47452 0 subsets accession name definition 0 0 45111 5 SOFA SO:0000000 Sequence_Ontology "" [] 0 1 45112 5 SOFA SO:0000001 region "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke] 0 0 45113 5 NULL SO:0000002 sequence_secondary_structure "A folded sequence." [SO:ke] 0 0 45114 5 NULL SO:0000003 G_quartet "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract] 0 0 45115 5 SOFA SO:0000004 interior_coding_exon "" [] 0 0 45116 5 SOFA SO:0000005 satellite_DNA "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45117 5 SOFA SO:0000006 PCR_product "A region amplified by a PCR reaction." [SO:ke] 0 0 45118 5 SOFA SO:0000007 read_pair "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls] 0 0 45119 5 NULL SO:0000008 gene_sensu_your_favorite_organism "" [] 0 1 45120 5 NULL SO:0000009 gene_class "" [] 0 1 45121 5 NULL SO:0000010 protein_coding "" [] 0 0 45122 5 NULL SO:0000011 non_protein_coding "" [] 0 0 45123 5 NULL SO:0000012 scRNA_primary_transcript "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html] 0 0 45124 5 SOFA SO:0000013 scRNA "A small non coding RNA sequence, present in the cytoplasm." [SO:ke] 0 0 45125 5 NULL SO:0000014 INR_motif "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867] 0 0 45126 5 NULL SO:0000015 DPE_motif "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739\\:12537576, PMID:16858867] 0 0 45127 5 NULL SO:0000016 BREu_motif "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867] 0 0 45128 5 NULL SO:0000017 PSE_motif "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739] 0 0 45129 5 NULL SO:0000018 linkage_group "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046] 0 0 45130 5 NULL SO:0000020 RNA_internal_loop "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke] 0 0 45131 5 NULL SO:0000021 asymmetric_RNA_internal_loop "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke] 0 0 45132 5 NULL SO:0000022 A_minor_RNA_motif "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke] 0 0 45133 5 NULL SO:0000023 K_turn_RNA_motif "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke] 0 0 45134 5 NULL SO:0000024 sarcin_like_RNA_motif "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662] 0 0 45135 5 NULL SO:0000025 symmetric_RNA_internal_loop "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke] 0 0 45136 5 NULL SO:0000026 RNA_junction_loop "" [] 0 0 45137 5 NULL SO:0000027 RNA_hook_turn "" [] 0 0 45138 5 NULL SO:0000028 base_pair "" [] 0 0 45139 5 NULL SO:0000029 WC_base_pair "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293] 0 0 45140 5 NULL SO:0000030 sugar_edge_base_pair "A type of non-canonical base-pairing." [PMID:12177293] 0 0 45141 5 NULL SO:0000031 aptamer "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu] 0 0 45142 5 NULL SO:0000032 DNA_aptamer "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu] 0 0 45143 5 NULL SO:0000033 RNA_aptamer "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu] 0 0 45144 5 NULL SO:0000034 morpholino_oligo "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/] 0 0 45145 5 NULL SO:0000035 riboswitch "A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954] 0 0 45146 5 NULL SO:0000036 matrix_attachment_site "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma] 0 0 45147 5 NULL SO:0000037 locus_control_region "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma] 0 0 45148 5 SOFA SO:0000038 match_set "A collection of match parts." [SO:ke] 0 1 45149 5 SOFA SO:0000039 match_part "A part of a match, for example an hsp from blast is a match_part." [SO:ke] 0 0 45150 5 NULL SO:0000040 genomic_clone "A clone of a DNA region of a genome." [SO:ma] 0 0 45151 5 NULL SO:0000041 sequence_operation "An operation that can be applied to a sequence, that results in a change." [SO:ke] 0 1 45152 5 NULL SO:0000042 pseudogene_attribute "An attribute of a pseudogene (SO:0000336)." [SO:ma] 0 1 45153 5 NULL SO:0000043 processed_pseudogene "A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 45154 5 NULL SO:0000044 pseudogene_by_unequal_crossing_over "A pseudogene caused by unequal crossing over at recombination." [SO:ke] 0 0 45155 5 NULL SO:0000045 delete "To remove a subsection of sequence." [SO:ke] 0 1 45156 5 NULL SO:0000046 insert "To insert a subsection of sequence." [SO:ke] 0 1 45157 5 NULL SO:0000047 invert "To invert a subsection of sequence." [SO:ke] 0 1 45158 5 NULL SO:0000048 substitute "To substitute a subsection of sequence for another." [SO:ke] 0 1 45159 5 NULL SO:0000049 translocate "To translocate a subsection of sequence." [SO:ke] 0 1 45160 5 SOFA SO:0000050 gene_part "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke] 0 1 45161 5 NULL SO:0000051 probe "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma] 0 0 45162 5 NULL SO:0000052 assortment_derived_deficiency "" [] 0 1 45163 5 NULL SO:0000053 sequence_variant_affecting_regulatory_region "A sequence_variant_effect which changes the regulatory region of a gene." [SO:ke] 0 1 45164 5 NULL SO:0000054 aneuploid "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke] 0 0 45165 5 NULL SO:0000055 hyperploid "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke] 0 0 45166 5 NULL SO:0000056 hypoploid "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke] 0 0 45167 5 SOFA SO:0000057 operator "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma] 0 0 45168 5 NULL SO:0000058 assortment_derived_aneuploid "" [] 0 1 45169 5 SOFA SO:0000059 nuclease_binding_site "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb] 0 0 45170 5 NULL SO:0000060 compound_chromosome_arm "" [] 0 0 45171 5 NULL SO:0000061 restriction_enzyme_binding_site "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb] 0 0 45172 5 NULL SO:0000062 deficient_intrachromosomal_transposition "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual] 0 0 45173 5 NULL SO:0000063 deficient_interchromosomal_transposition "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke] 0 0 45174 5 NULL SO:0000064 gene_by_transcript_attribute "" [] 0 1 45175 5 NULL SO:0000065 free_chromosome_arm "A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke] 0 0 45176 5 NULL SO:0000066 gene_by_polyadenylation_attribute "" [] 0 1 45177 5 NULL SO:0000067 gene_to_gene_feature "" [] 0 0 45178 5 NULL SO:0000068 overlapping "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke] 0 0 45179 5 NULL SO:0000069 inside_intron "An attribute to describe a gene when it is located within the intron of another gene." [SO:ke] 0 0 45180 5 NULL SO:0000070 inside_intron_antiparallel "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke] 0 0 45181 5 NULL SO:0000071 inside_intron_parallel "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke] 0 0 45182 5 NULL SO:0000072 end_overlapping_gene "" [] 0 1 45183 5 NULL SO:0000073 five_prime_three_prime_overlap "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke] 0 0 45184 5 NULL SO:0000074 five_prime_five_prime_overlap "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke] 0 0 45185 5 NULL SO:0000075 three_prime_three_prime_overlap "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke] 0 0 45186 5 NULL SO:0000076 three_prime_five_prime_overlap "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke] 0 0 45187 5 NULL SO:0000077 antisense "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke] 0 0 45188 5 NULL SO:0000078 polycistronic_transcript "A transcript that is polycistronic." [SO:xp] 0 0 45189 5 NULL SO:0000079 dicistronic_transcript "A transcript that is dicistronic." [SO:ke] 0 0 45190 5 NULL SO:0000080 operon_member "" [] 0 0 45191 5 NULL SO:0000081 gene_array_member "" [] 0 0 45192 5 NULL SO:0000082 processed_transcript_attribute "" [] 0 1 45193 5 NULL SO:0000083 macronuclear_sequence "" [] 0 0 45194 5 NULL SO:0000084 micronuclear_sequence "" [] 0 0 45195 5 NULL SO:0000085 gene_by_genome_location "" [] 0 1 45196 5 NULL SO:0000086 gene_by_organelle_of_genome "" [] 0 1 45197 5 NULL SO:0000087 nuclear_gene "A gene from nuclear sequence." [SO:xp] 0 0 45198 5 NULL SO:0000088 mt_gene "A gene located in mitochondrial sequence." [SO:xp] 0 0 45199 5 NULL SO:0000089 kinetoplast_gene "A gene located in kinetoplast sequence." [SO:xp] 0 0 45200 5 NULL SO:0000090 plastid_gene "A gene from plastid sequence." [SO:xp] 0 0 45201 5 NULL SO:0000091 apicoplast_gene "A gene from apicoplast sequence." [SO:xp] 0 0 45202 5 NULL SO:0000092 ct_gene "A gene from chloroplast sequence." [SO:xp] 0 0 45203 5 NULL SO:0000093 chromoplast_gene "A gene from chromoplast_sequence." [SO:xp] 0 0 45204 5 NULL SO:0000094 cyanelle_gene "A gene from cyanelle sequence." [SO:xp] 0 0 45205 5 NULL SO:0000095 leucoplast_gene "A plastid gene from leucoplast sequence." [SO:xp] 0 0 45206 5 NULL SO:0000096 proplastid_gene "A gene from proplastid sequence." [SO:ke] 0 0 45207 5 NULL SO:0000097 nucleomorph_gene "A gene from nucleomorph sequence." [SO:xp] 0 0 45208 5 NULL SO:0000098 plasmid_gene "A gene from plasmid sequence." [SO:xp] 0 0 45209 5 NULL SO:0000099 proviral_gene "A gene from proviral sequence." [SO:xp] 0 0 45210 5 NULL SO:0000100 endogenous_retroviral_gene "A proviral gene with origin endogenous retrovirus." [SO:xp] 0 0 45211 5 SOFA SO:0000101 transposable_element "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html] 0 0 45212 5 SOFA SO:0000102 expressed_sequence_match "A match to an EST or cDNA sequence." [SO:ke] 0 0 45213 5 SOFA SO:0000103 clone_insert_end "The end of the clone insert." [SO:ke] 0 0 45214 5 SOFA SO:0000104 polypeptide "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma] 0 0 45215 5 NULL SO:0000105 chromosome_arm "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152] 0 0 45216 5 NULL SO:0000106 non_capped_primary_transcript "" [] 0 1 45217 5 NULL SO:0000107 sequencing_primer "" [] 0 0 45218 5 NULL SO:0000108 mRNA_with_frameshift "An mRNA with a frameshift." [SO:xp] 0 0 45219 5 SOFA SO:0000109 sequence_variant_obs "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] 0 1 45220 5 SOFA SO:0000110 sequence_feature "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke] 1 0 45221 5 NULL SO:0000111 transposable_element_gene "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke] 0 0 45222 5 SOFA SO:0000112 primer "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke] 0 0 45223 5 SOFA SO:0000113 proviral_region "A viral sequence which has integrated into a host genome." [SO:ke] 0 0 45224 5 SOFA SO:0000114 methylated_cytosine "A methylated deoxy-cytosine." [SO:ke] 0 0 45225 5 NULL SO:0000115 transcript_feature "" [] 0 1 45226 5 NULL SO:0000116 edited "An attribute describing a sequence that is modified by editing." [SO:ke] 0 0 45227 5 NULL SO:0000117 transcript_with_readthrough_stop_codon "" [] 0 1 45228 5 NULL SO:0000118 transcript_with_translational_frameshift "A transcript with a translational frameshift." [SO:xp] 0 0 45229 5 NULL SO:0000119 regulated "An attribute to describe a sequence that is regulated." [SO:ke] 0 0 45230 5 SOFA SO:0000120 protein_coding_primary_transcript "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke] 0 0 45231 5 NULL SO:0000121 forward_primer "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] 0 0 45232 5 NULL SO:0000122 RNA_sequence_secondary_structure "A folded RNA sequence." [SO:ke] 0 0 45233 5 NULL SO:0000123 transcriptionally_regulated "An attribute describing a gene that is regulated at transcription." [SO:ma] 0 0 45234 5 NULL SO:0000124 transcriptionally_constitutive "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke] 0 0 45235 5 NULL SO:0000125 transcriptionally_induced "An inducer molecule is required for transcription to occur." [SO:ke] 0 0 45236 5 NULL SO:0000126 transcriptionally_repressed "A repressor molecule is required for transcription to stop." [SO:ke] 0 0 45237 5 NULL SO:0000127 silenced_gene "A gene that is silenced." [SO:xp] 0 0 45238 5 NULL SO:0000128 gene_silenced_by_DNA_modification "A gene that is silenced by DNA modification." [SO:xp] 0 0 45239 5 NULL SO:0000129 gene_silenced_by_DNA_methylation "A gene that is silenced by DNA methylation." [SO:xp] 0 0 45240 5 NULL SO:0000130 post_translationally_regulated "An attribute describing a gene that is regulated after it has been translated." [SO:ke] 0 0 45241 5 NULL SO:0000131 translationally_regulated "An attribute describing a gene that is regulated as it is translated." [SO:ke] 0 0 45242 5 NULL SO:0000132 reverse_primer "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] 0 0 45243 5 NULL SO:0000133 epigenetically_modified "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke] 0 0 45244 5 NULL SO:0000134 genomically_imprinted "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke] 0 0 45245 5 NULL SO:0000135 maternally_imprinted "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] 0 0 45246 5 NULL SO:0000136 paternally_imprinted "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] 0 0 45247 5 NULL SO:0000137 allelically_excluded "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke] 0 0 45248 5 NULL SO:0000138 gene_rearranged_at_DNA_level "An epigenetically modified gene, rearranged at the DNA level." [SO:xp] 0 0 45249 5 SOFA SO:0000139 ribosome_entry_site "Region in mRNA where ribosome assembles." [SO:ke] 0 0 45250 5 SOFA SO:0000140 attenuator "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as] 0 0 45251 5 SOFA SO:0000141 terminator "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45252 5 NULL SO:0000142 DNA_sequence_secondary_structure "A folded DNA sequence." [SO:ke] 0 0 45253 5 SOFA SO:0000143 assembly_component "A region of known length which may be used to manufacture a longer region." [SO:ke] 0 0 45254 5 NULL SO:0000144 primary_transcript_attribute "" [] 0 1 45255 5 NULL SO:0000145 recoded_codon "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp] 0 0 45256 5 NULL SO:0000146 capped "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke] 0 0 45257 5 SOFA SO:0000147 exon "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke] 0 0 45258 5 SOFA SO:0000148 supercontig "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls] 0 0 45259 5 SOFA SO:0000149 contig "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] 0 0 45260 5 SOFA SO:0000150 read "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd] 0 0 45261 5 SOFA SO:0000151 clone "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke] 0 0 45262 5 NULL SO:0000152 YAC "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma] 0 0 45263 5 NULL SO:0000153 BAC "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma] 0 0 45264 5 NULL SO:0000154 PAC "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome] 0 0 45265 5 NULL SO:0000155 plasmid "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma] 0 0 45266 5 NULL SO:0000156 cosmid "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma] 0 0 45267 5 NULL SO:0000157 phagemid "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \\"helper\\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma] 0 0 45268 5 NULL SO:0000158 fosmid "A cloning vector that utilizes the E. coli F factor." [SO:ma] 0 0 45269 5 SOFA SO:0000159 deletion "The point at which one or more contiguous nucleotides were excised." [SO:ke] 0 0 45270 5 NULL SO:0000160 lambda_clone "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] 0 1 45271 5 SOFA SO:0000161 methylated_adenine "A modified base in which adenine has been methylated." [SO:ke] 0 0 45272 5 SOFA SO:0000162 splice_site "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke] 0 0 45273 5 SOFA SO:0000163 five_prime_cis_splice_site "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] 0 0 45274 5 SOFA SO:0000164 three_prime_cis_splice_site "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] 0 0 45275 5 SOFA SO:0000165 enhancer "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45276 5 NULL SO:0000166 enhancer_bound_by_factor "An enhancer bound by a factor." [SO:xp] 0 0 45277 5 SOFA SO:0000167 promoter "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] 0 0 45278 5 NULL SO:0000168 restriction_enzyme_cut_site "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma] 0 1 45279 5 NULL SO:0000169 RNApol_I_promoter "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke] 0 0 45280 5 NULL SO:0000170 RNApol_II_promoter "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke] 0 0 45281 5 NULL SO:0000171 RNApol_III_promoter "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke] 0 0 45282 5 NULL SO:0000172 CAAT_signal "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45283 5 NULL SO:0000173 GC_rich_promoter_region "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45284 5 NULL SO:0000174 TATA_box "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867] 0 0 45285 5 NULL SO:0000175 minus_10_signal "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45286 5 NULL SO:0000176 minus_35_signal "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45287 5 SOFA SO:0000177 cross_genome_match "A nucleotide match against a sequence from another organism." [SO:ma] 0 0 45288 5 SOFA SO:0000178 operon "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma] 0 0 45289 5 SOFA SO:0000179 clone_insert_start "The start of the clone insert." [SO:ke] 0 0 45290 5 NULL SO:0000180 retrotransposon "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r] 0 0 45291 5 SOFA SO:0000181 translated_nucleotide_match "A match against a translated sequence." [SO:ke] 0 0 45292 5 NULL SO:0000182 DNA_transposon "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke] 0 0 45293 5 SOFA SO:0000183 non_transcribed_region "A region of the gene which is not transcribed." [SO:ke] 0 0 45294 5 NULL SO:0000184 U2_intron "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511] 0 0 45295 5 SOFA SO:0000185 primary_transcript "A transcript that in its initial state requires modification to be functional." [SO:ma] 0 0 45296 5 NULL SO:0000186 LTR_retrotransposon "A retrotransposon flanked by long terminal repeat sequences." [SO:ke] 0 0 45297 5 SOFA SO:0000187 repeat_family "A group of characterized repeat sequences." [SO:ke] 0 1 45298 5 SOFA SO:0000188 intron "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45299 5 NULL SO:0000189 non_LTR_retrotransposon "A retrotransposon without long terminal repeat sequences." [SO:ke] 0 0 45300 5 NULL SO:0000190 five_prime_intron "" [] 0 0 45301 5 NULL SO:0000191 interior_intron "" [] 0 0 45302 5 NULL SO:0000192 three_prime_intron "" [] 0 0 45303 5 SOFA SO:0000193 RFLP_fragment "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj] 0 0 45304 5 NULL SO:0000194 LINE_element "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] 0 0 45305 5 SOFA SO:0000195 coding_exon "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] 0 0 45306 5 SOFA SO:0000196 five_prime_coding_exon_coding_region "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm] 0 0 45307 5 SOFA SO:0000197 three_prime_coding_exon_coding_region "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm] 0 0 45308 5 SOFA SO:0000198 noncoding_exon "An exon that does not contain any codons." [SO:ke] 0 0 45309 5 DBVAR SO:0000199 translocation "A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." [NCBI:th, SO:ke] 0 0 45310 5 SOFA SO:0000200 five_prime_coding_exon "The 5' most coding exon." [SO:ke] 0 0 45311 5 NULL SO:0000201 interior_exon "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547] 0 0 45312 5 NULL SO:0000202 three_prime_coding_exon "The coding exon that is most 3-prime on a given transcript." [SO:ma] 0 0 45313 5 SOFA SO:0000203 UTR "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke] 0 0 45314 5 SOFA SO:0000204 five_prime_UTR "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45315 5 SOFA SO:0000205 three_prime_UTR "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45316 5 NULL SO:0000206 SINE_element "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke] 0 0 45317 5 NULL SO:0000207 simple_sequence_length_variation "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ." [SO:ke] 0 0 45318 5 NULL SO:0000208 terminal_inverted_repeat_element "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] 0 0 45319 5 SOFA SO:0000209 rRNA_primary_transcript "A primary transcript encoding a ribosomal RNA." [SO:ke] 0 0 45320 5 NULL SO:0000210 tRNA_primary_transcript "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke] 0 0 45321 5 NULL SO:0000211 alanine_tRNA_primary_transcript "A primary transcript encoding alanyl tRNA." [SO:ke] 0 0 45322 5 NULL SO:0000212 arginine_tRNA_primary_transcript "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke] 0 0 45323 5 NULL SO:0000213 asparagine_tRNA_primary_transcript "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke] 0 0 45324 5 NULL SO:0000214 aspartic_acid_tRNA_primary_transcript "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke] 0 0 45325 5 NULL SO:0000215 cysteine_tRNA_primary_transcript "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke] 0 0 45326 5 NULL SO:0000216 glutamic_acid_tRNA_primary_transcript "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke] 0 0 45327 5 NULL SO:0000217 glutamine_tRNA_primary_transcript "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke] 0 0 45328 5 NULL SO:0000218 glycine_tRNA_primary_transcript "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke] 0 0 45329 5 NULL SO:0000219 histidine_tRNA_primary_transcript "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke] 0 0 45330 5 NULL SO:0000220 isoleucine_tRNA_primary_transcript "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke] 0 0 45331 5 NULL SO:0000221 leucine_tRNA_primary_transcript "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke] 0 0 45332 5 NULL SO:0000222 lysine_tRNA_primary_transcript "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke] 0 0 45333 5 NULL SO:0000223 methionine_tRNA_primary_transcript "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke] 0 0 45334 5 NULL SO:0000224 phenylalanine_tRNA_primary_transcript "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke] 0 0 45335 5 NULL SO:0000225 proline_tRNA_primary_transcript "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke] 0 0 45336 5 NULL SO:0000226 serine_tRNA_primary_transcript "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] 0 0 45337 5 NULL SO:0000227 threonine_tRNA_primary_transcript "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke] 0 0 45338 5 NULL SO:0000228 tryptophan_tRNA_primary_transcript "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke] 0 0 45339 5 NULL SO:0000229 tyrosine_tRNA_primary_transcript "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke] 0 0 45340 5 NULL SO:0000230 valine_tRNA_primary_transcript "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke] 0 0 45341 5 NULL SO:0000231 snRNA_primary_transcript "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke] 0 0 45342 5 NULL SO:0000232 snoRNA_primary_transcript "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke] 0 0 45343 5 SOFA SO:0000233 mature_transcript "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke] 0 0 45344 5 SOFA SO:0000234 mRNA "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] 0 0 45345 5 SOFA SO:0000235 TF_binding_site "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke] 0 0 45346 5 SOFA SO:0000236 ORF "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma] 0 0 45347 5 NULL SO:0000237 transcript_attribute "" [] 0 0 45348 5 NULL SO:0000238 foldback_element "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] 0 0 45349 5 SOFA SO:0000239 flanking_region "The sequences extending on either side of a specific region." [SO:ke] 0 0 45350 5 NULL SO:0000240 chromosome_variation "" [] 0 0 45351 5 NULL SO:0000241 internal_UTR "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm] 0 0 45352 5 NULL SO:0000242 untranslated_region_polycistronic_mRNA "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke] 0 0 45353 5 NULL SO:0000243 internal_ribosome_entry_site "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke] 0 0 45354 5 NULL SO:0000244 four_cutter_restriction_site "" [] 0 1 45355 5 NULL SO:0000245 mRNA_by_polyadenylation_status "" [] 0 1 45356 5 NULL SO:0000246 polyadenylated "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke] 0 0 45357 5 NULL SO:0000247 mRNA_not_polyadenylated "" [] 0 1 45358 5 NULL SO:0000248 sequence_length_variation "A kind of kind of sequence alteration where the copies of a region present varies across a population." [SO:ke] 0 0 45359 5 NULL SO:0000249 six_cutter_restriction_site "" [] 0 1 45360 5 NULL SO:0000250 modified_RNA_base_feature "A post_transcriptionally modified base." [SO:ke] 0 0 45361 5 NULL SO:0000251 eight_cutter_restriction_site "" [] 0 1 45362 5 SOFA SO:0000252 rRNA "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] 0 0 45363 5 SOFA SO:0000253 tRNA "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] 0 0 45364 5 NULL SO:0000254 alanyl_tRNA "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke] 0 0 45365 5 NULL SO:0000255 rRNA_small_subunit_primary_transcript "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke] 0 0 45366 5 NULL SO:0000256 asparaginyl_tRNA "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke] 0 0 45367 5 NULL SO:0000257 aspartyl_tRNA "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke] 0 0 45368 5 NULL SO:0000258 cysteinyl_tRNA "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke] 0 0 45369 5 NULL SO:0000259 glutaminyl_tRNA "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke] 0 0 45370 5 NULL SO:0000260 glutamyl_tRNA "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke] 0 0 45371 5 NULL SO:0000261 glycyl_tRNA "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke] 0 0 45372 5 NULL SO:0000262 histidyl_tRNA "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke] 0 0 45373 5 NULL SO:0000263 isoleucyl_tRNA "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke] 0 0 45374 5 NULL SO:0000264 leucyl_tRNA "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke] 0 0 45375 5 NULL SO:0000265 lysyl_tRNA "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke] 0 0 45376 5 NULL SO:0000266 methionyl_tRNA "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke] 0 0 45377 5 NULL SO:0000267 phenylalanyl_tRNA "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke] 0 0 45378 5 NULL SO:0000268 prolyl_tRNA "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke] 0 0 45379 5 NULL SO:0000269 seryl_tRNA "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke] 0 0 45380 5 NULL SO:0000270 threonyl_tRNA "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke] 0 0 45381 5 NULL SO:0000271 tryptophanyl_tRNA "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke] 0 0 45382 5 NULL SO:0000272 tyrosyl_tRNA "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke] 0 0 45383 5 NULL SO:0000273 valyl_tRNA "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke] 0 0 45384 5 SOFA SO:0000274 snRNA "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems] 0 0 45385 5 SOFA SO:0000275 snoRNA "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc] 0 0 45386 5 SOFA SO:0000276 miRNA "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:11081512, PMID:12592000] 0 0 45387 5 NULL SO:0000277 bound_by_factor "An attribute describing a sequence that is bound by another molecule." [SO:ke] 0 0 45388 5 NULL SO:0000278 transcript_bound_by_nucleic_acid "A transcript that is bound by a nucleic acid." [SO:xp] 0 0 45389 5 NULL SO:0000279 transcript_bound_by_protein "A transcript that is bound by a protein." [SO:xp] 0 0 45390 5 NULL SO:0000280 engineered_gene "A gene that is engineered." [SO:xp] 0 0 45391 5 NULL SO:0000281 engineered_foreign_gene "A gene that is engineered and foreign." [SO:xp] 0 0 45392 5 NULL SO:0000282 mRNA_with_minus_1_frameshift "An mRNA with a minus 1 frameshift." [SO:xp] 0 0 45393 5 NULL SO:0000283 engineered_foreign_transposable_element_gene "A transposable_element that is engineered and foreign." [SO:xp] 0 0 45394 5 NULL SO:0000284 type_I_enzyme_restriction_site "The recognition site is bipartite and interrupted." [http://www.promega.com] 0 1 45395 5 NULL SO:0000285 foreign_gene "A gene that is foreign." [SO:xp] 0 0 45396 5 NULL SO:0000286 long_terminal_repeat "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45397 5 NULL SO:0000287 fusion_gene "A gene that is a fusion." [SO:xp] 0 0 45398 5 NULL SO:0000288 engineered_fusion_gene "A fusion gene that is engineered." [SO:xp] 0 0 45399 5 SOFA SO:0000289 microsatellite "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th] 0 0 45400 5 NULL SO:0000290 dinucleotide_repeat_microsatellite_feature "" [] 0 0 45401 5 NULL SO:0000291 trinucleotide_repeat_microsatellite_feature "" [] 0 0 45402 5 NULL SO:0000292 repetitive_element "" [] 0 1 45403 5 NULL SO:0000293 engineered_foreign_repetitive_element "A repetitive element that is engineered and foreign." [SO:xp] 0 0 45404 5 SOFA SO:0000294 inverted_repeat "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke] 0 0 45405 5 NULL SO:0000295 U12_intron "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511] 0 0 45406 5 SOFA SO:0000296 origin_of_replication "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45407 5 NULL SO:0000297 D_loop "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45408 5 NULL SO:0000298 recombination_feature "" [] 0 0 45409 5 NULL SO:0000299 specific_recombination_site "" [] 0 0 45410 5 NULL SO:0000300 recombination_feature_of_rearranged_gene "" [] 0 0 45411 5 NULL SO:0000301 vertebrate_immune_system_gene_recombination_feature "" [] 0 0 45412 5 NULL SO:0000302 J_gene_recombination_feature "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45413 5 SOFA SO:0000303 clip "Part of the primary transcript that is clipped off during processing." [SO:ke] 0 0 45414 5 NULL SO:0000304 type_II_enzyme_restriction_site "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com] 0 1 45415 5 SOFA SO:0000305 modified_DNA_base "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45416 5 SOFA SO:0000306 methylated_DNA_base_feature "A nucleotide modified by methylation." [SO:ke] 0 0 45417 5 SOFA SO:0000307 CpG_island "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd] 0 0 45418 5 NULL SO:0000308 sequence_feature_locating_method "" [] 0 1 45419 5 NULL SO:0000309 computed_feature "" [] 0 1 45420 5 NULL SO:0000310 predicted_ab_initio_computation "" [] 0 1 45421 5 NULL SO:0000311 computed_feature_by_similarity "." [SO:ma] 0 1 45422 5 NULL SO:0000312 experimentally_determined "Attribute to describe a feature that has been experimentally verified." [SO:ke] 0 0 45423 5 NULL SO:0000313 stem_loop "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45424 5 SOFA SO:0000314 direct_repeat "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke] 0 0 45425 5 SOFA SO:0000315 TSS "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] 0 0 45426 5 SOFA SO:0000316 CDS "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] 0 0 45427 5 NULL SO:0000317 cDNA_clone "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] 0 0 45428 5 SOFA SO:0000318 start_codon "First codon to be translated by a ribosome." [SO:ke] 0 0 45429 5 SOFA SO:0000319 stop_codon "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] 0 0 45430 5 NULL SO:0000320 intronic_splice_enhancer "Sequences within the intron that modulate splice site selection for some introns." [SO:ke] 0 0 45431 5 NULL SO:0000321 mRNA_with_plus_1_frameshift "An mRNA with a plus 1 frameshift." [SO:ke] 0 0 45432 5 NULL SO:0000322 nuclease_hypersensitive_site "" [] 0 0 45433 5 NULL SO:0000323 coding_start "The first base to be translated into protein." [SO:ke] 0 0 45434 5 SOFA SO:0000324 tag "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] 0 0 45435 5 SOFA SO:0000325 rRNA_large_subunit_primary_transcript "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] 0 0 45436 5 SOFA SO:0000326 SAGE_tag "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract] 0 0 45437 5 NULL SO:0000327 coding_end "The last base to be translated into protein. It does not include the stop codon." [SO:ke] 0 0 45438 5 NULL SO:0000328 microarray_oligo "" [] 0 0 45439 5 NULL SO:0000329 mRNA_with_plus_2_frameshift "An mRNA with a plus 2 frameshift." [SO:xp] 0 0 45440 5 SOFA SO:0000330 conserved_region "Region of sequence similarity by descent from a common ancestor." [SO:ke] 0 0 45441 5 SOFA SO:0000331 STS "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com] 0 0 45442 5 SOFA SO:0000332 coding_conserved_region "Coding region of sequence similarity by descent from a common ancestor." [SO:ke] 0 0 45443 5 SOFA SO:0000333 exon_junction "The boundary between two exons in a processed transcript." [SO:ke] 0 0 45444 5 SOFA SO:0000334 nc_conserved_region "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke] 0 0 45445 5 NULL SO:0000335 mRNA_with_minus_2_frameshift "A mRNA with a minus 2 frameshift." [SO:ke] 0 0 45446 5 SOFA SO:0000336 pseudogene "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \\"normal\\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \\"normal\\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] 0 0 45447 5 SOFA SO:0000337 RNAi_reagent "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] 0 0 45448 5 NULL SO:0000338 MITE "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083] 0 0 45449 5 NULL SO:0000339 recombination_hotspot "A region in a genome which promotes recombination." [SO:rd] 0 0 45450 5 SOFA SO:0000340 chromosome "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] 0 0 45451 5 SOFA SO:0000341 chromosome_band "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] 0 0 45452 5 NULL SO:0000342 site_specific_recombination_target_region "" [] 0 0 45453 5 SOFA SO:0000343 match "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] 0 0 45454 5 SOFA SO:0000344 splice_enhancer "Region of a transcript that regulates splicing." [SO:ke] 0 0 45455 5 SOFA SO:0000345 EST "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] 0 0 45456 5 NULL SO:0000346 loxP_site "" [] 0 0 45457 5 SOFA SO:0000347 nucleotide_match "A match against a nucleotide sequence." [SO:ke] 0 0 45458 5 NULL SO:0000348 nucleic_acid "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb] 0 0 45459 5 SOFA SO:0000349 protein_match "A match against a protein sequence." [SO:ke] 0 0 45460 5 NULL SO:0000350 FRT_site "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma] 0 0 45461 5 NULL SO:0000351 synthetic_sequence "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma] 0 0 45462 5 NULL SO:0000352 DNA "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb] 0 0 45463 5 SOFA SO:0000353 sequence_assembly "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] 0 0 45464 5 NULL SO:0000354 group_1_intron_homing_endonuclease_target_region "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke] 0 0 45465 5 NULL SO:0000355 haplotype_block "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma] 0 0 45466 5 NULL SO:0000356 RNA "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb] 0 0 45467 5 NULL SO:0000357 flanked "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke] 0 0 45468 5 NULL SO:0000359 floxed "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke] 0 0 45469 5 SOFA SO:0000360 codon "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke] 0 0 45470 5 NULL SO:0000361 FRT_flanked "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke] 0 0 45471 5 NULL SO:0000362 invalidated_by_chimeric_cDNA "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma] 0 0 45472 5 NULL SO:0000363 floxed_gene "A transgene that is floxed." [SO:xp] 0 0 45473 5 NULL SO:0000364 transposable_element_flanking_region "The region of sequence surrounding a transposable element." [SO:ke] 0 0 45474 5 NULL SO:0000365 integron "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as] 0 0 45475 5 SOFA SO:0000366 insertion_site "The junction where an insertion occurred." [SO:ke] 0 0 45476 5 NULL SO:0000367 attI_site "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as] 0 0 45477 5 SOFA SO:0000368 transposable_element_insertion_site "The junction in a genome where a transposable_element has inserted." [SO:ke] 0 0 45478 5 NULL SO:0000369 integrase_coding_region "" [] 0 1 45479 5 SOFA SO:0000370 small_regulatory_ncRNA "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma] 0 0 45480 5 NULL SO:0000371 conjugative_transposon "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html] 0 0 45481 5 SOFA SO:0000372 enzymatic_RNA "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] 0 0 45482 5 NULL SO:0000373 recombinationally_inverted_gene "A recombinationally rearranged gene by inversion." [SO:xp] 0 0 45483 5 SOFA SO:0000374 ribozyme "An RNA with catalytic activity." [SO:ma] 0 0 45484 5 SOFA SO:0000375 rRNA_5_8S "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002] 0 0 45485 5 NULL SO:0000376 RNA_6S "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013] 0 0 45486 5 NULL SO:0000377 CsrB_RsmB_RNA "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018] 0 0 45487 5 NULL SO:0000378 DsrA_RNA "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014] 0 0 45488 5 NULL SO:0000379 GcvB_RNA "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022] 0 0 45489 5 SOFA SO:0000380 hammerhead_ribozyme "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805] 0 0 45490 5 NULL SO:0000381 group_IIA_intron "" [] 0 0 45491 5 NULL SO:0000382 group_IIB_intron "" [] 0 0 45492 5 NULL SO:0000383 MicF_RNA "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033] 0 0 45493 5 NULL SO:0000384 OxyS_RNA "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035] 0 0 45494 5 SOFA SO:0000385 RNase_MRP_RNA "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030] 0 0 45495 5 SOFA SO:0000386 RNase_P_RNA "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010] 0 0 45496 5 NULL SO:0000387 RprA_RNA "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034] 0 0 45497 5 NULL SO:0000388 RRE_RNA "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036] 0 0 45498 5 NULL SO:0000389 spot_42_RNA "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021] 0 0 45499 5 SOFA SO:0000390 telomerase_RNA "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] 0 0 45500 5 SOFA SO:0000391 U1_snRNA "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003] 0 0 45501 5 SOFA SO:0000392 U2_snRNA "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004] 0 0 45502 5 SOFA SO:0000393 U4_snRNA "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] 0 0 45503 5 SOFA SO:0000394 U4atac_snRNA "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455] 0 0 45504 5 SOFA SO:0000395 U5_snRNA "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020] 0 0 45505 5 SOFA SO:0000396 U6_snRNA "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] 0 0 45506 5 SOFA SO:0000397 U6atac_snRNA "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract] 0 0 45507 5 SOFA SO:0000398 U11_snRNA "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129] 0 0 45508 5 SOFA SO:0000399 U12_snRNA "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007] 0 0 45509 5 NULL SO:0000400 sequence_attribute "An attribute describes a quality of sequence." [SO:ke] 1 0 45510 5 NULL SO:0000401 gene_attribute "" [] 0 0 45511 5 NULL SO:0000402 enhancer_attribute "" [] 0 1 45512 5 SOFA SO:0000403 U14_snoRNA "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119] 0 0 45513 5 SOFA SO:0000404 vault_RNA "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006] 0 0 45514 5 SOFA SO:0000405 Y_RNA "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019] 0 0 45515 5 NULL SO:0000406 twintron "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908] 0 0 45516 5 SOFA SO:0000407 rRNA_18S "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke] 0 0 45517 5 NULL SO:0000408 site "The interbase position where something (eg an aberration) occurred." [SO:ke] 0 1 45518 5 biosapiens,SOFA SO:0000409 binding_site "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] 0 0 45519 5 SOFA SO:0000410 protein_binding_site "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] 0 0 45520 5 NULL SO:0000411 rescue_region "A region that rescues." [SO:xp] 0 0 45521 5 SOFA SO:0000412 restriction_fragment "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] 0 0 45522 5 SOFA SO:0000413 sequence_difference "A region where the sequence differs from that of a specified sequence." [SO:ke] 0 0 45523 5 NULL SO:0000414 invalidated_by_genomic_contamination "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke] 0 0 45524 5 NULL SO:0000415 invalidated_by_genomic_polyA_primed_cDNA "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke] 0 0 45525 5 NULL SO:0000416 invalidated_by_partial_processing "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke] 0 0 45526 5 biosapiens SO:0000417 polypeptide_domain "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR] 0 0 45527 5 biosapiens,SOFA SO:0000418 signal_peptide "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45528 5 biosapiens,SOFA SO:0000419 mature_protein_region "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb] 0 0 45529 5 NULL SO:0000420 five_prime_terminal_inverted_repeat "" [] 0 0 45530 5 NULL SO:0000421 three_prime_terminal_inverted_repeat "" [] 0 0 45531 5 NULL SO:0000422 U5_LTR_region "" [] 0 0 45532 5 NULL SO:0000423 R_LTR_region "" [] 0 0 45533 5 NULL SO:0000424 U3_LTR_region "" [] 0 0 45534 5 NULL SO:0000425 five_prime_LTR "" [] 0 0 45535 5 NULL SO:0000426 three_prime_LTR "" [] 0 0 45536 5 NULL SO:0000427 R_five_prime_LTR_region "" [] 0 0 45537 5 NULL SO:0000428 U5_five_prime_LTR_region "" [] 0 0 45538 5 NULL SO:0000429 U3_five_prime_LTR_region "" [] 0 0 45539 5 NULL SO:0000430 R_three_prime_LTR_region "" [] 0 0 45540 5 NULL SO:0000431 U3_three_prime_LTR_region "" [] 0 0 45541 5 NULL SO:0000432 U5_three_prime_LTR_region "" [] 0 0 45542 5 NULL SO:0000433 non_LTR_retrotransposon_polymeric_tract "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke] 0 0 45543 5 NULL SO:0000434 target_site_duplication "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html] 0 0 45544 5 NULL SO:0000435 RR_tract "A polypurine tract within an LTR_retrotransposon." [SO:ke] 0 0 45545 5 SOFA SO:0000436 ARS "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma] 0 0 45546 5 NULL SO:0000437 assortment_derived_duplication "" [] 0 1 45547 5 NULL SO:0000438 gene_not_polyadenylated "" [] 0 1 45548 5 NULL SO:0000439 inverted_ring_chromosome "" [] 0 0 45549 5 NULL SO:0000440 vector_replicon "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma] 0 0 45550 5 SOFA SO:0000441 ss_oligo "A single stranded oligonucleotide." [SO:ke] 0 0 45551 5 SOFA SO:0000442 ds_oligo "A double stranded oligonucleotide." [SO:ke] 0 0 45552 5 NULL SO:0000443 polymer_attribute "An attribute to describe the kind of biological sequence." [SO:ke] 0 0 45553 5 NULL SO:0000444 three_prime_noncoding_exon "Non-coding exon in the 3' UTR." [SO:ke] 0 0 45554 5 NULL SO:0000445 five_prime_noncoding_exon "Non-coding exon in the 5' UTR." [SO:ke] 0 0 45555 5 NULL SO:0000446 UTR_intron "Intron located in the untranslated region." [SO:ke] 0 0 45556 5 NULL SO:0000447 five_prime_UTR_intron "An intron located in the 5' UTR." [SO:ke] 0 0 45557 5 NULL SO:0000448 three_prime_UTR_intron "An intron located in the 3' UTR." [SO:ke] 0 0 45558 5 NULL SO:0000449 random_sequence "A sequence of nucleotides or amino acids which, by design, has a \\"random\\" order of components, given a predetermined input frequency of these components." [SO:ma] 0 0 45559 5 NULL SO:0000450 interband "A light region between two darkly staining bands in a polytene chromosome." [SO:ma] 0 0 45560 5 NULL SO:0000451 gene_with_polyadenylated_mRNA "A gene that encodes a polyadenylated mRNA." [SO:xp] 0 0 45561 5 NULL SO:0000452 transgene_attribute "" [] 0 1 45562 5 NULL SO:0000453 chromosomal_transposition "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke] 0 0 45563 5 SOFA SO:0000454 rasiRNA "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284] 0 0 45564 5 NULL SO:0000455 gene_with_mRNA_with_frameshift "A gene that encodes an mRNA with a frameshift." [SO:xp] 0 0 45565 5 NULL SO:0000456 recombinationally_rearranged_gene "A gene that is recombinationally rearranged." [SO:ke] 0 0 45566 5 NULL SO:0000457 interchromosomal_duplication "A chromosome duplication involving an insertion from another chromosome." [SO:ke] 0 0 45567 5 NULL SO:0000458 D_gene_segment "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45568 5 NULL SO:0000459 gene_with_trans_spliced_transcript "A gene with a transcript that is trans-spliced." [SO:xp] 0 0 45569 5 NULL SO:0000460 vertebrate_immunoglobulin_T_cell_receptor_segment "" [] 0 0 45570 5 NULL SO:0000461 inversion_derived_bipartite_deficiency "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km] 0 0 45571 5 SOFA SO:0000462 pseudogenic_region "A non-functional descendant of a functional entity." [SO:cjm] 0 0 45572 5 NULL SO:0000463 encodes_alternately_spliced_transcripts "A gene that encodes more than one transcript." [SO:ke] 0 0 45573 5 SOFA SO:0000464 decayed_exon "A non-functional descendant of an exon." [SO:ke] 0 0 45574 5 NULL SO:0000465 inversion_derived_deficiency_plus_duplication "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km] 0 0 45575 5 NULL SO:0000466 V_gene_segment "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45576 5 NULL SO:0000467 post_translationally_regulated_by_protein_stability "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke] 0 0 45577 5 SOFA SO:0000468 golden_path_fragment "One of the pieces of sequence that make up a golden path." [SO:rd] 0 0 45578 5 NULL SO:0000469 post_translationally_regulated_by_protein_modification "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke] 0 0 45579 5 NULL SO:0000470 J_gene_segment "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45580 5 NULL SO:0000471 autoregulated "The gene product is involved in its own transcriptional regulation." [SO:ke] 0 0 45581 5 SOFA SO:0000472 tiling_path "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm] 0 0 45582 5 NULL SO:0000473 negatively_autoregulated "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke] 0 0 45583 5 SOFA SO:0000474 tiling_path_fragment "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke] 0 0 45584 5 NULL SO:0000475 positively_autoregulated "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke] 0 0 45585 5 NULL SO:0000476 contig_read "A DNA sequencer read which is part of a contig." [SO:ke] 0 0 45586 5 NULL SO:0000477 polycistronic_gene "A gene that is polycistronic." [SO:ke] 0 1 45587 5 NULL SO:0000478 C_gene_segment "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45588 5 NULL SO:0000479 trans_spliced_transcript "A transcript that is trans-spliced." [SO:xp] 0 0 45589 5 NULL SO:0000480 tiling_path_clone "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke] 0 0 45590 5 NULL SO:0000481 terminal_inverted_repeat "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke] 0 0 45591 5 NULL SO:0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster "" [] 0 0 45592 5 SOFA SO:0000483 nc_primary_transcript "A primary transcript that is never translated into a protein." [SO:ke] 0 0 45593 5 SOFA SO:0000484 three_prime_coding_exon_noncoding_region "The sequence of the 3' exon that is not coding." [SO:ke] 0 0 45594 5 NULL SO:0000485 DJ_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45595 5 SOFA SO:0000486 five_prime_coding_exon_noncoding_region "The sequence of the 5' exon preceding the start codon." [SO:ke] 0 0 45596 5 NULL SO:0000487 VDJ_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45597 5 NULL SO:0000488 VDJ_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45598 5 NULL SO:0000489 VJ_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45599 5 NULL SO:0000490 VJ_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45600 5 NULL SO:0000491 VJ_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45601 5 NULL SO:0000492 D_gene_recombination_feature "" [] 0 0 45602 5 NULL SO:0000493 three_prime_D_heptamer "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45603 5 NULL SO:0000494 three_prime_D_nonamer "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45604 5 NULL SO:0000495 three_prime_D_spacer "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45605 5 NULL SO:0000496 five_prime_D_heptamer "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45606 5 NULL SO:0000497 five_prime_D_nonamer "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45607 5 NULL SO:0000498 five_prime_D_spacer "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45608 5 SOFA SO:0000499 virtual_sequence "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke] 0 0 45609 5 NULL SO:0000500 Hoogsteen_base_pair "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293] 0 0 45610 5 NULL SO:0000501 reverse_Hoogsteen_base_pair "A type of non-canonical base-pairing." [SO:ke] 0 0 45611 5 SOFA SO:0000502 transcribed_region "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke] 0 1 45612 5 NULL SO:0000503 alternately_spliced_gene_encodeing_one_transcript "" [] 0 1 45613 5 NULL SO:0000504 D_DJ_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45614 5 NULL SO:0000505 D_DJ_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45615 5 NULL SO:0000506 D_DJ_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45616 5 NULL SO:0000507 pseudogenic_exon "A non functional descendant of an exon, part of a pseudogene." [SO:ke] 0 0 45617 5 NULL SO:0000508 D_DJ_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45618 5 NULL SO:0000509 D_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45619 5 NULL SO:0000510 VD_gene_segment "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45620 5 NULL SO:0000511 J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45621 5 NULL SO:0000512 inversion_derived_deficiency_plus_aneuploid "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] 0 0 45622 5 NULL SO:0000513 J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45623 5 NULL SO:0000514 J_nonamer "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45624 5 NULL SO:0000515 J_heptamer "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45625 5 NULL SO:0000516 pseudogenic_transcript "A non functional descendant of a transcript, part of a pseudogene." [SO:ke] 0 0 45626 5 NULL SO:0000517 J_spacer "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45627 5 NULL SO:0000518 V_DJ_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45628 5 NULL SO:0000519 V_DJ_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45629 5 NULL SO:0000520 V_VDJ_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45630 5 NULL SO:0000521 V_VDJ_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45631 5 NULL SO:0000522 V_VDJ_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45632 5 NULL SO:0000523 V_VJ_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45633 5 NULL SO:0000524 V_VJ_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45634 5 NULL SO:0000525 V_VJ_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45635 5 NULL SO:0000526 V_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45636 5 NULL SO:0000527 V_D_DJ_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45637 5 NULL SO:0000528 V_D_DJ_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45638 5 NULL SO:0000529 V_D_DJ_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45639 5 NULL SO:0000530 V_D_DJ_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45640 5 NULL SO:0000531 V_D_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45641 5 NULL SO:0000532 V_D_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45642 5 NULL SO:0000533 V_heptamer "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45643 5 NULL SO:0000534 V_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45644 5 NULL SO:0000535 V_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45645 5 NULL SO:0000536 V_nonamer "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45646 5 NULL SO:0000537 V_spacer "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45647 5 NULL SO:0000538 V_gene_recombination_feature "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45648 5 NULL SO:0000539 DJ_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45649 5 NULL SO:0000540 DJ_J_C_cluster "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45650 5 NULL SO:0000541 VDJ_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45651 5 NULL SO:0000542 V_DJ_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45652 5 NULL SO:0000543 alternately_spliced_gene_encoding_greater_than_one_transcript "" [] 0 1 45653 5 NULL SO:0000544 helitron "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569] 0 0 45654 5 NULL SO:0000545 recoding_pseudoknot "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937] 0 0 45655 5 NULL SO:0000546 designed_sequence "" [] 0 0 45656 5 NULL SO:0000547 inversion_derived_bipartite_duplication "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km] 0 0 45657 5 NULL SO:0000548 gene_with_edited_transcript "A gene that encodes a transcript that is edited." [SO:xp] 0 0 45658 5 NULL SO:0000549 inversion_derived_duplication_plus_aneuploid "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] 0 0 45659 5 NULL SO:0000550 aneuploid_chromosome "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke] 0 0 45660 5 SOFA SO:0000551 polyA_signal_sequence "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45661 5 NULL SO:0000552 Shine_Dalgarno_sequence "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh] 0 0 45662 5 SOFA SO:0000553 polyA_site "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45663 5 NULL SO:0000554 assortment_derived_deficiency_plus_duplication "" [] 0 1 45664 5 NULL SO:0000555 five_prime_clip "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45665 5 NULL SO:0000556 five_prime_D_recombination_signal_sequence "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45666 5 NULL SO:0000557 three_prime_clip "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45667 5 NULL SO:0000558 C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45668 5 NULL SO:0000559 D_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45669 5 NULL SO:0000560 D_J_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45670 5 NULL SO:0000561 heptamer_of_recombination_feature_of_vertebrate_immune_system_gene "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45671 5 NULL SO:0000562 nonamer_of_recombination_feature_of_vertebrate_immune_system_gene "" [] 0 0 45672 5 NULL SO:0000563 vertebrate_immune_system_gene_recombination_spacer "" [] 0 0 45673 5 NULL SO:0000564 V_DJ_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45674 5 NULL SO:0000565 V_VDJ_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45675 5 NULL SO:0000566 V_VJ_J_C_cluster "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45676 5 NULL SO:0000567 inversion_derived_aneuploid_chromosome "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km] 0 0 45677 5 NULL SO:0000568 bidirectional_promoter "An unregulated promoter that allows continuous expression." [SO:ke] 0 0 45678 5 NULL SO:0000569 retrotransposed "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke] 0 0 45679 5 NULL SO:0000570 three_prime_D_recombination_signal_sequence "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45680 5 NULL SO:0000571 miRNA_encoding "" [] 0 0 45681 5 NULL SO:0000572 DJ_gene_segment "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45682 5 NULL SO:0000573 rRNA_encoding "" [] 0 0 45683 5 NULL SO:0000574 VDJ_gene_segment "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45684 5 NULL SO:0000575 scRNA_encoding "" [] 0 0 45685 5 NULL SO:0000576 VJ_gene_segment "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] 0 0 45686 5 SOFA SO:0000577 centromere "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] 0 0 45687 5 NULL SO:0000578 snoRNA_encoding "" [] 0 0 45688 5 NULL SO:0000579 edited_transcript_feature "A locatable feature on a transcript that is edited." [SO:ma] 0 0 45689 5 NULL SO:0000580 methylation_guide_snoRNA_primary_transcript "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke] 0 0 45690 5 SOFA SO:0000581 cap "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] 0 0 45691 5 NULL SO:0000582 rRNA_cleavage_snoRNA_primary_transcript "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke] 0 0 45692 5 NULL SO:0000583 pre_edited_region "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] 0 0 45693 5 NULL SO:0000584 tmRNA "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023] 0 0 45694 5 NULL SO:0000585 C_D_box_snoRNA_encoding "" [] 0 0 45695 5 NULL SO:0000586 tmRNA_primary_transcript "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke] 0 0 45696 5 SOFA SO:0000587 group_I_intron "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028] 0 0 45697 5 SOFA SO:0000588 autocatalytically_spliced_intron "A self spliced intron." [SO:ke] 0 0 45698 5 NULL SO:0000589 SRP_RNA_primary_transcript "A primary transcript encoding a signal recognition particle RNA." [SO:ke] 0 0 45699 5 SOFA SO:0000590 SRP_RNA "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017] 0 0 45700 5 NULL SO:0000591 pseudoknot "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb] 0 0 45701 5 NULL SO:0000592 H_pseudoknot "A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov\\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract] 0 0 45702 5 SOFA SO:0000593 C_D_box_snoRNA "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] 0 0 45703 5 NULL SO:0000594 H_ACA_box_snoRNA "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] 0 0 45704 5 NULL SO:0000595 C_D_box_snoRNA_primary_transcript "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke] 0 0 45705 5 NULL SO:0000596 H_ACA_box_snoRNA_primary_transcript "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke] 0 0 45706 5 NULL SO:0000597 transcript_edited_by_U_insertion/deletion "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html] 0 1 45707 5 NULL SO:0000598 edited_by_C_insertion_and_dinucleotide_insertion "" [] 0 1 45708 5 NULL SO:0000599 edited_by_C_to_U_substitution "" [] 0 1 45709 5 NULL SO:0000600 edited_by_A_to_I_substitution "" [] 0 1 45710 5 NULL SO:0000601 edited_by_G_addition "" [] 0 1 45711 5 SOFA SO:0000602 guide_RNA "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html] 0 0 45712 5 SOFA SO:0000603 group_II_intron "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml] 0 0 45713 5 NULL SO:0000604 editing_block "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] 0 0 45714 5 SOFA SO:0000605 intergenic_region "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] 0 0 45715 5 NULL SO:0000606 editing_domain "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] 0 0 45716 5 NULL SO:0000607 unedited_region "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] 0 0 45717 5 NULL SO:0000608 H_ACA_box_snoRNA_encoding "" [] 0 0 45718 5 NULL SO:0000609 oligo_U_tail "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/] 0 0 45719 5 SOFA SO:0000610 polyA_sequence "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] 0 0 45720 5 SOFA SO:0000611 branch_site "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] 0 0 45721 5 SOFA SO:0000612 polypyrimidine_tract "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888] 0 0 45722 5 NULL SO:0000613 bacterial_RNApol_promoter "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke] 0 0 45723 5 NULL SO:0000614 bacterial_terminator "A terminator signal for bacterial transcription." [SO:ke] 0 0 45724 5 NULL SO:0000615 terminator_of_type_2_RNApol_III_promoter "A terminator signal for RNA polymerase III transcription." [SO:ke] 0 0 45725 5 SOFA SO:0000616 transcription_end_site "The base where transcription ends." [SO:ke] 0 0 45726 5 NULL SO:0000617 RNApol_III_promoter_type_1 "" [] 0 0 45727 5 NULL SO:0000618 RNApol_III_promoter_type_2 "" [] 0 0 45728 5 NULL SO:0000619 A_box "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke] 0 0 45729 5 NULL SO:0000620 B_box "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke] 0 0 45730 5 NULL SO:0000621 RNApol_III_promoter_type_3 "" [] 0 0 45731 5 NULL SO:0000622 C_box "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke] 0 0 45732 5 NULL SO:0000623 snRNA_encoding "" [] 0 0 45733 5 SOFA SO:0000624 telomere "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] 0 0 45734 5 SOFA SO:0000625 silencer "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] 0 0 45735 5 NULL SO:0000626 chromosomal_regulatory_element "" [] 0 0 45736 5 SOFA SO:0000627 insulator "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative] 0 0 45737 5 SOFA SO:0000628 chromosomal_structural_element "" [] 0 0 45738 5 NULL SO:0000629 five_prime_open_reading_frame "" [] 0 0 45739 5 NULL SO:0000630 upstream_AUG_codon "A start codon upstream of the ORF." [SO:ke] 0 0 45740 5 NULL SO:0000631 polycistronic_primary_transcript "A primary transcript encoding for more than one gene product." [SO:ke] 0 0 45741 5 NULL SO:0000632 monocistronic_primary_transcript "A primary transcript encoding for one gene product." [SO:ke] 0 0 45742 5 NULL SO:0000633 monocistronic_mRNA "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd] 0 0 45743 5 NULL SO:0000634 polycistronic_mRNA "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd] 0 0 45744 5 NULL SO:0000635 mini_exon_donor_RNA "A primary transcript that donates the spliced leader to other mRNA." [SO:ke] 0 0 45745 5 NULL SO:0000636 spliced_leader_RNA "" [] 0 0 45746 5 NULL SO:0000637 engineered_plasmid "A plasmid that is engineered." [SO:xp] 0 0 45747 5 NULL SO:0000638 transcribed_spacer_region "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html] 0 0 45748 5 NULL SO:0000639 internal_transcribed_spacer_region "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke] 0 0 45749 5 NULL SO:0000640 external_transcribed_spacer_region "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke] 0 0 45750 5 NULL SO:0000641 tetranucleotide_repeat_microsatellite_feature "" [] 0 0 45751 5 NULL SO:0000642 SRP_RNA_encoding "" [] 0 0 45752 5 SOFA SO:0000643 minisatellite "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml] 0 0 45753 5 SOFA SO:0000644 antisense_RNA "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] 0 0 45754 5 SOFA SO:0000645 antisense_primary_transcript "The reverse complement of the primary transcript." [SO:ke] 0 0 45755 5 SOFA SO:0000646 siRNA "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000] 0 0 45756 5 NULL SO:0000647 miRNA_primary_transcript "A primary transcript encoding a micro RNA." [SO:ke] 0 0 45757 5 SOFA SO:0000650 small_subunit_rRNA "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke] 0 0 45758 5 SOFA SO:0000651 large_subunit_rRNA "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke] 0 0 45759 5 SOFA SO:0000652 rRNA_5S "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001] 0 0 45760 5 SOFA SO:0000653 rRNA_28S "A component of the large ribosomal subunit." [SO:ke] 0 0 45761 5 NULL SO:0000654 maxicircle_gene "A mitochondrial gene located in a maxicircle." [SO:xp] 0 0 45762 5 SOFA SO:0000655 ncRNA "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] 0 0 45763 5 NULL SO:0000656 stRNA_encoding "" [] 0 0 45764 5 SOFA SO:0000657 repeat_region "A region of sequence containing one or more repeat units." [SO:ke] 0 0 45765 5 SOFA SO:0000658 dispersed_repeat "A repeat that is located at dispersed sites in the genome." [SO:ke] 0 0 45766 5 NULL SO:0000659 tmRNA_encoding "" [] 0 0 45767 5 NULL SO:0000660 DNA_invertase_target_sequence "" [] 0 1 45768 5 NULL SO:0000661 intron_attribute "" [] 0 1 45769 5 SOFA SO:0000662 spliceosomal_intron "An intron which is spliced by the spliceosome." [SO:ke] 0 0 45770 5 NULL SO:0000663 tRNA_encoding "" [] 0 0 45771 5 NULL SO:0000664 introgressed_chromosome_region "" [] 0 0 45772 5 NULL SO:0000665 monocistronic_transcript "A transcript that is monocistronic." [SO:xp] 0 0 45773 5 NULL SO:0000666 mobile_intron "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke] 0 0 45774 5 DBVAR,SOFA SO:0000667 insertion "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] 0 0 45775 5 SOFA SO:0000668 EST_match "A match against an EST sequence." [SO:ke] 0 0 45776 5 NULL SO:0000669 sequence_rearrangement_feature "" [] 0 0 45777 5 NULL SO:0000670 chromosome_breakage_sequence "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma] 0 0 45778 5 NULL SO:0000671 internal_eliminated_sequence "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma] 0 0 45779 5 NULL SO:0000672 macronucleus_destined_segment "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma] 0 0 45780 5 SOFA SO:0000673 transcript "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] 0 0 45781 5 NULL SO:0000674 non_canonical_splice_site "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke] 0 1 45782 5 NULL SO:0000675 canonical_splice_site "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke] 0 1 45783 5 NULL SO:0000676 canonical_three_prime_splice_site "The canonical 3' splice site has the sequence \\"AG\\"." [SO:ke] 0 0 45784 5 NULL SO:0000677 canonical_five_prime_splice_site "The canonical 5' splice site has the sequence \\"GT\\"." [SO:ke] 0 0 45785 5 NULL SO:0000678 non_canonical_three_prime_splice_site "A 3' splice site that does not have the sequence \\"AG\\"." [SO:ke] 0 0 45786 5 NULL SO:0000679 non_canonical_five_prime_splice_site "A 5' splice site which does not have the sequence \\"GT\\"." [SO:ke] 0 0 45787 5 NULL SO:0000680 non_canonical_start_codon "A start codon that is not the usual AUG sequence." [SO:ke] 0 0 45788 5 NULL SO:0000681 aberrant_processed_transcript "A transcript that has been processed \\"incorrectly\\", for example by the failure of splicing of one or more exons." [SO:ke] 0 0 45789 5 NULL SO:0000682 splicing_feature "" [] 0 1 45790 5 NULL SO:0000683 exonic_splice_enhancer "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov\\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract] 0 0 45791 5 SOFA SO:0000684 nuclease_sensitive_site "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma] 0 0 45792 5 NULL SO:0000685 DNAseI_hypersensitive_site "" [] 0 0 45793 5 NULL SO:0000686 translocation_element "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma] 0 0 45794 5 SOFA SO:0000687 deletion_junction "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] 0 0 45795 5 SOFA SO:0000688 golden_path "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls] 0 0 45796 5 SOFA SO:0000689 cDNA_match "A match against cDNA sequence." [SO:ke] 0 0 45797 5 NULL SO:0000690 gene_with_polycistronic_transcript "A gene that encodes a polycistronic transcript." [SO:xp] 0 0 45798 5 biosapiens SO:0000691 cleaved_initiator_methionine "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR] 0 0 45799 5 NULL SO:0000692 gene_with_dicistronic_transcript "A gene that encodes a dicistronic transcript." [SO:xp] 0 0 45800 5 NULL SO:0000693 gene_with_recoded_mRNA "A gene that encodes an mRNA that is recoded." [SO:xp] 0 0 45801 5 SOFA SO:0000694 SNP "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] 0 0 45802 5 SOFA SO:0000695 reagent "A sequence used in experiment." [SO:ke] 0 0 45803 5 SOFA SO:0000696 oligo "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] 0 0 45804 5 NULL SO:0000697 gene_with_stop_codon_read_through "A gene that encodes a transcript with stop codon readthrough." [SO:xp] 0 0 45805 5 NULL SO:0000698 gene_with_stop_codon_redefined_as_pyrrolysine "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp] 0 0 45806 5 SOFA SO:0000699 junction "A sequence_feature with an extent of zero." [SO:ke] 0 0 45807 5 SOFA SO:0000700 remark "A comment about the sequence." [SO:ke] 0 0 45808 5 SOFA SO:0000701 possible_base_call_error "A region of sequence where the validity of the base calling is questionable." [SO:ke] 0 0 45809 5 SOFA SO:0000702 possible_assembly_error "A region of sequence where there may have been an error in the assembly." [SO:ke] 0 0 45810 5 SOFA SO:0000703 experimental_result_region "A region of sequence implicated in an experimental result." [SO:ke] 0 0 45811 5 SOFA SO:0000704 gene "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] 0 0 45812 5 SOFA SO:0000705 tandem_repeat "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke] 0 0 45813 5 SOFA SO:0000706 trans_splice_acceptor_site "The 3' splice site of the acceptor primary transcript." [SO:ke] 0 0 45814 5 NULL SO:0000707 trans_splice_donor_site "The 5' five prime splice site region of the donor RNA." [SO:ke] 0 0 45815 5 NULL SO:0000708 SL1_acceptor_site "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw] 0 0 45816 5 NULL SO:0000709 SL2_acceptor_site "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 45817 5 NULL SO:0000710 gene_with_stop_codon_redefined_as_selenocysteine "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp] 0 0 45818 5 NULL SO:0000711 gene_with_mRNA_recoded_by_translational_bypass "A gene with mRNA recoded by translational bypass." [SO:xp] 0 0 45819 5 NULL SO:0000712 gene_with_transcript_with_translational_frameshift "A gene encoding a transcript that has a translational frameshift." [SO:xp] 0 0 45820 5 NULL SO:0000713 DNA_motif "A motif that is active in the DNA form of the sequence." [SO:ke] 0 0 45821 5 SOFA SO:0000714 nucleotide_motif "A region of nucleotide sequence corresponding to a known motif." [SO:ke] 0 0 45822 5 SOFA SO:0000715 RNA_motif "A motif that is active in RNA sequence." [SO:ke] 0 0 45823 5 NULL SO:0000716 dicistronic_mRNA "An mRNA that has the quality dicistronic." [SO:ke] 0 0 45824 5 SOFA SO:0000717 reading_frame "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb] 0 0 45825 5 NULL SO:0000718 blocked_reading_frame "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb] 0 0 45826 5 SOFA SO:0000719 ultracontig "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG] 0 0 45827 5 NULL SO:0000720 foreign_transposable_element "A transposable element that is foreign." [SO:ke] 0 0 45828 5 NULL SO:0000721 gene_with_dicistronic_primary_transcript "A gene that encodes a dicistronic primary transcript." [SO:xp] 0 0 45829 5 NULL SO:0000722 gene_with_dicistronic_mRNA "A gene that encodes a polycistronic mRNA." [SO:xp] 0 0 45830 5 NULL SO:0000723 iDNA "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma] 0 0 45831 5 SOFA SO:0000724 oriT "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45832 5 biosapiens,SOFA SO:0000725 transit_peptide "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 45833 5 NULL SO:0000726 repeat_unit "The simplest repeated component of a repeat region. A single repeat." [SO:ke] 0 0 45834 5 SOFA SO:0000727 CRM "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG] 0 0 45835 5 NULL SO:0000728 intein "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke] 0 0 45836 5 NULL SO:0000729 intein_containing "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke] 0 0 45837 5 SOFA SO:0000730 gap "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] 0 0 45838 5 NULL SO:0000731 fragmentary "An attribute to describe a feature that is incomplete." [SO:ke] 0 0 45839 5 NULL SO:0000732 predicted "An attribute describing an unverified region." [SO:ke] 0 0 45840 5 NULL SO:0000733 feature_attribute "An attribute describing a located_sequence_feature." [SO:ke] 0 0 45841 5 NULL SO:0000734 exemplar_mRNA "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php] 0 0 45842 5 NULL SO:0000735 sequence_location "" [] 0 0 45843 5 NULL SO:0000736 organelle_sequence "" [] 0 0 45844 5 NULL SO:0000737 mitochondrial_sequence "" [] 0 0 45845 5 NULL SO:0000738 nuclear_sequence "" [] 0 0 45846 5 NULL SO:0000739 nucleomorphic_sequence "" [] 0 0 45847 5 NULL SO:0000740 plastid_sequence "" [] 0 0 45848 5 NULL SO:0000741 kinetoplast "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055] 0 0 45849 5 NULL SO:0000742 maxicircle "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055] 0 0 45850 5 NULL SO:0000743 apicoplast_sequence "" [] 0 0 45851 5 NULL SO:0000744 chromoplast_sequence "" [] 0 0 45852 5 NULL SO:0000745 chloroplast_sequence "" [] 0 0 45853 5 NULL SO:0000746 cyanelle_sequence "" [] 0 0 45854 5 NULL SO:0000747 leucoplast_sequence "" [] 0 0 45855 5 NULL SO:0000748 proplastid_sequence "" [] 0 0 45856 5 NULL SO:0000749 plasmid_location "" [] 0 0 45857 5 NULL SO:0000750 amplification_origin "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma] 0 0 45858 5 NULL SO:0000751 proviral_location "" [] 0 0 45859 5 SOFA SO:0000752 gene_group_regulatory_region "" [] 0 0 45860 5 SOFA SO:0000753 clone_insert "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke] 0 0 45861 5 NULL SO:0000754 lambda_vector "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] 0 0 45862 5 NULL SO:0000755 plasmid_vector "" [] 0 0 45863 5 NULL SO:0000756 cDNA "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma] 0 0 45864 5 NULL SO:0000757 single_stranded_cDNA "" [] 0 0 45865 5 NULL SO:0000758 double_stranded_cDNA "" [] 0 0 45866 5 NULL SO:0000759 plasmid_clone "" [] 0 1 45867 5 NULL SO:0000760 YAC_clone "" [] 0 1 45868 5 NULL SO:0000761 phagemid_clone "" [] 0 1 45869 5 NULL SO:0000762 PAC_clone "" [] 0 1 45870 5 NULL SO:0000763 fosmid_clone "" [] 0 1 45871 5 NULL SO:0000764 BAC_clone "" [] 0 1 45872 5 NULL SO:0000765 cosmid_clone "" [] 0 1 45873 5 NULL SO:0000766 pyrrolysyl_tRNA "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke] 0 0 45874 5 NULL SO:0000767 clone_insert_start "" [] 0 1 45875 5 NULL SO:0000768 episome "A plasmid that may integrate with a chromosome." [SO:ma] 0 0 45876 5 NULL SO:0000769 tmRNA_coding_piece "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962] 0 0 45877 5 NULL SO:0000770 tmRNA_acceptor_piece "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw] 0 0 45878 5 NULL SO:0000771 QTL "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/] 0 0 45879 5 NULL SO:0000772 genomic_island "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke] 0 0 45880 5 NULL SO:0000773 pathogenic_island "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke] 0 0 45881 5 NULL SO:0000774 metabolic_island "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] 0 0 45882 5 NULL SO:0000775 adaptive_island "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke] 0 0 45883 5 NULL SO:0000776 symbiosis_island "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] 0 0 45884 5 SOFA SO:0000777 pseudogenic_rRNA "A non functional descendant of an rRNA." [SO:ke] 0 0 45885 5 SOFA SO:0000778 pseudogenic_tRNA "A non functional descendent of a tRNA." [SO:ke] 0 0 45886 5 NULL SO:0000779 engineered_episome "An episome that is engineered." [SO:xp] 0 0 45887 5 NULL SO:0000780 transposable_element_attribute "" [] 0 1 45888 5 NULL SO:0000781 transgenic "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke] 0 0 45889 5 NULL SO:0000782 natural "An attribute describing a feature that occurs in nature." [SO:ke] 0 0 45890 5 NULL SO:0000783 engineered "An attribute to describe a region that was modified in vitro." [SO:ke] 0 0 45891 5 NULL SO:0000784 foreign "An attribute to describe a region from another species." [SO:ke] 0 0 45892 5 NULL SO:0000785 cloned_region "" [] 0 0 45893 5 NULL SO:0000786 reagent_attribute "" [] 0 1 45894 5 NULL SO:0000787 clone_attribute "" [] 0 1 45895 5 NULL SO:0000788 cloned "" [] 0 1 45896 5 NULL SO:0000789 validated "An attribute to describe a feature that has been proven." [SO:ke] 0 0 45897 5 NULL SO:0000790 invalidated "An attribute describing a feature that is invalidated." [SO:ke] 0 0 45898 5 NULL SO:0000791 cloned_genomic "" [] 0 1 45899 5 NULL SO:0000792 cloned_cDNA "" [] 0 1 45900 5 NULL SO:0000793 engineered_DNA "" [] 0 1 45901 5 NULL SO:0000794 engineered_rescue_region "A rescue region that is engineered." [SO:xp] 0 0 45902 5 NULL SO:0000795 rescue_mini_gene "A mini_gene that rescues." [SO:xp] 0 0 45903 5 NULL SO:0000796 transgenic_transposable_element "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc] 0 0 45904 5 NULL SO:0000797 natural_transposable_element "TE that exists (or existed) in nature." [FB:mc] 0 0 45905 5 NULL SO:0000798 engineered_transposable_element "TE that has been modified by manipulations in vitro." [FB:mc] 0 0 45906 5 NULL SO:0000799 engineered_foreign_transposable_element "A transposable_element that is engineered and foreign." [FB:mc] 0 0 45907 5 NULL SO:0000800 assortment_derived_duplication "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm] 0 0 45908 5 NULL SO:0000801 assortment_derived_deficiency_plus_duplication "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm] 0 0 45909 5 NULL SO:0000802 assortment_derived_deficiency "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm] 0 0 45910 5 NULL SO:0000803 assortment_derived_aneuploid "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm] 0 0 45911 5 NULL SO:0000804 engineered_region "A region that is engineered." [SO:xp] 0 0 45912 5 NULL SO:0000805 engineered_foreign_region "A region that is engineered and foreign." [SO:xp] 0 0 45913 5 NULL SO:0000806 fusion "" [] 0 0 45914 5 NULL SO:0000807 engineered_tag "A tag that is engineered." [SO:xp] 0 0 45915 5 NULL SO:0000808 validated_cDNA_clone "A cDNA clone that has been validated." [SO:xp] 0 0 45916 5 NULL SO:0000809 invalidated_cDNA_clone "A cDNA clone that is invalid." [SO:xp] 0 0 45917 5 NULL SO:0000810 chimeric_cDNA_clone "A cDNA clone invalidated because it is chimeric." [SO:xp] 0 0 45918 5 NULL SO:0000811 genomically_contaminated_cDNA_clone "A cDNA clone invalidated by genomic contamination." [SO:xp] 0 0 45919 5 NULL SO:0000812 polyA_primed_cDNA_clone "A cDNA clone invalidated by polyA priming." [SO:xp] 0 0 45920 5 NULL SO:0000813 partially_processed_cDNA_clone "A cDNA invalidated clone by partial processing." [SO:xp] 0 0 45921 5 NULL SO:0000814 rescue "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke] 0 0 45922 5 NULL SO:0000815 mini_gene "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143] 0 0 45923 5 NULL SO:0000816 rescue_gene "A gene that rescues." [SO:xp] 0 0 45924 5 NULL SO:0000817 wild_type "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke] 0 0 45925 5 NULL SO:0000818 wild_type_rescue_gene "A gene that rescues." [SO:xp] 0 0 45926 5 NULL SO:0000819 mitochondrial_chromosome "A chromosome originating in a mitochondria." [SO:xp] 0 0 45927 5 NULL SO:0000820 chloroplast_chromosome "A chromosome originating in a chloroplast." [SO:xp] 0 0 45928 5 NULL SO:0000821 chromoplast_chromosome "A chromosome originating in a chromoplast." [SO:xp] 0 0 45929 5 NULL SO:0000822 cyanelle_chromosome "A chromosome originating in a cyanelle." [SO:xp] 0 0 45930 5 NULL SO:0000823 leucoplast_chromosome "A chromosome with origin in a leucoplast." [SO:xp] 0 0 45931 5 NULL SO:0000824 macronuclear_chromosome "A chromosome originating in a macronucleus." [SO:xp] 0 0 45932 5 NULL SO:0000825 micronuclear_chromosome "A chromosome originating in a micronucleus." [SO:xp] 0 0 45933 5 NULL SO:0000828 nuclear_chromosome "A chromosome originating in a nucleus." [SO:xp] 0 0 45934 5 NULL SO:0000829 nucleomorphic_chromosome "A chromosome originating in a nucleomorph." [SO:xp] 0 0 45935 5 SOFA SO:0000830 chromosome_part "A region of a chromosome." [SO:ke] 0 0 45936 5 SOFA SO:0000831 gene_member_region "A region of a gene." [SO:ke] 0 0 45937 5 NULL SO:0000832 promoter_region "A region of sequence which is part of a promoter." [SO:ke] 0 1 45938 5 SOFA SO:0000833 transcript_region "A region of a transcript." [SO:ke] 0 0 45939 5 SOFA SO:0000834 mature_transcript_region "A region of a mature transcript." [SO:ke] 0 0 45940 5 SOFA SO:0000835 primary_transcript_region "A part of a primary transcript." [SO:ke] 0 0 45941 5 SOFA SO:0000836 mRNA_region "A region of an mRNA." [SO:cb] 0 0 45942 5 SOFA SO:0000837 UTR_region "A region of UTR." [SO:ke] 0 0 45943 5 NULL SO:0000838 rRNA_primary_transcript_region "A region of an rRNA primary transcript." [SO:ke] 0 0 45944 5 biosapiens,SOFA SO:0000839 polypeptide_region "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] 0 0 45945 5 NULL SO:0000840 repeat_component "A region of a repeated sequence." [SO:ke] 0 0 45946 5 SOFA SO:0000841 spliceosomal_intron_region "A region within an intron." [SO:ke] 0 0 45947 5 SOFA SO:0000842 gene_component_region "" [] 0 0 45948 5 NULL SO:0000843 bacterial_RNApol_promoter_region "A region which is part of a bacterial RNA polymerase promoter." [SO:ke] 0 1 45949 5 NULL SO:0000844 RNApol_II_promoter_region "A region of sequence which is a promoter for RNA polymerase II." [SO:ke] 0 1 45950 5 NULL SO:0000845 RNApol_III_promoter_type_1_region "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke] 0 1 45951 5 NULL SO:0000846 RNApol_III_promoter_type_2_region "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke] 0 1 45952 5 NULL SO:0000847 tmRNA_region "A region of a tmRNA." [SO:cb] 0 0 45953 5 NULL SO:0000848 LTR_component "" [] 0 0 45954 5 NULL SO:0000849 three_prime_LTR_component "" [] 0 0 45955 5 NULL SO:0000850 five_prime_LTR_component "" [] 0 0 45956 5 SOFA SO:0000851 CDS_region "A region of a CDS." [SO:cb] 0 0 45957 5 SOFA SO:0000852 exon_region "A region of an exon." [RSC:cb] 0 0 45958 5 NULL SO:0000853 homologous_region "A region that is homologous to another region." [SO:ke] 0 0 45959 5 NULL SO:0000854 paralogous_region "A homologous_region that is paralogous to another region." [SO:ke] 0 0 45960 5 NULL SO:0000855 orthologous_region "A homologous_region that is orthologous to another region." [SO:ke] 0 0 45961 5 NULL SO:0000856 conserved "" [] 0 0 45962 5 NULL SO:0000857 homologous "Similarity due to common ancestry." [SO:ke] 0 0 45963 5 NULL SO:0000858 orthologous "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke] 0 0 45964 5 NULL SO:0000859 paralogous "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke] 0 0 45965 5 NULL SO:0000860 syntenic "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke] 0 0 45966 5 NULL SO:0000861 capped_primary_transcript "A primary transcript that is capped." [SO:xp] 0 0 45967 5 NULL SO:0000862 capped_mRNA "An mRNA that is capped." [SO:xp] 0 0 45968 5 NULL SO:0000863 mRNA_attribute "An attribute describing an mRNA feature." [SO:ke] 0 0 45969 5 NULL SO:0000864 exemplar "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke] 0 0 45970 5 NULL SO:0000865 frameshift "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke] 0 0 45971 5 NULL SO:0000866 minus_1_frameshift "A frameshift caused by deleting one base." [SO:ke] 0 0 45972 5 NULL SO:0000867 minus_2_frameshift "A frameshift caused by deleting two bases." [SO:ke] 0 0 45973 5 NULL SO:0000868 plus_1_frameshift "A frameshift caused by inserting one base." [SO:ke] 0 0 45974 5 NULL SO:0000869 plus_2_framshift "A frameshift caused by inserting two bases." [SO:ke] 0 0 45975 5 NULL SO:0000870 trans_spliced "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke] 0 0 45976 5 NULL SO:0000871 polyadenylated_mRNA "An mRNA that is polyadenylated." [SO:xp] 0 0 45977 5 NULL SO:0000872 trans_spliced_mRNA "An mRNA that is trans-spliced." [SO:xp] 0 0 45978 5 NULL SO:0000873 edited_transcript "A transcript that is edited." [SO:ke] 0 0 45979 5 NULL SO:0000874 edited_transcript_by_A_to_I_substitution "A transcript that has been edited by A to I substitution." [SO:ke] 0 0 45980 5 NULL SO:0000875 bound_by_protein "An attribute describing a sequence that is bound by a protein." [SO:ke] 0 0 45981 5 NULL SO:0000876 bound_by_nucleic_acid "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke] 0 0 45982 5 NULL SO:0000877 alternatively_spliced "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke] 0 0 45983 5 NULL SO:0000878 monocistronic "An attribute describing a sequence that contains the code for one gene product." [SO:ke] 0 0 45984 5 NULL SO:0000879 dicistronic "An attribute describing a sequence that contains the code for two gene products." [SO:ke] 0 0 45985 5 NULL SO:0000880 polycistronic "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke] 0 0 45986 5 NULL SO:0000881 recoded "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke] 0 0 45987 5 NULL SO:0000882 codon_redefined "An attribute describing the alteration of codon meaning." [SO:ke] 0 0 45988 5 NULL SO:0000883 stop_codon_read_through "A stop codon redefined to be a new amino acid." [SO:ke] 0 0 45989 5 NULL SO:0000884 stop_codon_redefined_as_pyrrolysine "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke] 0 0 45990 5 NULL SO:0000885 stop_codon_redefined_as_selenocysteine "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke] 0 0 45991 5 NULL SO:0000886 recoded_by_translational_bypass "Recoded mRNA where a block of nucleotides is not translated." [SO:ke] 0 0 45992 5 NULL SO:0000887 translationally_frameshifted "Recoding by frameshifting a particular site." [SO:ke] 0 0 45993 5 NULL SO:0000888 maternally_imprinted_gene "A gene that is maternally_imprinted." [SO:xp] 0 0 45994 5 NULL SO:0000889 paternally_imprinted_gene "A gene that is paternally imprinted." [SO:xp] 0 0 45995 5 NULL SO:0000890 post_translationally_regulated_gene "A gene that is post translationally regulated." [SO:xp] 0 0 45996 5 NULL SO:0000891 negatively_autoregulated_gene "A gene that is negatively autoreguated." [SO:xp] 0 0 45997 5 NULL SO:0000892 positively_autoregulated_gene "A gene that is positively autoregulated." [SO:xp] 0 0 45998 5 NULL SO:0000893 silenced "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke] 0 0 45999 5 NULL SO:0000894 silenced_by_DNA_modification "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke] 0 0 46000 5 NULL SO:0000895 silenced_by_DNA_methylation "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke] 0 0 46001 5 NULL SO:0000896 translationally_regulated_gene "A gene that is translationally regulated." [SO:xp] 0 0 46002 5 NULL SO:0000897 allelically_excluded_gene "A gene that is allelically_excluded." [SO:xp] 0 0 46003 5 NULL SO:0000898 epigenetically_modified_gene "A gene that is epigenetically modified." [SO:ke] 0 0 46004 5 NULL SO:0000899 nuclear_mitochondrial "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke] 0 1 46005 5 NULL SO:0000900 processed "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke] 0 1 46006 5 NULL SO:0000901 unequally_crossed_over "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke] 0 1 46007 5 NULL SO:0000902 transgene "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp] 0 0 46008 5 NULL SO:0000903 endogenous_retroviral_sequence "" [] 0 0 46009 5 NULL SO:0000904 rearranged_at_DNA_level "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke] 0 0 46010 5 NULL SO:0000905 status "An attribute describing the status of a feature, based on the available evidence." [SO:ke] 0 0 46011 5 NULL SO:0000906 independently_known "Attribute to describe a feature that is independently known - not predicted." [SO:ke] 0 0 46012 5 NULL SO:0000907 supported_by_sequence_similarity "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke] 0 0 46013 5 NULL SO:0000908 supported_by_domain_match "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke] 0 0 46014 5 NULL SO:0000909 supported_by_EST_or_cDNA "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke] 0 0 46015 5 NULL SO:0000910 orphan "" [] 0 0 46016 5 NULL SO:0000911 predicted_by_ab_initio_computation "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke] 0 0 46017 5 biosapiens SO:0000912 asx_turn "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46018 5 NULL SO:0000913 cloned_cDNA_insert "A clone insert made from cDNA." [SO:xp] 0 0 46019 5 NULL SO:0000914 cloned_genomic_insert "A clone insert made from genomic DNA." [SO:xp] 0 0 46020 5 NULL SO:0000915 engineered_insert "A clone insert that is engineered." [SO:xp] 0 0 46021 5 NULL SO:0000916 edit_operation "" [] 0 1 46022 5 NULL SO:0000917 insert_U "An edit to insert a U." [SO:ke] 0 1 46023 5 NULL SO:0000918 delete_U "An edit to delete a uridine." [SO:ke] 0 1 46024 5 NULL SO:0000919 substitute_A_to_I "An edit to substitute an I for an A." [SO:ke] 0 1 46025 5 NULL SO:0000920 insert_C "An edit to insert a cytidine." [SO:ke] 0 1 46026 5 NULL SO:0000921 insert_dinucleotide "An edit to insert a dinucleotide." [SO:ke] 0 1 46027 5 NULL SO:0000922 substitute_C_to_U "An edit to substitute an U for a C." [SO:ke] 0 1 46028 5 NULL SO:0000923 insert_G "An edit to insert a G." [SO:ke] 0 1 46029 5 NULL SO:0000924 insert_GC "An edit to insert a GC dinucleotide." [SO:ke] 0 1 46030 5 NULL SO:0000925 insert_GU "An edit to insert a GU dinucleotide." [SO:ke] 0 1 46031 5 NULL SO:0000926 insert_CU "An edit to insert a CU dinucleotide." [SO:ke] 0 1 46032 5 NULL SO:0000927 insert_AU "An edit to insert a AU dinucleotide." [SO:ke] 0 1 46033 5 NULL SO:0000928 insert_AA "An edit to insert a AA dinucleotide." [SO:ke] 0 1 46034 5 NULL SO:0000929 edited_mRNA "An mRNA that is edited." [SO:xp] 0 0 46035 5 NULL SO:0000930 guide_RNA_region "A region of guide RNA." [SO:ma] 0 0 46036 5 NULL SO:0000931 anchor_region "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk] 0 0 46037 5 NULL SO:0000932 pre_edited_mRNA "" [] 0 0 46038 5 NULL SO:0000933 intermediate "An attribute to describe a feature between stages of processing." [SO:ke] 0 0 46039 5 NULL SO:0000934 miRNA_target_site "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds] 0 0 46040 5 NULL SO:0000935 edited_CDS "A CDS that is edited." [SO:xp] 0 0 46041 5 NULL SO:0000936 vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment "" [] 0 0 46042 5 NULL SO:0000937 vertebrate_immune_system_feature "" [] 0 1 46043 5 NULL SO:0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster "" [] 0 0 46044 5 NULL SO:0000939 vertebrate_immune_system_gene_recombination_signal_feature "" [] 0 0 46045 5 NULL SO:0000940 recombinationally_rearranged "" [] 0 0 46046 5 NULL SO:0000941 recombinationally_rearranged_vertebrate_immune_system_gene "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp] 0 0 46047 5 NULL SO:0000942 attP_site "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as] 0 0 46048 5 NULL SO:0000943 attB_site "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as] 0 0 46049 5 NULL SO:0000944 attL_site "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as] 0 0 46050 5 NULL SO:0000945 attR_site "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as] 0 0 46051 5 NULL SO:0000946 integration_excision_site "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as] 0 0 46052 5 NULL SO:0000947 resolution_site "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as] 0 0 46053 5 NULL SO:0000948 inversion_site "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma] 0 0 46054 5 NULL SO:0000949 dif_site "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as] 0 0 46055 5 NULL SO:0000950 attC_site "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as] 0 0 46056 5 NULL SO:0000951 eukaryotic_terminator "" [] 0 0 46057 5 NULL SO:0000952 oriV "An origin of vegetative replication in plasmids and phages." [SO:as] 0 0 46058 5 NULL SO:0000953 oriC "An origin of bacterial chromosome replication." [SO:as] 0 0 46059 5 NULL SO:0000954 DNA_chromosome "Structural unit composed of a self-replicating, DNA molecule." [SO:ma] 0 0 46060 5 NULL SO:0000955 double_stranded_DNA_chromosome "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma] 0 0 46061 5 NULL SO:0000956 single_stranded_DNA_chromosome "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma] 0 0 46062 5 NULL SO:0000957 linear_double_stranded_DNA_chromosome "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma] 0 0 46063 5 NULL SO:0000958 circular_double_stranded_DNA_chromosome "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma] 0 0 46064 5 NULL SO:0000959 linear_single_stranded_DNA_chromosome "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma] 0 0 46065 5 NULL SO:0000960 circular_single_stranded_DNA_chromosome "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] 0 0 46066 5 NULL SO:0000961 RNA_chromosome "Structural unit composed of a self-replicating, RNA molecule." [SO:ma] 0 0 46067 5 NULL SO:0000962 single_stranded_RNA_chromosome "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma] 0 0 46068 5 NULL SO:0000963 linear_single_stranded_RNA_chromosome "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma] 0 0 46069 5 NULL SO:0000964 linear_double_stranded_RNA_chromosome "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma] 0 0 46070 5 NULL SO:0000965 double_stranded_RNA_chromosome "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma] 0 0 46071 5 NULL SO:0000966 circular_single_stranded_RNA_chromosome "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] 0 0 46072 5 NULL SO:0000967 circular_double_stranded_RNA_chromosome "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma] 0 0 46073 5 NULL SO:0000968 sequence_replication_mode "" [] 0 1 46074 5 NULL SO:0000969 rolling_circle "" [] 0 1 46075 5 NULL SO:0000970 theta_replication "" [] 0 1 46076 5 NULL SO:0000971 DNA_replication_mode "" [] 0 1 46077 5 NULL SO:0000972 RNA_replication_mode "" [] 0 1 46078 5 NULL SO:0000973 insertion_sequence "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as] 0 0 46079 5 NULL SO:0000975 minicircle_gene "" [] 0 0 46080 5 NULL SO:0000976 cryptic "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke] 0 0 46081 5 NULL SO:0000977 anchor_binding_site "" [] 0 0 46082 5 NULL SO:0000978 template_region "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk] 0 0 46083 5 NULL SO:0000979 gRNA_encoding "A non-protein_coding gene that encodes a guide_RNA." [SO:ma] 0 0 46084 5 NULL SO:0000980 minicircle "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055] 0 0 46085 5 NULL SO:0000981 rho_dependent_bacterial_terminator "" [] 0 0 46086 5 NULL SO:0000982 rho_independent_bacterial_terminator "" [] 0 0 46087 5 NULL SO:0000983 strand_attribute "" [] 0 0 46088 5 NULL SO:0000984 single "" [] 0 0 46089 5 NULL SO:0000985 double "" [] 0 0 46090 5 NULL SO:0000986 topology_attribute "" [] 0 0 46091 5 NULL SO:0000987 linear "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb] 0 0 46092 5 NULL SO:0000988 circular "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb] 0 0 46093 5 NULL SO:0000989 class_II_RNA "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] 0 0 46094 5 NULL SO:0000990 class_I_RNA "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] 0 0 46095 5 NULL SO:0000991 genomic_DNA "" [] 0 0 46096 5 NULL SO:0000992 BAC_cloned_genomic_insert "" [] 0 0 46097 5 NULL SO:0000993 consensus "" [] 0 0 46098 5 NULL SO:0000994 consensus_region "" [] 0 0 46099 5 NULL SO:0000995 consensus_mRNA "" [] 0 0 46100 5 NULL SO:0000996 predicted_gene "" [] 0 0 46101 5 NULL SO:0000997 gene_fragment "" [] 0 0 46102 5 NULL SO:0000998 recursive_splice_site "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661] 0 0 46103 5 NULL SO:0000999 BAC_end "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke] 0 0 46104 5 SOFA SO:0001000 rRNA_16S "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke] 0 0 46105 5 SOFA SO:0001001 rRNA_23S "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke] 0 0 46106 5 SOFA SO:0001002 rRNA_25S "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb] 0 0 46107 5 NULL SO:0001003 solo_LTR "A recombination product between the 2 LTR of the same element." [SO:ke] 0 0 46108 5 NULL SO:0001004 low_complexity "" [] 0 0 46109 5 NULL SO:0001005 low_complexity_region "" [] 0 0 46110 5 NULL SO:0001006 prophage "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \\"island\\"." [GOC:jl] 0 0 46111 5 NULL SO:0001007 cryptic_prophage "A remnant of an integrated prophage in the host genome or an \\"island\\" in the host genome that includes phage like-genes." [GOC:jl] 0 0 46112 5 NULL SO:0001008 tetraloop "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke] 0 0 46113 5 NULL SO:0001009 DNA_constraint_sequence "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\\]&dispmax=50] 0 0 46114 5 NULL SO:0001010 i_motif "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739] 0 0 46115 5 NULL SO:0001011 PNA_oligo "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke] 0 0 46116 5 NULL SO:0001012 DNAzyme "A DNA sequence with catalytic activity." [SO:cb] 0 0 46117 5 NULL SO:0001013 MNP "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431] 0 0 46118 5 NULL SO:0001014 intron_domain "" [] 0 0 46119 5 NULL SO:0001015 wobble_base_pair "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617] 0 0 46120 5 NULL SO:0001016 internal_guide_sequence "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb] 0 0 46121 5 NULL SO:0001017 silent_mutation "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke] 0 0 46122 5 NULL SO:0001018 epitope "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb] 0 0 46123 5 SOFA SO:0001019 copy_number_variation "A variation that increases or decreases the copy number of a given region." [SO:ke] 0 0 46124 5 NULL SO:0001020 sequence_variant_affecting_copy_number "" [] 0 1 46125 5 NULL SO:0001021 chromosome_breakpoint "" [] 0 0 46126 5 NULL SO:0001022 inversion_breakpoint "The point within a chromosome where an inversion begins or ends." [SO:cb] 0 0 46127 5 NULL SO:0001023 allele "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop] 0 0 46128 5 NULL SO:0001024 haplotype "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop] 0 0 46129 5 NULL SO:0001025 polymorphic_sequence_variant "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop] 0 0 46130 5 NULL SO:0001026 genome "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop] 0 0 46131 5 NULL SO:0001027 genotype "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop] 0 0 46132 5 NULL SO:0001028 diplotype "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop] 0 0 46133 5 NULL SO:0001029 direction_attribute "" [] 0 0 46134 5 NULL SO:0001030 forward "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke] 0 0 46135 5 NULL SO:0001031 reverse "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke] 0 0 46136 5 NULL SO:0001032 mitochondrial_DNA "" [] 0 0 46137 5 NULL SO:0001033 chloroplast_DNA "" [] 0 0 46138 5 NULL SO:0001034 miRtron "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma] 0 0 46139 5 NULL SO:0001035 piRNA "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke] 0 0 46140 5 NULL SO:0001036 arginyl_tRNA "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke] 0 0 46141 5 SOFA SO:0001037 mobile_genetic_element "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355] 0 0 46142 5 NULL SO:0001038 extrachromosomal_mobile_genetic_element "An MGE that is not integrated into the host chromosome." [SO:ke] 0 0 46143 5 SOFA SO:0001039 integrated_mobile_genetic_element "An MGE that is integrated into the host chromosome." [SO:ke] 0 0 46144 5 NULL SO:0001040 integrated_plasmid "A plasmid sequence that is integrated within the host chromosome." [SO:ke] 0 0 46145 5 NULL SO:0001041 viral_sequence "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke] 0 0 46146 5 NULL SO:0001042 phage_sequence "The nucleotide sequence of a virus that infects bacteria." [SO:ke] 0 0 46147 5 NULL SO:0001043 attCtn_site "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at] 0 0 46148 5 NULL SO:0001044 nuclear_mt_pseudogene "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp] 0 0 46149 5 NULL SO:0001045 cointegrated_plasmid "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at] 0 0 46150 5 NULL SO:0001046 IRLinv_site "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at] 0 0 46151 5 NULL SO:0001047 IRRinv_site "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at] 0 0 46152 5 NULL SO:0001048 inversion_site_part "A region located within an inversion site." [SO:ke] 0 0 46153 5 NULL SO:0001049 defective_conjugative_transposon "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane] 0 0 46154 5 NULL SO:0001050 repeat_fragment "A portion of a repeat, interrupted by the insertion of another element." [SO:ke] 0 0 46155 5 NULL SO:0001051 nested_region "" [] 0 1 46156 5 NULL SO:0001052 nested_repeat "" [] 0 1 46157 5 NULL SO:0001053 nested_transposon "" [] 0 1 46158 5 NULL SO:0001054 transposon_fragment "A portion of a transposon, interrupted by the insertion of another element." [SO:ke] 0 0 46159 5 SOFA SO:0001055 transcriptional_cis_regulatory_region "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative] 0 0 46160 5 SOFA SO:0001056 splicing_regulatory_region "A regulatory_region that modulates splicing." [SO:ke] 0 0 46161 5 NULL SO:0001057 enhanceosome "" [] 0 1 46162 5 NULL SO:0001058 promoter_targeting_sequence "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative] 0 0 46163 5 SOFA SO:0001059 sequence_alteration "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] 0 0 46164 5 NULL SO:0001060 sequence_variant "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] 1 0 46165 5 biosapiens SO:0001061 propeptide_cleavage_site "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR] 0 0 46166 5 biosapiens SO:0001062 propeptide "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR] 0 0 46167 5 biosapiens,SOFA SO:0001063 immature_peptide_region "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR] 0 0 46168 5 biosapiens SO:0001064 active_peptide "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual] 0 0 46169 5 biosapiens SO:0001066 compositionally_biased_region_of_peptide "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual] 0 0 46170 5 biosapiens SO:0001067 polypeptide_motif "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual] 0 0 46171 5 biosapiens SO:0001068 polypeptide_repeat "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR] 0 0 46172 5 biosapiens SO:0001070 polypeptide_structural_region "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb] 0 0 46173 5 biosapiens SO:0001071 membrane_structure "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR] 0 0 46174 5 biosapiens SO:0001072 extramembrane_polypeptide_region "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb] 0 0 46175 5 biosapiens SO:0001073 cytoplasmic_polypeptide_region "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb] 0 0 46176 5 biosapiens SO:0001074 non_cytoplasmic_polypeptide_region "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb] 0 0 46177 5 biosapiens SO:0001075 intramembrane_polypeptide_region "Polypeptide region present in the lipid bilayer." [EBIBS:GAR] 0 0 46178 5 biosapiens SO:0001076 membrane_peptide_loop "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb] 0 0 46179 5 biosapiens SO:0001077 transmembrane_polypeptide_region "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual] 0 0 46180 5 biosapiens SO:0001078 polypeptide_secondary_structure "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR] 0 0 46181 5 biosapiens SO:0001079 polypeptide_structural_motif "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR] 0 0 46182 5 biosapiens SO:0001080 coiled_coil "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual] 0 0 46183 5 biosapiens SO:0001081 helix_turn_helix "A motif comprising two helices separated by a turn." [EBIBS:GAR] 0 0 46184 5 biosapiens SO:0001082 polypeptide_sequencing_information "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR] 0 0 46185 5 biosapiens SO:0001083 non_adjacent_residues "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual] 0 0 46186 5 biosapiens SO:0001084 non_terminal_residue "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual] 0 0 46187 5 biosapiens SO:0001085 sequence_conflict "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual] 0 0 46188 5 biosapiens SO:0001086 sequence_uncertainty "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual] 0 0 46189 5 biosapiens SO:0001087 cross_link "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual] 0 1 46190 5 biosapiens SO:0001088 disulfide_bond "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual] 0 1 46191 5 biosapiens SO:0001089 post_translationally_modified_region "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual] 0 0 46192 5 biosapiens SO:0001090 covalent_binding_site "Binding involving a covalent bond." [EBIBS:GAR] 0 1 46193 5 biosapiens SO:0001091 non_covalent_binding_site "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR] 0 1 46194 5 biosapiens SO:0001092 polypeptide_metal_contact "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual] 0 0 46195 5 biosapiens SO:0001093 protein_protein_contact "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual] 0 0 46196 5 biosapiens SO:0001094 polypeptide_calcium_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR] 0 0 46197 5 biosapiens SO:0001095 polypeptide_cobalt_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb] 0 0 46198 5 biosapiens SO:0001096 polypeptide_copper_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb] 0 0 46199 5 biosapiens SO:0001097 polypeptide_iron_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb] 0 0 46200 5 biosapiens SO:0001098 polypeptide_magnesium_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb] 0 0 46201 5 biosapiens SO:0001099 polypeptide_manganese_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb] 0 0 46202 5 biosapiens SO:0001100 polypeptide_molybdenum_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb] 0 0 46203 5 biosapiens SO:0001101 polypeptide_nickel_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR] 0 0 46204 5 biosapiens SO:0001102 polypeptide_tungsten_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb] 0 0 46205 5 biosapiens SO:0001103 polypeptide_zinc_ion_contact_site "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb] 0 0 46206 5 biosapiens SO:0001104 catalytic_residue "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual] 0 0 46207 5 biosapiens SO:0001105 polypeptide_ligand_contact "Residues which interact with a ligand." [EBIBS:GAR] 0 0 46208 5 biosapiens SO:0001106 asx_motif "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46209 5 biosapiens SO:0001107 beta_bulge "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46210 5 biosapiens SO:0001108 beta_bulge_loop "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46211 5 biosapiens SO:0001109 beta_bulge_loop_five "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46212 5 biosapiens SO:0001110 beta_bulge_loop_six "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46213 5 biosapiens SO:0001111 beta_strand "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual] 0 0 46214 5 biosapiens SO:0001112 antiparallel_beta_strand "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual] 0 0 46215 5 biosapiens SO:0001113 parallel_beta_strand "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual] 0 0 46216 5 biosapiens SO:0001114 peptide_helix "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR] 0 0 46217 5 biosapiens SO:0001115 left_handed_peptide_helix "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR] 0 0 46218 5 biosapiens SO:0001116 right_handed_peptide_helix "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR] 0 0 46219 5 biosapiens SO:0001117 alpha_helix "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR] 0 0 46220 5 biosapiens SO:0001118 pi_helix "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR] 0 0 46221 5 biosapiens SO:0001119 three_ten_helix "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR] 0 0 46222 5 biosapiens SO:0001120 polypeptide_nest_motif "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46223 5 biosapiens SO:0001121 polypeptide_nest_left_right_motif "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46224 5 biosapiens SO:0001122 polypeptide_nest_right_left_motif "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46225 5 biosapiens SO:0001123 schellmann_loop "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46226 5 biosapiens SO:0001124 schellmann_loop_seven "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46227 5 biosapiens SO:0001125 schellmann_loop_six "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46228 5 biosapiens SO:0001126 serine_threonine_motif "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46229 5 biosapiens SO:0001127 serine_threonine_staple_motif "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46230 5 biosapiens SO:0001128 polypeptide_turn_motif "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type] 0 0 46231 5 biosapiens SO:0001129 asx_turn_left_handed_type_one "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46232 5 biosapiens SO:0001130 asx_turn_left_handed_type_two "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46233 5 biosapiens SO:0001131 asx_turn_right_handed_type_two "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46234 5 biosapiens SO:0001132 asx_turn_right_handed_type_one "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46235 5 biosapiens SO:0001133 beta_turn "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46236 5 biosapiens SO:0001134 beta_turn_left_handed_type_one "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46237 5 biosapiens SO:0001135 beta_turn_left_handed_type_two "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46238 5 biosapiens SO:0001136 beta_turn_right_handed_type_one "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46239 5 biosapiens SO:0001137 beta_turn_right_handed_type_two "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46240 5 biosapiens SO:0001138 gamma_turn "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46241 5 biosapiens SO:0001139 gamma_turn_classic "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46242 5 biosapiens SO:0001140 gamma_turn_inverse "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46243 5 biosapiens SO:0001141 serine_threonine_turn "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46244 5 biosapiens SO:0001142 st_turn_left_handed_type_one "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46245 5 biosapiens SO:0001143 st_turn_left_handed_type_two "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46246 5 biosapiens SO:0001144 st_turn_right_handed_type_one "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46247 5 biosapiens SO:0001145 st_turn_right_handed_type_two "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 46248 5 biosapiens SO:0001146 polypeptide_variation_site "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke] 0 0 46249 5 biosapiens SO:0001147 natural_variant_site "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual] 0 0 46250 5 biosapiens SO:0001148 mutated_variant_site "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual] 0 0 46251 5 biosapiens SO:0001149 alternate_sequence_site "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual] 0 0 46252 5 biosapiens SO:0001150 beta_turn_type_six "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb] 0 0 46253 5 biosapiens SO:0001151 beta_turn_type_six_a "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] 0 0 46254 5 biosapiens SO:0001152 beta_turn_type_six_a_one "" [] 0 0 46255 5 biosapiens SO:0001153 beta_turn_type_six_a_two "" [] 0 0 46256 5 biosapiens SO:0001154 beta_turn_type_six_b "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] 0 0 46257 5 biosapiens SO:0001155 beta_turn_type_eight "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb] 0 0 46258 5 NULL SO:0001156 DRE_motif "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576] 0 0 46259 5 NULL SO:0001157 DMv4_motif "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941\\:12537576] 0 0 46260 5 NULL SO:0001158 E_box_motif "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576\\:16827941] 0 0 46261 5 NULL SO:0001159 DMv5_motif "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\\:16827941] 0 0 46262 5 NULL SO:0001160 DMv3_motif "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576\\:16827941] 0 0 46263 5 NULL SO:0001161 DMv2_motif "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576\\:16827941] 0 0 46264 5 NULL SO:0001162 MTE "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576\\:15231738, PMID:16858867] 0 0 46265 5 NULL SO:0001163 INR1_motif "A promoter motif with consensus sequence TCATTCG." [PMID:16827941] 0 0 46266 5 NULL SO:0001164 DPE1_motif "A promoter motif with consensus sequence CGGACGT." [PMID:16827941] 0 0 46267 5 NULL SO:0001165 DMv1_motif "A promoter motif with consensus sequence CARCCCT." [PMID:16827941] 0 0 46268 5 NULL SO:0001166 GAGA_motif "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941] 0 0 46269 5 NULL SO:0001167 NDM2_motif "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941] 0 0 46270 5 NULL SO:0001168 NDM3_motif "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941] 0 0 46271 5 NULL SO:0001169 ds_RNA_viral_sequence "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke] 0 0 46272 5 NULL SO:0001170 polinton "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396] 0 0 46273 5 NULL SO:0001171 rRNA_21S "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb] 0 0 46274 5 NULL SO:0001172 tRNA_region "A region of a tRNA." [RSC:cb] 0 0 46275 5 NULL SO:0001173 anticodon_loop "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207] 0 0 46276 5 NULL SO:0001174 anticodon "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb] 0 0 46277 5 NULL SO:0001175 CCA_tail "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207] 0 0 46278 5 NULL SO:0001176 DHU_loop "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920] 0 0 46279 5 NULL SO:0001177 T_loop "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207] 0 0 46280 5 NULL SO:0001178 pyrrolysine_tRNA_primary_transcript "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb] 0 0 46281 5 NULL SO:0001179 U3_snoRNA "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012] 0 0 46282 5 NULL SO:0001180 AU_rich_element "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223] 0 0 46283 5 NULL SO:0001181 Bruno_response_element "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231] 0 0 46284 5 NULL SO:0001182 iron_responsive_element "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843] 0 0 46285 5 NULL SO:0001183 morpholino_backbone "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb] 0 0 46286 5 NULL SO:0001184 PNA "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb] 0 0 46287 5 NULL SO:0001185 enzymatic "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] 0 0 46288 5 NULL SO:0001186 ribozymic "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb] 0 0 46289 5 NULL SO:0001187 pseudouridylation_guide_snoRNA "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] 0 0 46290 5 NULL SO:0001188 LNA "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010] 0 0 46291 5 NULL SO:0001189 LNA_oligo "An oligo composed of LNA residues." [RSC:cb] 0 0 46292 5 NULL SO:0001190 TNA "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019] 0 0 46293 5 NULL SO:0001191 TNA_oligo "An oligo composed of TNA residues." [RSC:cb] 0 0 46294 5 NULL SO:0001192 GNA "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015] 0 0 46295 5 NULL SO:0001193 GNA_oligo "An oligo composed of GNA residues." [RSC:cb] 0 0 46296 5 NULL SO:0001194 R_GNA "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016] 0 0 46297 5 NULL SO:0001195 R_GNA_oligo "An oligo composed of (R)-GNA residues." [RSC:cb] 0 0 46298 5 NULL SO:0001196 S_GNA "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017] 0 0 46299 5 NULL SO:0001197 S_GNA_oligo "An oligo composed of (S)-GNA residues." [RSC:cb] 0 0 46300 5 NULL SO:0001198 ds_DNA_viral_sequence "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke] 0 0 46301 5 NULL SO:0001199 ss_RNA_viral_sequence "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke] 0 0 46302 5 NULL SO:0001200 negative_sense_ssRNA_viral_sequence "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke] 0 0 46303 5 NULL SO:0001201 positive_sense_ssRNA_viral_sequence "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke] 0 0 46304 5 NULL SO:0001202 ambisense_ssRNA_viral_sequence "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke] 0 0 46305 5 NULL SO:0001203 RNA_polymerase_promoter "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb] 0 0 46306 5 NULL SO:0001204 Phage_RNA_Polymerase_Promoter "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb] 0 0 46307 5 NULL SO:0001205 SP6_RNA_Polymerase_Promoter "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb] 0 0 46308 5 NULL SO:0001206 T3_RNA_Polymerase_Promoter "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb] 0 0 46309 5 NULL SO:0001207 T7_RNA_Polymerase_Promoter "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb] 0 0 46310 5 NULL SO:0001208 five_prime_EST "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] 0 0 46311 5 NULL SO:0001209 three_prime_EST "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] 0 0 46312 5 NULL SO:0001210 translational_frameshift "The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] 0 0 46313 5 NULL SO:0001211 plus_1_translational_frameshift "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] 0 0 46314 5 NULL SO:0001212 plus_2_translational_frameshift "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] 0 0 46315 5 NULL SO:0001213 group_III_intron "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794] 0 0 46316 5 SOFA SO:0001214 noncoding_region_of_exon "The maximal intersection of exon and UTR." [SO:ke] 0 0 46317 5 SOFA SO:0001215 coding_region_of_exon "The region of an exon that encodes for protein sequence." [SO:ke] 0 0 46318 5 NULL SO:0001216 endonuclease_spliced_intron "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke] 0 0 46319 5 NULL SO:0001217 protein_coding_gene "" [] 0 0 46320 5 NULL SO:0001218 transgenic_insertion "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm] 0 0 46321 5 NULL SO:0001219 retrogene "" [] 0 0 46322 5 NULL SO:0001220 silenced_by_RNA_interference "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb] 0 0 46323 5 NULL SO:0001221 silenced_by_histone_modification "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb] 0 0 46324 5 NULL SO:0001222 silenced_by_histone_methylation "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb] 0 0 46325 5 NULL SO:0001223 silenced_by_histone_deacetylation "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb] 0 0 46326 5 NULL SO:0001224 gene_silenced_by_RNA_interference "A gene that is silenced by RNA interference." [SO:xp] 0 0 46327 5 NULL SO:0001225 gene_silenced_by_histone_modification "A gene that is silenced by histone modification." [SO:xp] 0 0 46328 5 NULL SO:0001226 gene_silenced_by_histone_methylation "A gene that is silenced by histone methylation." [SO:xp] 0 0 46329 5 NULL SO:0001227 gene_silenced_by_histone_deacetylation "A gene that is silenced by histone deacetylation." [SO:xp] 0 0 46330 5 NULL SO:0001228 dihydrouridine "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb] 0 0 46331 5 NULL SO:0001229 pseudouridine "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb] 0 0 46332 5 NULL SO:0001230 inosine "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb] 0 0 46333 5 NULL SO:0001231 seven_methylguanine "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb] 0 0 46334 5 NULL SO:0001232 ribothymidine "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb] 0 0 46335 5 NULL SO:0001233 methylinosine "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb] 0 0 46336 5 NULL SO:0001234 mobile "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb] 0 0 46337 5 SOFA SO:0001235 replicon "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] 0 0 46338 5 SOFA SO:0001236 base "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] 0 0 46339 5 NULL SO:0001237 amino_acid "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb] 0 0 46340 5 NULL SO:0001238 major_TSS "" [] 0 0 46341 5 NULL SO:0001239 minor_TSS "" [] 0 0 46342 5 NULL SO:0001240 TSS_region "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw] 0 0 46343 5 NULL SO:0001241 encodes_alternate_transcription_start_sites "" [] 0 0 46344 5 NULL SO:0001243 miRNA_primary_transcript_region "A part of an miRNA primary_transcript." [SO:ke] 0 0 46345 5 NULL SO:0001244 pre_miRNA "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke] 0 0 46346 5 NULL SO:0001245 miRNA_stem "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] 0 0 46347 5 NULL SO:0001246 miRNA_loop "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] 0 0 46348 5 NULL SO:0001247 synthetic_oligo "An oligo composed of synthetic nucleotides." [SO:ke] 0 0 46349 5 SOFA SO:0001248 assembly "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] 0 0 46350 5 NULL SO:0001249 fragment_assembly "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke] 0 0 46351 5 NULL SO:0001250 fingerprint_map "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke] 0 0 46352 5 NULL SO:0001251 STS_map "An STS map is a physical map organized by the unique STS landmarks." [SO:ke] 0 0 46353 5 NULL SO:0001252 RH_map "A radiation hybrid map is a physical map." [SO:ke] 0 0 46354 5 NULL SO:0001253 sonicate_fragment "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke] 0 0 46355 5 NULL SO:0001254 polyploid "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke] 0 0 46356 5 NULL SO:0001255 autopolyploid "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke] 0 0 46357 5 NULL SO:0001256 allopolyploid "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke] 0 0 46358 5 NULL SO:0001257 homing_endonuclease_binding_site "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke] 0 0 46359 5 NULL SO:0001258 octamer_motif "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662] 0 0 46360 5 NULL SO:0001259 apicoplast_chromosome "A chromosome originating in an apicoplast." [SO:xp] 0 0 46361 5 NULL SO:0001260 sequence_collection "A collection of discontinuous sequences." [SO:ke] 1 0 46362 5 NULL SO:0001261 overlapping_feature_set "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke] 0 0 46363 5 NULL SO:0001262 overlapping_EST_set "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke] 0 0 46364 5 NULL SO:0001263 ncRNA_gene "" [] 0 0 46365 5 NULL SO:0001264 gRNA_gene "" [] 0 0 46366 5 NULL SO:0001265 miRNA_gene "" [] 0 0 46367 5 NULL SO:0001266 scRNA_gene "" [] 0 0 46368 5 NULL SO:0001267 snoRNA_gene "" [] 0 0 46369 5 NULL SO:0001268 snRNA_gene "" [] 0 0 46370 5 NULL SO:0001269 SRP_RNA_gene "" [] 0 0 46371 5 NULL SO:0001271 tmRNA_gene "" [] 0 0 46372 5 NULL SO:0001272 tRNA_gene "" [] 0 0 46373 5 NULL SO:0001273 modified_adenosine "A modified adenine is an adenine base feature that has been altered." [SO:ke] 0 0 46374 5 NULL SO:0001274 modified_inosine "A modified inosine is an inosine base feature that has been altered." [SO:ke] 0 0 46375 5 NULL SO:0001275 modified_cytidine "A modified cytidine is a cytidine base feature which has been altered." [SO:ke] 0 0 46376 5 NULL SO:0001276 modified_guanosine "" [] 0 0 46377 5 NULL SO:0001277 modified_uridine "" [] 0 0 46378 5 NULL SO:0001278 one_methylinosine "1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] 0 0 46379 5 NULL SO:0001279 one_two_prime_O_dimethylinosine "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] 0 0 46380 5 NULL SO:0001280 two_prime_O_methylinosine "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] 0 0 46381 5 NULL SO:0001281 three_methylcytidine "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46382 5 NULL SO:0001282 five_methylcytidine "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46383 5 NULL SO:0001283 two_prime_O_methylcytidine "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46384 5 NULL SO:0001284 two_thiocytidine "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46385 5 NULL SO:0001285 N4_acetylcytidine "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46386 5 NULL SO:0001286 five_formylcytidine "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46387 5 NULL SO:0001287 five_two_prime_O_dimethylcytidine "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46388 5 NULL SO:0001288 N4_acetyl_2_prime_O_methylcytidine "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46389 5 NULL SO:0001289 lysidine "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46390 5 NULL SO:0001290 N4_methylcytidine "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46391 5 NULL SO:0001291 N4_2_prime_O_dimethylcytidine "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46392 5 NULL SO:0001292 five_hydroxymethylcytidine "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46393 5 NULL SO:0001293 five_formyl_two_prime_O_methylcytidine "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46394 5 NULL SO:0001294 N4_N4_2_prime_O_trimethylcytidine "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] 0 0 46395 5 NULL SO:0001295 one_methyladenosine "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46396 5 NULL SO:0001296 two_methyladenosine "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46397 5 NULL SO:0001297 N6_methyladenosine "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46398 5 NULL SO:0001298 two_prime_O_methyladenosine "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46399 5 NULL SO:0001299 two_methylthio_N6_methyladenosine "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46400 5 NULL SO:0001300 N6_isopentenyladenosine "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46401 5 NULL SO:0001301 two_methylthio_N6_isopentenyladenosine "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46402 5 NULL SO:0001302 N6_cis_hydroxyisopentenyl_adenosine "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46403 5 NULL SO:0001303 two_methylthio_N6_cis_hydroxyisopentenyl_adenosine "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46404 5 NULL SO:0001304 N6_glycinylcarbamoyladenosine "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46405 5 NULL SO:0001305 N6_threonylcarbamoyladenosine "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46406 5 NULL SO:0001306 two_methylthio_N6_threonyl_carbamoyladenosine "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46407 5 NULL SO:0001307 N6_methyl_N6_threonylcarbamoyladenosine "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46408 5 NULL SO:0001308 N6_hydroxynorvalylcarbamoyladenosine "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46409 5 NULL SO:0001309 two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46410 5 NULL SO:0001310 two_prime_O_ribosyladenosine_phosphate "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46411 5 NULL SO:0001311 N6_N6_dimethyladenosine "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46412 5 NULL SO:0001312 N6_2_prime_O_dimethyladenosine "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46413 5 NULL SO:0001313 N6_N6_2_prime_O_trimethyladenosine "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46414 5 NULL SO:0001314 one_two_prime_O_dimethyladenosine "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46415 5 NULL SO:0001315 N6_acetyladenosine "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] 0 0 46416 5 NULL SO:0001316 seven_deazaguanosine "7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/] 0 0 46417 5 NULL SO:0001317 queuosine "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] 0 0 46418 5 NULL SO:0001318 epoxyqueuosine "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] 0 0 46419 5 NULL SO:0001319 galactosyl_queuosine "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] 0 0 46420 5 NULL SO:0001320 mannosyl_queuosine "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] 0 0 46421 5 NULL SO:0001321 seven_cyano_seven_deazaguanosine "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] 0 0 46422 5 NULL SO:0001322 seven_aminomethyl_seven_deazaguanosine "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] 0 0 46423 5 NULL SO:0001323 archaeosine "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] 0 0 46424 5 NULL SO:0001324 one_methylguanosine "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46425 5 NULL SO:0001325 N2_methylguanosine "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46426 5 NULL SO:0001326 seven_methylguanosine "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46427 5 NULL SO:0001327 two_prime_O_methylguanosine "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46428 5 NULL SO:0001328 N2_N2_dimethylguanosine "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46429 5 NULL SO:0001329 N2_2_prime_O_dimethylguanosine "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46430 5 NULL SO:0001330 N2_N2_2_prime_O_trimethylguanosine "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46431 5 NULL SO:0001331 two_prime_O_ribosylguanosine_phosphate "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46432 5 NULL SO:0001332 wybutosine "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46433 5 NULL SO:0001333 peroxywybutosine "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46434 5 NULL SO:0001334 hydroxywybutosine "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46435 5 NULL SO:0001335 undermodified_hydroxywybutosine "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46436 5 NULL SO:0001336 wyosine "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46437 5 NULL SO:0001337 methylwyosine "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46438 5 NULL SO:0001338 N2_7_dimethylguanosine "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46439 5 NULL SO:0001339 N2_N2_7_trimethylguanosine "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46440 5 NULL SO:0001340 one_two_prime_O_dimethylguanosine "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46441 5 NULL SO:0001341 four_demethylwyosine "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46442 5 NULL SO:0001342 isowyosine "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46443 5 NULL SO:0001343 N2_7_2prirme_O_trimethylguanosine "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46444 5 NULL SO:0001344 five_methyluridine "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46445 5 NULL SO:0001345 two_prime_O_methyluridine "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46446 5 NULL SO:0001346 five_two_prime_O_dimethyluridine "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46447 5 NULL SO:0001347 one_methylpseudouridine "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46448 5 NULL SO:0001348 two_prime_O_methylpseudouridine "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46449 5 NULL SO:0001349 two_thiouridine "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46450 5 NULL SO:0001350 four_thiouridine "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46451 5 NULL SO:0001351 five_methyl_2_thiouridine "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46452 5 NULL SO:0001352 two_thio_two_prime_O_methyluridine "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46453 5 NULL SO:0001353 three_three_amino_three_carboxypropyl_uridine "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46454 5 NULL SO:0001354 five_hydroxyuridine "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46455 5 NULL SO:0001355 five_methoxyuridine "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46456 5 NULL SO:0001356 uridine_five_oxyacetic_acid "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46457 5 NULL SO:0001357 uridine_five_oxyacetic_acid_methyl_ester "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46458 5 NULL SO:0001358 five_carboxyhydroxymethyl_uridine "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46459 5 NULL SO:0001359 five_carboxyhydroxymethyl_uridine_methyl_ester "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46460 5 NULL SO:0001360 five_methoxycarbonylmethyluridine "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46461 5 NULL SO:0001361 five_methoxycarbonylmethyl_two_prime_O_methyluridine "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46462 5 NULL SO:0001362 five_methoxycarbonylmethyl_two_thiouridine "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46463 5 NULL SO:0001363 five_aminomethyl_two_thiouridine "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46464 5 NULL SO:0001364 five_methylaminomethyluridine "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46465 5 NULL SO:0001365 five_methylaminomethyl_two_thiouridine "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46466 5 NULL SO:0001366 five_methylaminomethyl_two_selenouridine "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46467 5 NULL SO:0001367 five_carbamoylmethyluridine "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46468 5 NULL SO:0001368 five_carbamoylmethyl_two_prime_O_methyluridine "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46469 5 NULL SO:0001369 five_carboxymethylaminomethyluridine "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46470 5 NULL SO:0001370 five_carboxymethylaminomethyl_two_prime_O_methyluridine "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46471 5 NULL SO:0001371 five_carboxymethylaminomethyl_two_thiouridine "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46472 5 NULL SO:0001372 three_methyluridine "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46473 5 NULL SO:0001373 one_methyl_three_three_amino_three_carboxypropyl_pseudouridine "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46474 5 NULL SO:0001374 five_carboxymethyluridine "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46475 5 NULL SO:0001375 three_two_prime_O_dimethyluridine "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46476 5 NULL SO:0001376 five_methyldihydrouridine "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46477 5 NULL SO:0001377 three_methylpseudouridine "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46478 5 NULL SO:0001378 five_taurinomethyluridine "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46479 5 NULL SO:0001379 five_taurinomethyl_two_thiouridine "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46480 5 NULL SO:0001380 five_isopentenylaminomethyl_uridine "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46481 5 NULL SO:0001381 five_isopentenylaminomethyl_two_thiouridine "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46482 5 NULL SO:0001382 five_isopentenylaminomethyl_two_prime_O_methyluridine "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] 0 0 46483 5 NULL SO:0001383 histone_binding_site "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke] 0 0 46484 5 NULL SO:0001384 CDS_fragment "" [] 0 0 46485 5 NULL SO:0001385 modified_amino_acid_feature "A post translationally modified amino acid feature." [SO:ke] 0 0 46486 5 NULL SO:0001386 modified_glycine "A post translationally modified glycine amino acid feature." [SO:ke] 0 0 46487 5 NULL SO:0001387 modified_L_alanine "A post translationally modified alanine amino acid feature." [SO:ke] 0 0 46488 5 NULL SO:0001388 modified_L_asparagine "A post translationally modified asparagine amino acid feature." [SO:ke] 0 0 46489 5 NULL SO:0001389 modified_L_aspartic_acid "A post translationally modified aspartic acid amino acid feature." [SO:ke] 0 0 46490 5 NULL SO:0001390 modified_L_cysteine "A post translationally modified cysteine amino acid feature." [SO:ke] 0 0 46491 5 NULL SO:0001391 modified_L_glutamic_acid "" [] 0 0 46492 5 NULL SO:0001392 modified_L_threonine "A post translationally modified threonine amino acid feature." [SO:ke] 0 0 46493 5 NULL SO:0001393 modified_L_tryptophan "A post translationally modified tryptophan amino acid feature." [SO:ke] 0 0 46494 5 NULL SO:0001394 modified_L_glutamine "A post translationally modified glutamine amino acid feature." [SO:ke] 0 0 46495 5 NULL SO:0001395 modified_L_methionine "A post translationally modified methionine amino acid feature." [SO:ke] 0 0 46496 5 NULL SO:0001396 modified_L_isoleucine "A post translationally modified isoleucine amino acid feature." [SO:ke] 0 0 46497 5 NULL SO:0001397 modified_L_phenylalanine "A post translationally modified phenylalanine amino acid feature." [SO:ke] 0 0 46498 5 NULL SO:0001398 modified_L_histidine "A post translationally modified histidine amino acid feature." [SO:ke] 0 0 46499 5 NULL SO:0001399 modified_L_serine "A post translationally modified serine amino acid feature." [SO:ke] 0 0 46500 5 NULL SO:0001400 modified_L_lysine "A post translationally modified lysine amino acid feature." [SO:ke] 0 0 46501 5 NULL SO:0001401 modified_L_leucine "A post translationally modified leucine amino acid feature." [SO:ke] 0 0 46502 5 NULL SO:0001402 modified_L_selenocysteine "A post translationally modified selenocysteine amino acid feature." [SO:ke] 0 0 46503 5 NULL SO:0001403 modified_L_valine "A post translationally modified valine amino acid feature." [SO:ke] 0 0 46504 5 NULL SO:0001404 modified_L_proline "A post translationally modified proline amino acid feature." [SO:ke] 0 0 46505 5 NULL SO:0001405 modified_L_tyrosine "A post translationally modified tyrosine amino acid feature." [SO:ke] 0 0 46506 5 NULL SO:0001406 modified_L_arginine "A post translationally modified arginine amino acid feature." [SO:ke] 0 0 46507 5 NULL SO:0001407 peptidyl "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke] 0 0 46508 5 NULL SO:0001408 cleaved_for_gpi_anchor_region "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh] 0 0 46509 5 SOFA SO:0001409 biomaterial_region "A region which is intended for use in an experiment." [SO:cb] 0 0 46510 5 SOFA SO:0001410 experimental_feature "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] 0 0 46511 5 SOFA SO:0001411 biological_region "A region defined by its disposition to be involved in a biological process." [SO:cb] 0 0 46512 5 SOFA SO:0001412 topologically_defined_region "A region that is defined according to its relations with other regions within the same sequence." [SO:cb] 0 0 46513 5 NULL SO:0001413 translocation_breakpoint "The point within a chromosome where a translocation begins or ends." [SO:cb] 0 0 46514 5 NULL SO:0001414 insertion_breakpoint "The point within a chromosome where a insertion begins or ends." [SO:cb] 0 0 46515 5 NULL SO:0001415 deletion_breakpoint "The point within a chromosome where a deletion begins or ends." [SO:cb] 0 0 46516 5 NULL SO:0001416 five_prime_flanking_region "A flanking region located five prime of a specific region." [SO:chado] 0 0 46517 5 NULL SO:0001417 three_prime_flanking_region "A flanking region located three prime of a specific region." [SO:chado] 0 0 46518 5 NULL SO:0001418 transcribed_fragment "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke] 0 0 46519 5 SOFA SO:0001419 cis_splice_site "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke] 0 0 46520 5 SOFA SO:0001420 trans_splice_site "Primary transcript region bordering trans-splice junction." [SO:ke] 0 0 46521 5 NULL SO:0001421 splice_junction "The boundary between an intron and an exon." [SO:ke] 0 0 46522 5 NULL SO:0001422 conformational_switch "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke] 0 0 46523 5 NULL SO:0001423 dye_terminator_read "A read produced by the dye terminator method of sequencing." [SO:ke] 0 0 46524 5 NULL SO:0001424 pyrosequenced_read "A read produced by pyrosequencing technology." [SO:ke] 0 0 46525 5 NULL SO:0001425 ligation_based_read "A read produced by ligation based sequencing technologies." [SO:ke] 0 0 46526 5 NULL SO:0001426 polymerase_synthesis_read "A read produced by the polymerase based sequence by synthesis method." [SO:ke] 0 0 46527 5 NULL SO:0001427 cis_regulatory_frameshift_element "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd] 0 0 46528 5 NULL SO:0001428 expressed_sequence_assembly "A sequence assembly derived from expressed sequences." [SO:ke] 0 0 46529 5 NULL SO:0001429 DNA_binding_site "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke] 0 0 46530 5 NULL SO:0001431 cryptic_gene "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke] 0 0 46531 5 NULL SO:0001432 sequence_variant_affecting_polyadenylation "" [] 0 1 46532 5 NULL SO:0001433 three_prime_RACE_clone "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw] 0 0 46533 5 NULL SO:0001434 cassette_pseudogene "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke] 0 0 46534 5 NULL SO:0001435 alanine "" [] 0 0 46535 5 NULL SO:0001436 valine "" [] 0 0 46536 5 NULL SO:0001437 leucine "" [] 0 0 46537 5 NULL SO:0001438 isoleucine "" [] 0 0 46538 5 NULL SO:0001439 proline "" [] 0 0 46539 5 NULL SO:0001440 tryptophan "" [] 0 0 46540 5 NULL SO:0001441 phenylalanine "" [] 0 0 46541 5 NULL SO:0001442 methionine "" [] 0 0 46542 5 NULL SO:0001443 glycine "" [] 0 0 46543 5 NULL SO:0001444 serine "" [] 0 0 46544 5 NULL SO:0001445 threonine "" [] 0 0 46545 5 NULL SO:0001446 tyrosine "" [] 0 0 46546 5 NULL SO:0001447 cysteine "" [] 0 0 46547 5 NULL SO:0001448 glutamine "" [] 0 0 46548 5 NULL SO:0001449 asparagine "" [] 0 0 46549 5 NULL SO:0001450 lysine "" [] 0 0 46550 5 NULL SO:0001451 arginine "" [] 0 0 46551 5 NULL SO:0001452 histidine "" [] 0 0 46552 5 NULL SO:0001453 aspartic_acid "" [] 0 0 46553 5 NULL SO:0001454 glutamic_acid "" [] 0 0 46554 5 NULL SO:0001455 selenocysteine "" [] 0 0 46555 5 NULL SO:0001456 pyrrolysine "" [] 0 0 46556 5 NULL SO:0001457 transcribed_cluster "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke] 0 0 46557 5 NULL SO:0001458 unigene_cluster "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke] 0 0 46558 5 NULL SO:0001459 CRISPR "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd] 0 0 46559 5 NULL SO:0001460 insulator_binding_site "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] 0 0 46560 5 NULL SO:0001461 enhancer_binding_site "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] 0 0 46561 5 NULL SO:0001462 contig_collection "A collection of contigs." [SO:ke] 0 0 46562 5 NULL SO:0001463 lincRNA "A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke] 0 0 46563 5 NULL SO:0001464 UST "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw] 0 0 46564 5 NULL SO:0001465 three_prime_UST "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw] 0 0 46565 5 NULL SO:0001466 five_prime_UST "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw] 0 0 46566 5 NULL SO:0001467 RST "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw] 0 0 46567 5 NULL SO:0001468 three_prime_RST "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw] 0 0 46568 5 NULL SO:0001469 five_prime_RST "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw] 0 0 46569 5 NULL SO:0001470 UST_match "A match against an UST sequence." [SO:nlw] 0 0 46570 5 NULL SO:0001471 RST_match "A match against an RST sequence." [SO:nlw] 0 0 46571 5 NULL SO:0001472 primer_match "A nucleotide match to a primer sequence." [SO:nlw] 0 0 46572 5 NULL SO:0001473 miRNA_antiguide "A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke] 0 0 46573 5 NULL SO:0001474 trans_splice_junction "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke] 0 0 46574 5 NULL SO:0001475 outron "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke] 0 0 46575 5 NULL SO:0001476 natural_plasmid "A plasmid that occurs naturally." [SO:xp] 0 0 46576 5 NULL SO:0001477 gene_trap_construct "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh] 0 0 46577 5 NULL SO:0001478 promoter_trap_construct "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh] 0 0 46578 5 NULL SO:0001479 enhancer_trap_construct "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh] 0 0 46579 5 NULL SO:0001480 PAC_end "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh] 0 0 46580 5 NULL SO:0001481 RAPD "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh] 0 0 46581 5 NULL SO:0001482 shadow_enhancer "" [] 0 0 46582 5 SOFA SO:0001483 SNV "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm] 0 0 46583 5 NULL SO:0001484 X_element_combinatorial_repeat "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html] 0 0 46584 5 NULL SO:0001485 Y_prime_element "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http\\://www.yeastgenome.org/help/glossary.html] 0 0 46585 5 NULL SO:0001486 standard_draft "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126] 0 0 46586 5 NULL SO:0001487 high_quality_draft "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126] 0 0 46587 5 NULL SO:0001488 improved_high_quality_draft "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126] 0 0 46588 5 NULL SO:0001489 annotation_directed_improved_draft "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126] 0 0 46589 5 NULL SO:0001490 noncontiguous_finished "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126] 0 0 46590 5 NULL SO:0001491 finished_genome "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126] 0 0 46591 5 NULL SO:0001492 intronic_regulatory_region "A regulatory region that is part of an intron." [SO:ke] 0 0 46592 5 NULL SO:0001493 centromere_DNA_Element_I "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754] 0 0 46593 5 NULL SO:0001494 centromere_DNA_Element_II "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754] 0 0 46594 5 NULL SO:0001495 centromere_DNA_Element_III "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754] 0 0 46595 5 NULL SO:0001496 telomeric_repeat "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065] 0 0 46596 5 NULL SO:0001497 X_element "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434] 0 0 46597 5 NULL SO:0001498 YAC_end "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke] 0 0 46598 5 NULL SO:0001499 whole_genome_sequence_status "The status of whole genome sequence." [DOI:10.1126] 0 0 46599 5 NULL SO:0001500 heritable_phenotypic_marker "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene] 0 0 46600 5 NULL SO:0001501 peptide_collection "A collection of peptide sequences." [BBOP:nlw] 0 0 46601 5 NULL SO:0001502 high_identity_region "An experimental feature with high sequence identity to another sequence." [SO:ke] 0 0 46602 5 NULL SO:0001503 processed_transcript "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen] 0 0 46603 5 NULL SO:0001504 assortment_derived_variation "A chromosome variation derived from an event during meiosis." [SO:ke] 0 0 46604 5 NULL SO:0001505 reference_genome "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke] 0 0 46605 5 NULL SO:0001506 variant_genome "A collection of sequences (often chromosomes) of an individual." [SO:ke] 0 0 46606 5 NULL SO:0001507 variant_collection "A collection of one or more sequences of an individual." [SO:ke] 0 0 46607 5 NULL SO:0001508 alteration_attribute "" [] 0 0 46608 5 NULL SO:0001509 chromosomal_variation_attribute "" [] 0 0 46609 5 NULL SO:0001510 intrachromosomal "" [] 0 0 46610 5 NULL SO:0001511 interchromosomal "" [] 0 0 46611 5 NULL SO:0001512 insertion_attribute "A quality of a chromosomal insertion,." [SO:ke] 0 0 46612 5 NULL SO:0001513 tandem "" [] 0 0 46613 5 NULL SO:0001514 direct "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke] 0 0 46614 5 NULL SO:0001515 inverted "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke] 0 0 46615 5 NULL SO:0001516 free "The quality of a duplication where the new region exists independently of the original." [SO:ke] 0 0 46616 5 NULL SO:0001517 inversion_attribute "" [] 0 0 46617 5 NULL SO:0001518 pericentric "" [] 0 0 46618 5 NULL SO:0001519 paracentric "" [] 0 0 46619 5 NULL SO:0001520 translocaton_attribute "" [] 0 0 46620 5 NULL SO:0001521 reciprocal "" [] 0 0 46621 5 NULL SO:0001522 insertional "" [] 0 0 46622 5 NULL SO:0001523 duplication_attribute "" [] 0 0 46623 5 NULL SO:0001524 chromosomally_aberrant_genome "" [] 0 0 46624 5 NULL SO:0001525 assembly_error_correction "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke] 0 0 46625 5 NULL SO:0001526 base_call_error_correction "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke] 0 0 46626 5 SOFA SO:0001527 peptide_localization_signal "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] 0 0 46627 5 NULL SO:0001528 nuclear_localization_signal "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke] 0 0 46628 5 NULL SO:0001529 endosomal_localization_signal "A polypeptide region that targets a polypeptide to the endosome." [SO:ke] 0 0 46629 5 NULL SO:0001530 lysosomal_localization_signal "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke] 0 0 46630 5 NULL SO:0001531 nuclear_export_signal "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke] 0 0 46631 5 NULL SO:0001532 recombination_signal_sequence "A region recognized by a recombinase." [SO:ke] 0 0 46632 5 NULL SO:0001533 cryptic_splice_site "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke] 0 0 46633 5 NULL SO:0001534 nuclear_rim_localization_signal "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke] 0 0 46634 5 NULL SO:0001535 p_element "A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke] 0 0 46635 5 NULL SO:0001536 functional_variant "A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke] 0 0 46636 5 NULL SO:0001537 structural_variant "A sequence variant that changes one or more sequence features." [SO:ke] 0 0 46637 5 NULL SO:0001538 transcript_function_variant "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke] 0 0 46638 5 NULL SO:0001539 translational_product_function_variant "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke] 0 0 46639 5 NULL SO:0001540 level_of_transcript_variant "A sequence variant which alters the level of a transcript." [SO:ke] 0 0 46640 5 NULL SO:0001541 decreased_transcript_level_variant "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] 0 0 46641 5 NULL SO:0001542 increased_transcript_level_variant "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] 0 0 46642 5 NULL SO:0001543 transcript_processing_variant "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke] 0 0 46643 5 NULL SO:0001544 editing_variant "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke] 0 0 46644 5 NULL SO:0001545 polyadenylation_variant "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke] 0 0 46645 5 NULL SO:0001546 transcript_stability_variant "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke] 0 0 46646 5 NULL SO:0001547 decreased_transcript_stability_variant "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke] 0 0 46647 5 NULL SO:0001548 increased_transcript_stability_variant "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke] 0 0 46648 5 NULL SO:0001549 transcription_variant "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke] 0 0 46649 5 NULL SO:0001550 rate_of_transcription_variant "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke] 0 0 46650 5 NULL SO:0001551 increased_transcription_rate_variant "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke] 0 0 46651 5 NULL SO:0001552 decreased_transcription_rate_variant "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke] 0 0 46652 5 NULL SO:0001553 translational_product_level_variant "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke] 0 0 46653 5 NULL SO:0001554 polypeptide_function_variant "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke] 0 0 46654 5 NULL SO:0001555 decreased_translational_product_level "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke] 0 0 46655 5 NULL SO:0001556 increased_translational_product_level "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke] 0 0 46656 5 NULL SO:0001557 polypeptide_gain_of_function_variant "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke] 0 0 46657 5 NULL SO:0001558 polypeptide_localization_variant "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke] 0 0 46658 5 NULL SO:0001559 polypeptide_loss_of_function_variant "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke] 0 0 46659 5 NULL SO:0001560 inactive_ligand_binding_site "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke] 0 0 46660 5 NULL SO:0001561 polypeptide_partial_loss_of_function "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke] 0 0 46661 5 NULL SO:0001562 polypeptide_post_translational_processing_variant "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke] 0 0 46662 5 NULL SO:0001563 copy_number_change "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke] 0 0 46663 5 NULL SO:0001564 gene_variant "A sequence variant where the structure of the gene is changed." [SO:ke] 0 0 46664 5 NULL SO:0001565 gene_fusion "A sequence variant whereby a two genes have become joined." [SO:ke] 0 0 46665 5 NULL SO:0001566 regulatory_region_variant "A sequence variant located within a regulatory region." [SO:ke] 0 0 46666 5 NULL SO:0001567 stop_retained_variant "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke] 0 0 46667 5 NULL SO:0001568 splicing_variant "A sequence variant that changes the process of splicing." [SO:ke] 0 0 46668 5 NULL SO:0001569 cryptic_splice_site_variant "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 0 46669 5 NULL SO:0001570 cryptic_splice_acceptor "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke] 0 0 46670 5 NULL SO:0001571 cryptic_splice_donor "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke] 0 0 46671 5 NULL SO:0001572 exon_loss_variant "A sequence variant whereby an exon is lost from the transcript." [SO:ke] 0 0 46672 5 NULL SO:0001573 intron_gain_variant "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 0 46673 5 NULL SO:0001574 splice_acceptor_variant "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke] 0 0 46674 5 NULL SO:0001575 splice_donor_variant "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke] 0 0 46675 5 NULL SO:0001576 transcript_variant "A sequence variant that changes the structure of the transcript." [SO:ke] 0 0 46676 5 NULL SO:0001577 complex_transcript_variant "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html] 0 0 46677 5 NULL SO:0001578 stop_lost "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke] 0 0 46678 5 NULL SO:0001579 transcript_sequence_variant "" [] 0 1 46679 5 NULL SO:0001580 coding_sequence_variant "A sequence variant that changes the coding sequence." [SO:ke] 0 0 46680 5 NULL SO:0001582 initiator_codon_variant "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke] 0 0 46681 5 NULL SO:0001583 missense_variant "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke] 0 0 46682 5 NULL SO:0001585 conservative_missense_variant "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke] 0 0 46683 5 NULL SO:0001586 non_conservative_missense_variant "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke] 0 0 46684 5 NULL SO:0001587 stop_gained "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke] 0 0 46685 5 NULL SO:0001589 frameshift_variant "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] 0 0 46686 5 NULL SO:0001590 terminator_codon_variant "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke] 0 0 46687 5 NULL SO:0001591 frame_restoring_variant "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] 0 0 46688 5 NULL SO:0001592 minus_1_frameshift_variant "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] 0 0 46689 5 NULL SO:0001593 minus_2_frameshift_variant "" [] 0 0 46690 5 NULL SO:0001594 plus_1_frameshift_variant "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] 0 0 46691 5 NULL SO:0001595 plus_2_frameshift_variant "" [] 0 0 46692 5 NULL SO:0001596 transcript_secondary_structure_variant "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke] 0 0 46693 5 NULL SO:0001597 compensatory_transcript_secondary_structure_variant "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke] 0 0 46694 5 NULL SO:0001598 translational_product_structure_variant "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke] 0 0 46695 5 NULL SO:0001599 3D_polypeptide_structure_variant "A sequence variant that changes the resulting polypeptide structure." [SO:ke] 0 0 46696 5 NULL SO:0001600 complex_3D_structural_variant "A sequence variant that changes the resulting polypeptide structure." [SO:ke] 0 0 46697 5 NULL SO:0001601 conformational_change_variant "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke] 0 0 46698 5 NULL SO:0001602 complex_change_of_translational_product_variant "" [] 0 0 46699 5 NULL SO:0001603 polypeptide_sequence_variant "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke] 0 0 46700 5 NULL SO:0001604 amino_acid_deletion "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke] 0 0 46701 5 NULL SO:0001605 amino_acid_insertion "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke] 0 0 46702 5 NULL SO:0001606 amino_acid_substitution "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke] 0 0 46703 5 NULL SO:0001607 conservative_amino_acid_substitution "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke] 0 0 46704 5 NULL SO:0001608 non_conservative_amino_acid_substitution "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke] 0 0 46705 5 NULL SO:0001609 elongated_polypeptide "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke] 0 0 46706 5 NULL SO:0001610 elongated_polypeptide_C_terminal "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] 0 0 46707 5 NULL SO:0001611 elongated_polypeptide_N_terminal "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] 0 0 46708 5 NULL SO:0001612 elongated_in_frame_polypeptide_C_terminal "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] 0 0 46709 5 NULL SO:0001613 elongated_out_of_frame_polypeptide_C_terminal "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] 0 0 46710 5 NULL SO:0001614 elongated_in_frame_polypeptide_N_terminal_elongation "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] 0 0 46711 5 NULL SO:0001615 elongated_out_of_frame_polypeptide_N_terminal "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] 0 0 46712 5 NULL SO:0001616 polypeptide_fusion "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke] 0 0 46713 5 NULL SO:0001617 polypeptide_truncation "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke] 0 0 46714 5 NULL SO:0001618 inactive_catalytic_site "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke] 0 0 46715 5 NULL SO:0001619 non_coding_transcript_variant "A transcript variant of a non coding RNA gene." [SO:ke] 0 0 46716 5 NULL SO:0001620 mature_miRNA_variant "A transcript variant located with the sequence of the mature miRNA." [SO:ke] 0 0 46717 5 NULL SO:0001621 NMD_transcript_variant "A variant in a transcript that is the target of NMD." [SO:ke] 0 0 46718 5 NULL SO:0001622 UTR_variant "A transcript variant that is located within the UTR." [SO:ke] 0 0 46719 5 NULL SO:0001623 5_prime_UTR_variant "A UTR variant of the 5' UTR." [SO:ke] 0 0 46720 5 NULL SO:0001624 3_prime_UTR_variant "A UTR variant of the 3' UTR." [SO:ke] 0 0 46721 5 NULL SO:0001626 incomplete_terminal_codon_variant "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke] 0 0 46722 5 NULL SO:0001627 intron_variant "A transcript variant occurring within an intron." [SO:ke] 0 0 46723 5 NULL SO:0001628 intergenic_variant "A sequence variant located in the intergenic region, between genes." [SO:ke] 0 0 46724 5 NULL SO:0001629 splice_site_variant "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html] 0 0 46725 5 NULL SO:0001630 splice_region_variant "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html] 0 0 46726 5 NULL SO:0001631 upstream_gene_variant "A sequence variant located 5' of a gene." [SO:ke] 0 0 46727 5 NULL SO:0001632 downstream_gene_variant "A sequence variant located 3' of a gene." [SO:ke] 0 0 46728 5 NULL SO:0001633 5KB_downstream_variant "A sequence variant located within 5 KB of the end of a gene." [SO:ke] 0 0 46729 5 NULL SO:0001634 500B_downstream_variant "A sequence variant located within a half KB of the end of a gene." [SO:ke] 0 0 46730 5 NULL SO:0001635 5KB_upstream_variant "A sequence variant located within 5KB 5' of a gene." [SO:ke] 0 0 46731 5 NULL SO:0001636 2KB_upstream_variant "A sequence variant located within 2KB 5' of a gene." [SO:ke] 0 0 46732 5 NULL SO:0001637 rRNA_gene "A gene that encodes for ribosomal RNA." [SO:ke] 0 0 46733 5 NULL SO:0001638 piRNA_gene "A gene that encodes for an piwi associated RNA." [SO:ke] 0 0 46734 5 NULL SO:0001639 RNase_P_RNA_gene "A gene that encodes an RNase P RNA." [SO:ke] 0 0 46735 5 NULL SO:0001640 RNase_MRP_RNA_gene "A gene that encodes a RNase_MRP_RNA." [SO:ke] 0 0 46736 5 NULL SO:0001641 lincRNA_gene "A gene that encodes large intervening non-coding RNA." [SO:ke] 0 0 46737 5 NULL SO:0001642 mathematically_defined_repeat "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill] 0 0 46738 5 NULL SO:0001643 telomerase_RNA_gene "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke] 0 0 46739 5 NULL SO:0001644 targeting_vector "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467] 0 0 46740 5 NULL SO:0001645 genetic_marker "A measurable sequence feature that varies within a population." [SO:db] 0 0 46741 5 NULL SO:0001646 DArT_marker "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke] 0 0 46742 5 SOFA SO:0001647 kozak_sequence "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke] 0 0 46743 5 NULL SO:0001648 nested_transposon "A transposon that is disrupted by the insertion of another element." [SO:ke] 0 0 46744 5 NULL SO:0001649 nested_repeat "A repeat that is disrupted by the insertion of another element." [SO:ke] 0 0 46745 5 NULL SO:0001650 inframe_variant "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke] 0 0 46746 5 NULL SO:0001653 retinoic_acid_responsive_element "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671] 0 0 46747 5 SOFA SO:0001654 nucleotide_to_protein_binding_site "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] 0 0 46748 5 NULL SO:0001655 nucleotide_binding_site "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb] 0 0 46749 5 NULL SO:0001656 metal_binding_site "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb] 0 0 46750 5 NULL SO:0001657 ligand_binding_site "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke] 0 0 46751 5 NULL SO:0001658 nested_tandem_repeat "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF] 0 0 46752 5 NULL SO:0001659 promoter_element "" [] 0 0 46753 5 NULL SO:0001660 core_promoter_element "" [] 0 0 46754 5 NULL SO:0001661 RNA_polymerase_II_TATA_box "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867] 0 0 46755 5 NULL SO:0001662 RNA_polymerase_III_TATA_box "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke] 0 0 46756 5 NULL SO:0001663 BREd_motif "A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867] 0 0 46757 5 NULL SO:0001664 DCE "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867] 0 0 46758 5 NULL SO:0001665 DCE_SI "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke] 0 0 46759 5 NULL SO:0001666 DCE_SII "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke] 0 0 46760 5 NULL SO:0001667 DCE_SIII "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke] 0 0 46761 5 NULL SO:0001668 proximal_promoter_element "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml] 0 0 46762 5 NULL SO:0001669 RNApol_II_core_promoter "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867] 0 0 46763 5 NULL SO:0001670 distal_promoter_element "" [] 0 0 46764 5 NULL SO:0001671 bacterial_RNApol_promoter_sigma_70 "" [] 0 0 46765 5 NULL SO:0001672 bacterial_RNApol_promoter_sigma54 "" [] 0 0 46766 5 NULL SO:0001673 minus_12_signal "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] 0 0 46767 5 NULL SO:0001674 minus_24_signal "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] 0 0 46768 5 NULL SO:0001675 A_box_type_1 "An A box within an RNA polymerase III type 1 promoter." [SO:ke] 0 0 46769 5 NULL SO:0001676 A_box_type_2 "An A box within an RNA polymerase III type 2 promoter." [SO:ke] 0 0 46770 5 NULL SO:0001677 intermediate_element "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659] 0 0 46771 5 NULL SO:0001678 regulatory_promoter_element "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659] 0 0 46772 5 SOFA SO:0001679 transcription_regulatory_region "A regulatory region that is involved in the control of the process of transcription." [SO:ke] 0 0 46773 5 NULL SO:0001680 translation_regulatory_region "A regulatory region that is involved in the control of the process of translation." [SO:ke] 0 0 46774 5 NULL SO:0001681 recombination_regulatory_region "A regulatory region that is involved in the control of the process of recombination." [SO:ke] 0 0 46775 5 NULL SO:0001682 replication_regulatory_region "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke] 0 0 46776 5 SOFA SO:0001683 sequence_motif "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] 0 0 46777 5 NULL SO:0001684 experimental_feature_attribute "An attribute of an experimentally derived feature." [SO:ke] 0 0 46778 5 NULL SO:0001685 score "The score of an experimentally derived feature such as a p-value." [SO:ke] 0 0 46779 5 NULL SO:0001686 quality_value "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke] 0 0 46780 5 NULL SO:0001687 restriction_enzyme_recognition_site "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke] 0 0 46781 5 NULL SO:0001688 restriction_enzyme_cleavage_junction "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke] 0 0 46782 5 NULL SO:0001689 five_prime_restriction_enzyme_junction "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke] 0 0 46783 5 NULL SO:0001690 three_prime_restriction_enzyme_junction "" [] 0 0 46784 5 NULL SO:0001691 blunt_end_restriction_enzyme_cleavage_site "A restriction enzyme recognition site that, when cleaved, results in no overhangs." [SBOL:jgquinn, SO:ke] 0 0 46785 5 NULL SO:0001692 sticky_end_restriction_enzyme_cleavage_site "" [] 0 0 46786 5 NULL SO:0001693 blunt_end_restriction_enzyme_cleavage_junction "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke] 0 0 46787 5 NULL SO:0001694 single_strand_restriction_enzyme_cleavage_site "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke] 0 0 46788 5 NULL SO:0001695 restriction_enzyme_single_strand_overhang "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke] 0 0 46789 5 NULL SO:0001696 experimentally_defined_binding_region "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke] 0 0 46790 5 NULL SO:0001697 ChIP_seq_region "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke] 0 0 46791 5 NULL SO:0001698 ASPE_primer "\\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801] 0 0 46792 5 NULL SO:0001699 dCAPS_primer "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033] 0 0 46793 5 NULL SO:0001700 histone_modification "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone] 0 0 46794 5 NULL SO:0001701 histone_methylation_site "A histone modification site where the modification is the methylation of the residue." [SO:ke] 0 0 46795 5 NULL SO:0001702 histone_acetylation_site "A histone modification where the modification is the acylation of the residue." [SO:ke] 0 0 46796 5 NULL SO:0001703 H3K9_acetylation_site "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46797 5 NULL SO:0001704 H3K14_acetylation_site "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46798 5 NULL SO:0001705 H3K4_monomethylation_site "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46799 5 NULL SO:0001706 H3K4_trimethylation "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46800 5 NULL SO:0001707 H3K9_trimethylation_site "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46801 5 NULL SO:0001708 H3K27_monomethylation_site "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46802 5 NULL SO:0001709 H3K27_trimethylation_site "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46803 5 NULL SO:0001710 H3K79_monomethylation_site "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46804 5 NULL SO:0001711 H3K79_dimethylation_site "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46805 5 NULL SO:0001712 H3K79_trimethylation_site "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46806 5 NULL SO:0001713 H4K20_monomethylation_site "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46807 5 NULL SO:0001714 H2BK5_monomethylation_site "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone] 0 0 46808 5 NULL SO:0001715 ISRE "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac] 0 0 46809 5 NULL SO:0001716 histone_ubiqitination_site "A histone modification site where ubiquitin may be added." [SO:ke] 0 0 46810 5 NULL SO:0001717 H2B_ubiquitination_site "A histone modification site on H2B where ubiquitin may be added." [SO:ke] 0 0 46811 5 NULL SO:0001718 H3K18_acetylation_site "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] 0 0 46812 5 NULL SO:0001719 H3K23_acylation_site "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] 0 0 46813 5 SOFA SO:0001720 epigenetically_modified_region "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] 0 0 46814 5 NULL SO:0001721 H3K27_acylation_site "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] 0 0 46815 5 NULL SO:0001722 H3K36_monomethylation_site "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke] 0 0 46816 5 NULL SO:0001723 H3K36_dimethylation_site "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke] 0 0 46817 5 NULL SO:0001724 H3K36_trimethylation_site "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke] 0 0 46818 5 NULL SO:0001725 H3K4_dimethylation_site "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke] 0 0 46819 5 NULL SO:0001726 H3K27_dimethylation_site "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke] 0 0 46820 5 NULL SO:0001727 H3K9_monomethylation_site "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke] 0 0 46821 5 NULL SO:0001728 H3K9_dimethylation_site "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke] 0 0 46822 5 NULL SO:0001729 H4K16_acylation_site "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke] 0 0 46823 5 NULL SO:0001730 H4K5_acylation_site "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke] 0 0 46824 5 NULL SO:0001731 H4K8_acylation_site "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE] 0 0 46825 5 NULL SO:0001732 H3K27_methylation_site "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] 0 0 46826 5 NULL SO:0001733 H3K36_methylation_site "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] 0 0 46827 5 NULL SO:0001734 H3K4_methylation_site "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke] 0 0 46828 5 NULL SO:0001735 H3K79_methylation_site "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] 0 0 46829 5 NULL SO:0001736 H3K9_methylation_site "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke] 0 0 46830 5 NULL SO:0001737 histone_acylation_region "A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke] 0 0 46831 5 NULL SO:0001738 H4K_acylation_region "A region of the H4 histone whereby multiple lysines are acylated." [SO:ke] 0 0 46832 5 NULL SO:0001739 gene_with_non_canonical_start_codon "A gene with a start codon other than AUG." [SO:xp] 0 0 46833 5 NULL SO:0001740 gene_with_start_codon_CUG "A gene with a translational start codon of CUG." [SO:mc] 0 0 46834 5 NULL SO:0001741 pseudogenic_gene_segment "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd] 0 0 46835 5 DBVAR SO:0001742 copy_number_gain "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke] 0 0 46836 5 DBVAR SO:0001743 copy_number_loss "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke] 0 0 46837 5 DBVAR SO:0001744 UPD "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM] 0 0 46838 5 NULL SO:0001745 maternal_uniparental_disomy "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm] 0 0 46839 5 NULL SO:0001746 paternal_uniparental_disomy "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm] 0 0 46840 5 NULL SO:0001747 open_chromatin_region "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb] 0 0 46841 5 NULL SO:0001748 SL3_acceptor_site "A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46842 5 NULL SO:0001749 SL4_acceptor_site "A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46843 5 NULL SO:0001750 SL5_acceptor_site "A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46844 5 NULL SO:0001751 SL6_acceptor_site "A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46845 5 NULL SO:0001752 SL7_acceptor_site "A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46846 5 NULL SO:0001753 SL8_acceptor_site "A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46847 5 NULL SO:0001754 SL9_acceptor_site "A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46848 5 NULL SO:0001755 SL10_acceptor_site "A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46849 5 NULL SO:0001756 SL11_acceptor_site "A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46850 5 NULL SO:0001757 SL12_acceptor_site "A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] 0 0 46851 5 NULL SO:0001758 duplicated_pseudogene "A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene] 0 0 46852 5 NULL SO:0001759 unitary_pseudogene "A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, http://en.wikipedia.org/wiki/Pseudogene, SO:ke] 0 0 46853 5 NULL SO:0001760 non_processed_pseudogene "A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, SO:ke] 0 0 46854 5 NULL SO:0001761 variant_quality "A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke] 0 0 46855 5 NULL SO:0001762 variant_origin "A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke] 0 0 46856 5 NULL SO:0001763 variant_frequency "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke] 0 0 46857 5 NULL SO:0001764 unique_variant "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke] 0 0 46858 5 NULL SO:0001765 rare_variant "" [] 0 0 46859 5 NULL SO:0001766 polymorphic_variant "" [] 0 0 46860 5 NULL SO:0001767 common_variant "" [] 0 0 46861 5 NULL SO:0001768 fixed_variant "" [] 0 0 46862 5 NULL SO:0001769 variant_phenotype "A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke] 0 0 46863 5 NULL SO:0001770 benign_variant "" [] 0 0 46864 5 NULL SO:0001771 disease_associated_variant "" [] 0 0 46865 5 NULL SO:0001772 disease_causing_variant "" [] 0 0 46866 5 NULL SO:0001773 lethal_variant "" [] 0 0 46867 5 NULL SO:0001774 quantitative_variant "" [] 0 0 46868 5 NULL SO:0001775 maternal_variant "" [] 0 0 46869 5 NULL SO:0001776 paternal_variant "" [] 0 0 46870 5 NULL SO:0001777 somatic_variant "" [] 0 0 46871 5 NULL SO:0001778 germline_variant "" [] 0 0 46872 5 NULL SO:0001779 pedigree_specific_variant "" [] 0 0 46873 5 NULL SO:0001780 population_specific_variant "" [] 0 0 46874 5 NULL SO:0001781 de_novo_variant "" [] 0 0 46875 5 NULL SO:0001782 TF_binding_site_variant "A sequence variant located within a transcription factor binding site." [EBI:fc] 0 0 46876 5 DBVAR SO:0001784 complex_structural_alteration "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints." [FB:reference_manual, NCBI:th, SO:ke] 0 0 46877 5 DBVAR SO:0001785 structural_alteration "" [] 0 0 46878 5 DBVAR SO:0001786 loss_of_heterozygosity "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke] 0 0 46879 5 NULL SO:0001787 splice_donor_5th_base_variant "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr] 0 0 46880 5 NULL SO:0001788 U_box "An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446] 0 0 46881 5 NULL SO:0001789 mating_type_region "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke] 0 0 46882 5 SOFA SO:0001790 paired_end_fragment "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke] 0 0 46883 5 NULL SO:0001791 exon_variant "A sequence variant that changes exon sequence." [SO:ke] 0 0 46884 5 NULL SO:0001792 non_coding_transcript_exon_variant "A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke] 0 0 46885 5 NULL SO:0001793 clone_end "A read from an end of the clone sequence." [SO:ke] 0 0 46886 5 NULL SO:0001794 point_centromere "A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw] 0 0 46887 5 NULL SO:0001795 regional_centromere "A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw] 0 0 46888 5 NULL SO:0001796 regional_centromere_central_core "A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw] 0 0 46889 5 NULL SO:0001797 centromeric_repeat "A repeat region found within the modular centromere." [SO:ke] 0 0 46890 5 NULL SO:0001798 regional_centromere_inner_repeat_region "The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw] 0 0 46891 5 NULL SO:0001799 regional_centromere_outer_repeat_region "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw] 0 0 46892 5 NULL SO:0001800 tasiRNA "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017] 0 0 46893 5 NULL SO:0001801 tasiRNA_primary_transcript "A primary transcript encoding a tasiRNA." [PMID:16145017] 0 0 46894 5 NULL SO:0001802 increased_polyadenylation_variant "A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke] 0 0 46895 5 NULL SO:0001803 decreased_polyadenylation_variant "A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke] 0 0 46896 5 NULL SO:0001804 DDB_box "A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632] 0 0 46897 5 NULL SO:0001805 destruction_box "A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691] 0 0 46898 5 NULL SO:0001806 ER_retention_signal "A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689] 0 0 46899 5 NULL SO:0001807 KEN_box "A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916] 0 0 46900 5 NULL SO:0001808 mitochondrial_targeting_signal "A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah] 0 0 46901 5 NULL SO:0001809 signal_anchor "A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php] 0 0 46902 5 NULL SO:0001810 PIP_box "A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646] 0 0 46903 5 NULL SO:0001811 phosphorylation_site "A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah] 0 0 46904 5 NULL SO:0001812 transmembrane_helix "A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah] 0 0 46905 5 NULL SO:0001813 vacuolar_sorting_signal "A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah] 0 0 46906 5 NULL SO:0001814 coding_variant_quality "" [] 0 0 46907 5 NULL SO:0001815 synonymous "" [] 0 0 46908 5 NULL SO:0001816 non_synonymous "" [] 0 0 46909 5 NULL SO:0001817 inframe "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke] 0 0 46910 5 NULL SO:0001818 protein_altering_variant "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr] 0 0 46911 5 NULL SO:0001819 synonymous_variant "A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke] 0 0 46912 5 NULL SO:0001820 inframe_indel "A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke] 0 0 46913 5 NULL SO:0001821 inframe_insertion "An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr] 0 0 46914 5 NULL SO:0001822 inframe_deletion "An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr] 0 0 46915 5 NULL SO:0001823 conservative_inframe_insertion "An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr] 0 0 46916 5 NULL SO:0001824 disruptive_inframe_insertion "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr] 0 0 46917 5 NULL SO:0001825 conservative_inframe_deletion "An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr] 0 0 46918 5 NULL SO:0001826 disruptive_inframe_deletion "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr] 0 0 46919 5 NULL SO:0001827 mRNA_read "A sequencer read of an mRNA substrate." [SO:ke] 0 0 46920 5 NULL SO:0001828 genomic_DNA_read "A sequencer read of a genomic DNA substrate." [SO:ke] 0 0 46921 5 NULL SO:0001829 mRNA_contig "A contig composed of mRNA_reads." [SO:ke] 0 0 46922 5 NULL SO:0001830 AFLP_fragment "A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea] 0 0 46923 5 NULL SO:0001831 protein_hmm_match "A match to a protein HMM such as pfam." [SO:ke] 0 0 46924 5 NULL SO:0001832 immunoglobulin_region "A region of immunoglobulin sequence, either constant or variable." [SO:ke] 0 0 46925 5 NULL SO:0001833 V_region "The variable region of an immunoglobulin polypeptide sequence." [SO:ke] 0 0 46926 5 NULL SO:0001834 C_region "The constant region of an immunoglobulin polypeptide sequence." [SO:ke] 0 0 46927 5 NULL SO:0001835 N_region "Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke] 0 0 46928 5 NULL SO:0001836 S_region "The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke] 0 0 46929 5 NULL SO:0001837 mobile_element_insertion "A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga] 0 0 46930 5 NULL SO:0001838 novel_sequence_insertion "An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th] 0 0 46931 5 NULL SO:0001839 CSL_response_element "A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542] 0 0 46932 5 NULL SO:0001840 GATA_box "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208] 0 0 46933 5 NULL SO:0001841 polymorphic_pseudogene "A pseudogene in the reference genome, though known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, JAX:hd] 0 0 46934 5 NULL SO:0001842 AP_1_binding_site "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983] 0 0 46935 5 NULL SO:0001843 CRE "A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993] 0 0 46936 5 NULL SO:0001844 CuRE "A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922] 0 0 46937 5 NULL SO:0001845 DRE "A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127] 0 0 46938 5 NULL SO:0001846 FLEX_element "A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934] 0 0 46939 5 NULL SO:0001847 forkhead_motif "A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092] 0 0 46940 5 NULL SO:0001848 homol_D_box "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:21673110, PMID:7501449, PMID:8458332] 0 0 46941 5 NULL SO:0001849 homol_E_box "A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449] 0 0 46942 5 NULL SO:0001850 HSE "A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565] 0 0 46943 5 NULL SO:0001851 iron_repressed_GATA_element "A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681] 0 0 46944 5 NULL SO:0001852 mating_type_M_box "A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811] 0 0 46945 5 NULL SO:0001853 androgen_response_element "A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522] 0 0 46946 5 NULL SO:0001854 smFISH_probe "A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792] 0 0 46947 5 NULL SO:0001855 MCB "A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853] 0 0 46948 5 NULL SO:0001856 CCAAT_motif "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626] 0 0 46949 5 NULL SO:0001857 Ace2_UAS "A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171] 0 0 46950 5 NULL SO:0001858 TR_box "A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709] 0 0 46951 5 NULL SO:0001859 STREP_motif "A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717] 0 0 46952 5 NULL SO:0001860 rDNA_intergenic_spacer_element "A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645] 0 0 46953 5 NULL SO:0001861 sterol_regulatory_element "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923] 0 0 46954 5 NULL SO:0001862 GT_dinucleotide_repeat "A dinucleotide repeat region composed of GT repeating elements." [SO:ke] 0 0 46955 5 NULL SO:0001863 GTT_trinucleotide_repeat "A trinucleotide repeat region composed of GTT repeating elements." [SO:ke] 0 0 46956 5 NULL SO:0001864 Sap1_recognition_motif "A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412] 0 0 46957 5 NULL SO:0001865 CDRE_motif "An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959] 0 0 46958 5 NULL SO:0001866 BAC_read_contig "A contig of BAC reads." [GMOD:ea] 0 0 46959 5 NULL SO:0001867 candidate_gene "A gene suspected of being involved in the expression of a trait." [GMOD:ea] 0 0 46960 5 NULL SO:0001868 positional_candidate_gene "A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea] 0 0 46961 5 NULL SO:0001869 functional_candidate_gene "A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea] 0 0 46962 5 NULL SO:0001870 enhancerRNA "A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm] 0 0 46963 5 NULL SO:0001871 PCB "A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492] 0 0 46964 5 NULL SO:0001872 rearrangement_region "A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416] 0 0 46965 5 NULL SO:0001873 interchromosomal_breakpoint "A rearrangement breakpoint between two different chromosomes." [NCBI:th] 0 0 46966 5 NULL SO:0001874 intrachromosomal_breakpoint "A rearrangement breakpoint within the same chromosome." [NCBI:th] 0 0 46967 5 NULL SO:0001875 unassigned_supercontig "A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea] 0 0 46968 5 NULL SO:0001876 partial_genomic_sequence_assembly "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea] 0 0 46969 5 NULL SO:0001877 lnc_RNA "A non-coding RNA over 200nucleotides in length." [HGNC:mw] 0 0 46970 5 NULL SO:0001878 feature_variant "A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke] 0 0 46971 5 NULL SO:0001879 feature_ablation "A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke] 0 0 46972 5 NULL SO:0001880 feature_amplification "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke] 0 0 46973 5 NULL SO:0001881 feature_translocation "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke] 0 0 46974 5 NULL SO:0001882 feature_fusion "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke] 0 0 46975 5 NULL SO:0001883 transcript_translocation "A feature translocation where the region contains a transcript." [SO:ke] 0 0 46976 5 NULL SO:0001884 regulatory_region_translocation "A feature translocation where the region contains a regulatory region." [SO:ke] 0 0 46977 5 NULL SO:0001885 TFBS_translocation "A feature translocation where the region contains a transcription factor binding site." [SO:ke] 0 0 46978 5 NULL SO:0001886 transcript_fusion "A feature fusion where the deletion brings together transcript regions." [SO:ke] 0 0 46979 5 NULL SO:0001887 regulatory_region_fusion "A feature fusion where the deletion brings together regulatory regions." [SO:ke] 0 0 46980 5 NULL SO:0001888 TFBS_fusion "A fusion where the deletion brings together transcription factor binding sites." [SO:ke] 0 0 46981 5 NULL SO:0001889 transcript_amplification "A feature amplification of a region containing a transcript." [SO:ke] 0 0 46982 5 NULL SO:0001890 transcript_regulatory_region_fusion "A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke] 0 0 46983 5 NULL SO:0001891 regulatory_region_amplification "A feature amplification of a region containing a regulatory region." [SO:ke] 0 0 46984 5 NULL SO:0001892 TFBS_amplification "A feature amplification of a region containing a transcription factor binding site." [SO:ke] 0 0 46985 5 NULL SO:0001893 transcript_ablation "A feature ablation whereby the deleted region includes a transcript feature." [SO:ke] 0 0 46986 5 NULL SO:0001894 regulatory_region_ablation "A feature ablation whereby the deleted region includes a regulatory region." [SO:ke] 0 0 46987 5 NULL SO:0001895 TFBS_ablation "A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke] 0 0 46988 5 NULL SO:0001896 transposable_element_CDS "A CDS that is part of a transposable element." [SO:ke] 0 0 46989 5 NULL SO:0001897 transposable_element_pseudogene "A pseudogene contained within a transposable element." [SO:ke] 0 0 46990 5 NULL SO:0001898 dg_repeat "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw] 0 0 46991 5 NULL SO:0001899 dh_repeat "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw] 0 0 46992 5 NULL SO:0001900 M26_binding_site "A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137] 0 0 46993 5 NULL SO:0001901 AACCCT_box "A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687] 0 0 46994 5 NULL SO:0001902 splice_region "A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm] 0 0 46995 5 NULL SO:0001903 intronic_lncRNA "A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke] 0 0 46996 5 NULL SO:0001904 antisense_lncRNA "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999] 0 0 46997 5 NULL SO:0001905 regional_centromere_outer_repeat_transcript "A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah] 0 0 46998 5 NULL SO:0001906 feature_truncation "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke] 0 0 46999 5 NULL SO:0001907 feature_elongation "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke] 0 0 47000 5 NULL SO:0001908 internal_feature_elongation "A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke] 0 0 47001 5 NULL SO:0001909 frameshift_elongation "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke] 0 0 47002 5 NULL SO:0001910 frameshift_truncation "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke] 0 0 47003 5 NULL SO:0001911 copy_number_increase "A sequence variant where copies of a feature are increased relative to the reference." [SO:ke] 0 0 47004 5 NULL SO:0001912 copy_number_decrease "A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke] 0 0 47005 5 NULL SO:0001913 bacterial_RNApol_promoter_sigma_ecf "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc] 0 0 47006 5 NULL SO:0001914 rDNA_replication_fork_barrier "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529] 0 0 47007 5 NULL SO:0001915 transcription_start_cluster "A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson] 0 0 47008 5 NULL SO:0001916 CAGE_tag "A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson] 0 0 47009 5 NULL SO:0001917 CAGE_cluster "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson] 0 0 47010 5 NULL SO:0001918 5_methylcytosine "A cytosine methylated at the 5 carbon." [SO:rtapella] 0 0 47011 5 NULL SO:0001919 4_methylcytosine "A cytosine methylated at the 4 nitrogen." [SO:rtapella] 0 0 47012 5 NULL SO:0001920 N6_methyladenine "An adenine methylated at the 6 nitrogen." [SO:rtapella] 0 0 47013 5 NULL SO:0001921 mitochondrial_contig "A contig of mitochondria derived sequences." [GMOD:ea] 0 0 47014 5 NULL SO:0001922 mitochondrial_supercontig "A scaffold composed of mitochondrial contigs." [GMOD:ea] 0 0 47015 5 NULL SO:0001923 TERRA "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915] 0 0 47016 5 NULL SO:0001924 ARRET "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915] 0 0 47017 5 NULL SO:0001925 ARIA "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats." [PMID:22139915] 0 0 47018 5 NULL SO:0001926 anti_ARRET "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts." [PMID:22139915] 0 0 47019 5 NULL SO:0001927 telomeric_transcript "A non-coding transcript derived from the transcript of the telomere." [PMID:22139915] 0 0 47020 5 NULL SO:0001928 distal_duplication "A duplication of the distal region of a chromosome." [SO:bm] 0 0 47021 5 NULL SO:0001929 mitochondrial_DNA_read "A sequencer read of a mitochondrial DNA sample." [GMOD:ea] 0 0 47022 5 NULL SO:0001930 chloroplast_DNA_read "A sequencer read of a chloroplast DNA sample." [GMOD:ea] 0 0 47023 5 NULL SO:0001931 consensus_gDNA "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea] 0 0 47024 5 NULL SO:0001932 restriction_enzyme_five_prime_single_strand_overhang "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke] 0 0 47025 5 NULL SO:0001933 restriction_enzyme_three_prime_single_strand_overhang "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke] 0 0 47026 5 NULL SO:0001934 monomeric_repeat "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke] 0 0 47027 5 NULL SO:0001935 H3K20_trimethylation_site "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj] 0 0 47028 5 NULL SO:0001936 H3K36_acetylation_site "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj] 0 0 47029 5 NULL SO:0001937 H2BK12_acetylation_site "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj] 0 0 47030 5 NULL SO:0001938 H2AK5_acetylation_site "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj] 0 0 47031 5 NULL SO:0001939 H4K12_acetylation_site "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj] 0 0 47032 5 NULL SO:0001940 H2BK120_acetylation_site "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj] 0 0 47033 5 NULL SO:0001941 H4K91_acetylation_site "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj] 0 0 47034 5 NULL SO:0001942 H2BK20_acetylation_site "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj] 0 0 47035 5 NULL SO:0001943 H3K4ac_acetylation_site "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj] 0 0 47036 5 NULL SO:0001944 H2AK9_acetylation_site "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj] 0 0 47037 5 NULL SO:0001945 H3K56_acetylation_site "A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj] 0 0 47038 5 NULL SO:0001946 H2BK15_acetylation_site "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj] 0 0 47039 5 NULL SO:0001947 H3R2_monomethylation_site "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj] 0 0 47040 5 NULL SO:0001948 H3R2_dimethylation_site "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj] 0 0 47041 5 NULL SO:0001949 H4R3_dimethylation_site "A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj] 0 0 47042 5 NULL SO:0001950 H4K4_trimethylation_site "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj] 0 0 47043 5 NULL SO:0001951 H3K23_dimethylation_site "A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj] 0 0 47044 5 NULL SO:0001952 promoter_flanking_region "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj] 0 0 47045 5 NULL SO:0001953 restriction_enzyme_assembly_scar "A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke] 0 0 47046 5 NULL SO:0001954 restriction_enzyme_region "A region related to restriction enzyme function." [SO:ke] 0 0 47047 5 NULL SO:0001955 protein_stability_element "A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke] 0 0 47048 5 NULL SO:0001956 protease_site "A polypeptide_region that codes for a protease cleavage site." [SO:ke] 0 0 47049 5 NULL SO:0001957 RNA_stability_element "RNA secondary structure that affects the stability of an RNA molecule." [SO:ke] 0 1 47050 5 NULL SO:0001958 lariat_intron "A kind of intron whereby the excision is driven by lariat formation." [SO:ke] 0 0 47051 5 NULL SO:0001959 TCT_motif "A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl] 0 0 47052 5 NULL SO:0001960 5_hydroxymethylcytosine "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke] 0 0 47053 5 NULL SO:0001961 5_formylcytosine "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke] 0 0 47054 5 NULL SO:0001962 modified_adenine "A modified adenine DNA base feature." [SO:ke] 0 0 47055 5 NULL SO:0001963 modified_cytosine "A modified cytosine DNA base feature." [SO:ke] 0 0 47056 5 NULL SO:0001964 modified_guanine "A modified guanine DNA base feature." [SO:ke] 0 0 47057 5 NULL SO:0001965 8_oxoguanine "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke] 0 0 47058 5 NULL SO:0001966 5_carboxylcytosine "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke] 0 0 47059 5 NULL SO:0001967 8_oxoadenine "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke] 0 0 47060 5 NULL SO:0001968 coding_transcript_variant "A transcript variant of a protein coding gene." [SO:ke] 0 0 47061 5 NULL SO:0001969 coding_transcript_intron_variant "A transcript variant occurring within an intron of a coding transcript." [SO:ke] 0 0 47062 5 NULL SO:0001970 non_coding_transcript_intron_variant "A transcript variant occurring within an intron of a non coding transcript." [SO:ke] 0 0 47063 5 NULL SO:0001971 zinc_finger_binding_site "" [] 0 0 47064 5 NULL SO:0001972 histone_4_acylation_site "A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke] 0 0 47065 5 NULL SO:0001973 histone_3_acetylation_site "A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke] 0 0 47066 5 NULL SO:0001974 CTCF_binding_site "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj] 0 0 47067 5 NULL SO:0001975 five_prime_sticky_end_restriction_enzyme_cleavage_site "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke] 0 0 47068 5 NULL SO:0001976 three_prime_sticky_end_restriction_enzyme_cleavage_site "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke] 0 0 47069 5 NULL SO:0001977 ribonuclease_site "A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke] 0 0 47070 5 NULL SO:0001978 signature "A region of sequence where developer information is encoded." [SO:ke] 0 0 47071 5 NULL SO:0001979 RNA_stability_element "A motif that affects the stability of RNA." [PMID:22495308, SO:ke] 0 0 47072 5 NULL SO:0001980 G_box "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml] 0 0 47073 5 NULL SO:0001981 L_box "An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml] 0 0 47074 5 NULL SO:0001982 I-box "A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml] 0 0 47075 5 NULL SO:0001983 5_prime_UTR_premature_start_codon_variant "A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am] 0 0 47076 5 NULL SO:0001984 silent_mating_type_cassette_array "A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah] 0 0 47077 5 NULL SO:0001985 Okazaki_fragment "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152] 0 0 47078 5 NULL SO:0001986 upstream_transcript_variant "A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr] 0 0 47079 5 NULL SO:0001987 downstream_transcript_variant "" [] 0 0 47080 5 NULL SO:0001988 5_prime_UTR_premature_start_codon_gain_variant "A 5' UTR variant where a premature start codon is gained." [Sanger:am] 0 0 47081 5 NULL SO:0001989 5_prime_UTR_premature_start_codon_loss_variant "A 5' UTR variant where a premature start codon is lost." [SANGER:am] 0 0 47082 5 NULL SO:0001990 five_prime_UTR_premature_start_codon_location_variant "A 5' UTR variant where a premature start codon is moved." [SANGER:am] 0 0 47083 5 NULL SO:0001991 consensus_AFLP_fragment "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea] 0 0 47084 5 NULL SO:0001992 nonsynonymous_variant "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke] 0 0 47085 5 NULL SO:0001993 extended_cis_splice_site "Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am] 0 0 47086 5 NULL SO:0001994 intron_base_5 "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am] 0 0 47087 5 NULL SO:0001995 extended_intronic_splice_region_variant "A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am] 0 0 47088 5 NULL SO:0001996 extended_intronic_splice_region "Region of intronic sequence within 10 bases of an exon." [SANGER:am] 0 0 47089 5 NULL SO:0001997 subtelomere "A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al] 0 0 47090 5 NULL SO:0001998 sgRNA "A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893] 0 0 47091 5 NULL SO:0001999 mating_type_region_motif "DNA motif that is a component of a mating type region." [SO:ke] 0 0 47092 5 NULL SO:0002001 Y_region "A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd] 0 0 47093 5 NULL SO:0002002 Z1_region "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd] 0 0 47094 5 NULL SO:0002003 Z2_region "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd] 0 0 47095 5 NULL SO:0002004 ARS_consensus_sequence "The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd] 0 0 47096 5 NULL SO:0002005 DSR_motif "The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662] 0 0 47097 5 NULL SO:0002006 zinc_repressed_element "A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh] 0 0 47098 5 NULL SO:0002007 MNV "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th] 0 0 47099 5 NULL SO:0002008 rare_amino_acid_variant "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke] 0 0 47100 5 NULL SO:0002009 selenocysteine_loss "A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid." [SO:ke] 0 0 47101 5 NULL SO:0002010 pyrrolysine_loss "A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke] 0 0 47102 5 NULL SO:0002011 intragenic_variant "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." [SO:ke] 0 0 47103 5 NULL SO:0002012 start_lost "A codon variant that changes at least one base of the canonical start codon." [SO:ke] 0 0 47104 5 NULL SO:0002013 5_prime_UTR_truncation "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence." [SO:ke] 0 0 47105 5 NULL SO:0002014 5_prime_UTR_elongation "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke] 0 0 47106 5 NULL SO:0002015 3_prime_UTR_truncation "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence." [SO:ke] 0 0 47107 5 NULL SO:0002016 3_prime_UTR_elongation "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke] 0 0 47108 5 NULL SO:0002017 conserved_intergenic_variant "A sequence variant located in a conserved intergenic region, between genes." [SO:ke] 0 0 47109 5 NULL SO:0002018 conserved_intron_variant "A transcript variant occurring within a conserved region of an intron." [SO:ke] 0 0 47110 5 NULL SO:0002019 start_retained_variant "A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke] 0 0 47111 5 NULL SO:0002020 boundary_element "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502] 0 0 47112 5 NULL SO:0002021 mating_type_region_replication_fork_barrier "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787] 0 0 47113 5 NULL SO:0002022 priRNA "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al] 0 0 47114 5 NULL SO:0002023 multiplexing_sequence_identifier "A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170] 0 0 47115 5 NULL SO:0002024 W_region "The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR." [SGD:jd] 0 0 47116 5 NULL SO:0002025 cis_acting_homologous_chromosome_pairing_region "A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw] 0 0 47117 5 NULL SO:0002026 intein_encoding_region "The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123] 0 0 47118 5 NULL SO:0002027 uORF "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah] 0 0 47119 5 NULL SO:0002028 sORF "An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah] 0 0 47120 5 NULL SO:0002029 tnaORF "A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw] 0 0 47121 5 NULL SO:0002030 X_region "One of two segments of homology found at all three mating loci (HML, MAT and HMR)." [SGD:jd] 0 0 47122 5 NULL SO:0002031 shRNA "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke] 0 0 47123 5 NULL SO:0002032 moR "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA." [SO:ke] 0 0 47124 5 NULL SO:0002033 loR "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA." [SO:ke] 0 0 47125 5 NULL SO:0002034 miR_encoding_snoRNA_primary_transcript "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] 0 0 47126 5 NULL SO:0002035 lncRNA_primary_transcript "A primary transcript encoding a lncRNA." [SO:ke] 0 0 47127 5 NULL SO:0002036 miR_encoding_lncRNA_primary_transcript "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] 0 0 47128 5 NULL SO:0002037 miR_encoding_tRNA_primary_transcript "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] 0 0 47129 5 NULL SO:0002038 shRNA_primary_transcript "A primary transcript encoding an shRNA." [SO:ke] 0 0 47130 5 NULL SO:0002039 miR_encoding_shRNA_primary_transcript "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] 0 0 47131 5 NULL SO:0002040 vaultRNA_primary_transcript "A primary transcript encoding a vaultRNA." [SO:ke] 0 0 47132 5 NULL SO:0002041 miR_encoding_vaultRNA_primary_transcript "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] 0 0 47133 5 NULL SO:0002042 Y_RNA_primary_transcript "A primary transcript encoding a Y-RNA." [SO:ke] 0 0 47134 5 NULL SO:0002043 miR_encoding_Y_RNA_primary_transcript "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke] 0 0 47135 5 NULL SO:0002044 TCS_element "A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT." [PMID:1489142, PMID:20118212, SO:ke] 0 0 47136 5 NULL SO:0002045 pheromone_response_element "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]." [PMID:1489142, SO:ke] 0 0 47137 5 NULL SO:0002046 FRE "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae." [PMID:1489142, SO:ke] 0 0 47138 5 NULL SO:0002047 transcription_pause_site "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli." [PMID:24789973, SO:ke] 0 0 47139 5 NULL SO:0002048 disabled_reading_frame "A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons)." [SGD:se] 0 0 47140 5 NULL SO:0002049 H3K27_acetylation_site "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:rs] 0 0 47141 5 NULL SO:0002050 constitutive_promoter "A promoter that allows for continual transcription of gene." [SO:ke] 0 0 47142 5 NULL SO:0002051 inducible_promoter "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors." [SO:ke] 0 0 47143 5 NULL SO:0002052 dominant_negative_variant "A variant where the mutated gene product adversely affects the other (wild type) gene product." [SO:ke] 0 0 47144 5 NULL SO:0002053 gain_of_function_variant "A sequence variant whereby new or enhanced function is conferred on the gene product." [SO:ke] 0 0 47145 5 NULL SO:0002054 loss_of_function_variant "A sequence variant whereby the gene product has diminished or abolished function." [SO:ke] 0 0 47146 5 NULL SO:0002055 null_mutation "A variant whereby the gene product is not functional or the gene product is not produced." [SO:ke] 0 0 47147 5 NULL SO:0002056 intronic_splicing_silencer "An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke] 0 0 47148 5 NULL SO:0002057 intronic_splicing_enhancer "" [] 0 1 47149 5 NULL SO:0002058 exonic_splicing_silencer "An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke] 0 0 47150 5 NULL SO:0002059 recombination_enhancer "A regulatory_region that promotes or induces the process of recombination." [PMID:8861911, SGD:se] 0 0 47151 5 NULL SO:0002060 interchromosomal_translocation "A translocation where the regions involved are from different chromosomes." [NCBI:th] 0 0 47152 5 NULL SO:0002061 intrachromosomal_translocation "A translocation where the regions involved are from the same chromosome." [NCBI:th] 0 0 47153 5 NULL SO:0002062 complex_chromosomal_rearrangement "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis." [NCBI:th] 0 0 47154 5 NULL SO:0002063 Alu_insertion "An insertion of sequence from the Alu family of mobile elements." [NCBI:th] 0 0 47155 5 NULL SO:0002064 LINE1_insertion "An insertion from the Line1 family of mobile elements." [NCBI:th] 0 0 47156 5 NULL SO:0002065 SVA_insertion "An insertion of sequence from the SVA family of mobile elements." [NCBI:th] 0 0 47157 5 NULL SO:0002066 mobile_element_deletion "A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element)." [NCBI:th] 0 0 47158 5 NULL SO:0002067 HERV_deletion "A deletion of the HERV mobile element with respect to a reference." [NCBI:th] 0 0 47159 5 NULL SO:0002068 SVA_deletion "A deletion of an SVA mobile element." [NCBI:th] 0 0 47160 5 NULL SO:0002069 LINE1_deletion "A deletion of a LINE1 mobile element with respect to a reference." [NCBI:th] 0 0 47161 5 NULL SO:0002070 Alu_deletion "A deletion of an Alu mobile element with respect to a reference." [NCBI:th] 0 0 47162 5 NULL SO:0002071 CDS_supported_by_peptide_spectrum_match "A CDS that is supported by proteomics data." [SO:ke] 0 0 47163 5 NULL SO:0002072 sequence_comparison "" [] 0 0 47164 5 NULL SO:0002073 no_sequence_alteration "A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence." [SO:ke] 0 0 47165 5 NULL SO:0002074 intergenic_1kb_variant "A variant that falls in an intergenic region that is 1 kb or less between 2 genes." [SO:ke] 0 0 47166 5 NULL SO:0002075 incomplete_transcript_variant "A sequence variant that intersects an incompletely annotated transcript." [SO:ke] 0 0 47167 5 NULL SO:0002076 incomplete_transcript_3UTR_variant "A sequence variant that intersects the 3' UTR of an incompletely annotated transcript." [SO:ke] 0 0 47168 5 NULL SO:0002077 incomplete_transcript_5UTR_variant "A sequence variant that intersects the 5' UTR of an incompletely annotated transcript." [SO:ke] 0 0 47169 5 NULL SO:0002078 incomplete_transcript_intronic_variant "A sequence variant that intersects the intron of an incompletely annotated transcript." [SO:ke] 0 0 47170 5 NULL SO:0002079 incomplete_transcript_splice_region_variant "A sequence variant that intersects the splice region of an incompletely annotated transcript." [SO:ke] 0 0 47171 5 NULL SO:0002080 incomplete_transcript_exonic_variant "A sequence variant that intersects the exon of an incompletely annotated transcript." [SO:ke] 0 0 47172 5 NULL SO:0002081 incomplete_transcript_CDS "A sequence variant that intersects the coding regions of an incompletely annotated transcript." [SO:ke] 0 0 47173 5 NULL SO:0002082 incomplete_transcript_coding_splice_variant "A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript." [SO:ke] 0 0 47174 5 NULL SO:0002083 2KB_downstream_variant "A sequence variant located within 2KB 3' of a gene." [SO:ke] 0 0 47175 5 NULL SO:0002084 exonic_splice_region_variant "A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary." [SO:ke] 0 0 47176 5 NULL SO:0002085 unidirectional_gene_fusion "A sequence variant whereby a two genes, on alternate strands have become joined." [SO:ke] 0 0 47177 5 NULL SO:0002086 bidirectional_gene_fusion "A sequence variant whereby a two genes, on alternate strands have become joined." [SO:ke] 0 0 47178 5 NULL SO:0002087 pseudogenic_CDS "A non functional descendant of the coding portion of a coding transcript, part of a pseudogene." [SO:ke] 0 0 47179 5 NULL SO:0002088 non_coding_transcript_splice_region_variant "A transcript variant occurring within the splice region (1-3 bases of the exon or 3-8 bases of the intron) of a non coding transcript." [SO:ke] 0 0 47180 5 NULL SO:0002089 3_prime_UTR_exon_variant "A UTR variant of exonic sequence of the 3' UTR." [SO:ke] 0 0 47181 5 NULL SO:0002090 3_prime_UTR_intron_variant "A UTR variant of intronic sequence of the 3' UTR." [SO:ke] 0 0 47182 5 NULL SO:0002091 5_prime_UTR_intron_variant "A UTR variant of intronic sequence of the 5' UTR." [SO:ke] 0 0 47183 5 NULL SO:0002092 5_prime_UTR_exon_variant "A UTR variant of exonic sequence of the 5' UTR." [SO:ke] 0 0 47184 5 NULL SO:0002093 structural_interaction_variant "A variant that impacts the internal interactions of the resulting polypeptide structure." [SO:ke] 0 0 47185 5 NULL SO:0002094 non_allelic_homologous_recombination_region "A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination." [] 0 0 47186 5 NULL SO:0002095 scaRNA "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs)." [] 0 0 47187 5 NULL SO:0002096 short_tandem_repeat_variation "A kind of sequence variant whereby a tandem repeat is expanded or contracted with regard to a reference." [SO:ke] 0 0 47188 5 NULL SO:0002097 vertebrate_immune_system_pseudogene "A pseudogene derived from a vertebrate immune system gene." [SO:ke] 0 0 47189 5 NULL SO:0002098 immunoglobulin_pseudogene "A pseudogene derived from an immunoglobulin gene." [SO:ke] 0 0 47190 5 NULL SO:0002099 T_cell_receptor_pseudogene "A pseudogene derived from a T-cell receptor gene." [SO:ke] 0 0 47191 5 NULL SO:0002100 IG_C_pseudogene "A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] 0 0 47192 5 NULL SO:0002101 IG_J_pseudogene "A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] 0 0 47193 5 NULL SO:0002102 IG_V_pseudogene "A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] 0 0 47194 5 NULL SO:0002103 TR_V_pseudogene "A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] 0 0 47195 5 NULL SO:0002104 TR_J_pseudogene "A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html, IGMT:http\\://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php] 0 0 47196 5 NULL SO:0002105 translated_processed_pseudogene "A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47197 5 NULL SO:0002106 translated_unprocessed_pseudogene "A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47198 5 NULL SO:0002107 transcribed_unprocessed_pseudogene "A unprocessed pseudogene supported by locus-specific evidence of transcription." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47199 5 NULL SO:0002108 transcribed_unitary_pseudogene "A unitary pseudogene overlapped by locus-specific evidence of transcription." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47200 5 NULL SO:0002109 transcribed_processed_pseudogene "A processed_pseudogene overlapped by locus-specific evidence of transcription." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47201 5 NULL SO:0002110 polymorphic_pseudogene_with_retained_intron "A polymorphic pseudogene in the reference genome, containing a retained intron, known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47202 5 NULL SO:0002111 pseudogene_processed_transcript "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus)." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47203 5 NULL SO:0002112 coding_transcript_with_retained_intron "A protein coding transcript containing a retained intron." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47204 5 NULL SO:0002113 lnRNA_with_retained_intron "A lncRNA transcript containing a retained intron." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47205 5 NULL SO:0002114 NMD_transcript "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptable to nonsense mediated decay." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47206 5 NULL SO:0002115 pseudogenic_transcript_with_retained_intron "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47207 5 NULL SO:0002116 polymorphic_pseudogene_processed_transcript "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47208 5 NULL SO:0002117 "" [] 0 1 47209 5 NULL SO:0002118 NMD_polymorphic_pseudogene_transcript "A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles." [GENCODE:http\\://www.gencodegenes.org/gencode_biotypes.html] 0 0 47210 5 NULL SO:0002119 allelic_frequency "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population." [SO:ke] 0 0 47211 5 SOFA SO:0005836 regulatory_region "A region of sequence that is involved in the control of a biological process." [SO:ke] 0 0 47212 5 NULL SO:0005837 U14_snoRNA_primary_transcript "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119] 0 0 47213 5 NULL SO:0005841 methylation_guide_snoRNA "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] 0 0 47214 5 NULL SO:0005843 rRNA_cleavage_RNA "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc] 0 0 47215 5 NULL SO:0005845 exon_of_single_exon_gene "An exon that is the only exon in a gene." [RSC:cb] 0 0 47216 5 NULL SO:0005847 cassette_array_member "" [] 0 0 47217 5 NULL SO:0005848 gene_cassette_member "" [] 0 0 47218 5 NULL SO:0005849 gene_subarray_member "" [] 0 0 47219 5 NULL SO:0005850 primer_binding_site "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] 0 0 47220 5 NULL SO:0005851 gene_array "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma] 0 0 47221 5 NULL SO:0005852 gene_subarray "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma] 0 0 47222 5 NULL SO:0005853 gene_cassette "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se] 0 0 47223 5 NULL SO:0005854 gene_cassette_array "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma] 0 0 47224 5 SOFA SO:0005855 gene_group "A collection of related genes." [SO:ma] 0 0 47225 5 NULL SO:0005856 selenocysteine_tRNA_primary_transcript "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] 0 0 47226 5 NULL SO:0005857 selenocysteinyl_tRNA "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke] 0 0 47227 5 NULL SO:0005858 syntenic_region "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml] 0 0 47228 5 biosapiens SO:0100001 biochemical_region_of_peptide "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR] 0 0 47229 5 biosapiens SO:0100002 molecular_contact_region "A region that is involved a contact with another molecule." [EBIBS:GAR] 0 0 47230 5 biosapiens SO:0100003 intrinsically_unstructured_polypeptide_region "A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR] 0 0 47231 5 biosapiens SO:0100004 catmat_left_handed_three "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 47232 5 biosapiens SO:0100005 catmat_left_handed_four "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 47233 5 biosapiens SO:0100006 catmat_right_handed_three "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 47234 5 biosapiens SO:0100007 catmat_right_handed_four "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 47235 5 biosapiens SO:0100008 alpha_beta_motif "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] 0 0 47236 5 biosapiens SO:0100009 lipoprotein_signal_peptide "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR] 0 0 47237 5 biosapiens SO:0100010 no_output "An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR] 0 0 47238 5 biosapiens,SOFA SO:0100011 cleaved_peptide_region "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR] 0 0 47239 5 biosapiens SO:0100012 peptide_coil "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR] 0 0 47240 5 biosapiens SO:0100013 hydrophobic_region_of_peptide "Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR] 0 0 47241 5 biosapiens SO:0100014 n_terminal_region "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR] 0 0 47242 5 biosapiens SO:0100015 c_terminal_region "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR] 0 0 47243 5 biosapiens SO:0100016 central_hydrophobic_region_of_signal_peptide "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR] 0 0 47244 5 biosapiens SO:0100017 polypeptide_conserved_motif "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR] 0 0 47245 5 biosapiens SO:0100018 polypeptide_binding_motif "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR] 0 0 47246 5 biosapiens SO:0100019 polypeptide_catalytic_motif "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR] 0 0 47247 5 biosapiens SO:0100020 polypeptide_DNA_contact "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke] 0 0 47248 5 biosapiens SO:0100021 polypeptide_conserved_region "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR] 0 0 47249 5 SOFA SO:1000002 substitution "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke] 0 0 47250 5 SOFA SO:1000005 complex_substitution "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \\"complex\\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 0 47251 5 SOFA SO:1000008 point_mutation "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop] 0 0 47252 5 NULL SO:1000009 transition "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 0 47253 5 NULL SO:1000010 pyrimidine_transition "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke] 0 0 47254 5 NULL SO:1000011 C_to_T_transition "A transition of a cytidine to a thymine." [SO:ke] 0 0 47255 5 NULL SO:1000012 C_to_T_transition_at_pCpG_site "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 0 47256 5 NULL SO:1000013 T_to_C_transition "" [] 0 0 47257 5 NULL SO:1000014 purine_transition "A substitution of a purine, A or G, for another purine." [SO:ke] 0 0 47258 5 NULL SO:1000015 A_to_G_transition "A transition of an adenine to a guanine." [SO:ke] 0 0 47259 5 NULL SO:1000016 G_to_A_transition "A transition of a guanine to an adenine." [SO:ke] 0 0 47260 5 NULL SO:1000017 transversion "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 0 47261 5 NULL SO:1000018 pyrimidine_to_purine_transversion "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke] 0 0 47262 5 NULL SO:1000019 C_to_A_transversion "A transversion from cytidine to adenine." [SO:ke] 0 0 47263 5 NULL SO:1000020 C_to_G_transversion "" [] 0 0 47264 5 NULL SO:1000021 T_to_A_transversion "A transversion from T to A." [SO:ke] 0 0 47265 5 NULL SO:1000022 T_to_G_transversion "A transversion from T to G." [SO:ke] 0 0 47266 5 NULL SO:1000023 purine_to_pyrimidine_transversion "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke] 0 0 47267 5 NULL SO:1000024 A_to_C_transversion "A transversion from adenine to cytidine." [SO:ke] 0 0 47268 5 NULL SO:1000025 A_to_T_transversion "A transversion from adenine to thymine." [SO:ke] 0 0 47269 5 NULL SO:1000026 G_to_C_transversion "A transversion from guanine to cytidine." [SO:ke] 0 0 47270 5 NULL SO:1000027 G_to_T_transversion "A transversion from guanine to thymine." [SO:ke] 0 0 47271 5 NULL SO:1000028 intrachromosomal_mutation "A chromosomal structure variation within a single chromosome." [SO:ke] 0 0 47272 5 NULL SO:1000029 chromosomal_deletion "An incomplete chromosome." [SO:ke] 0 0 47273 5 NULL SO:1000030 chromosomal_inversion "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke] 0 0 47274 5 NULL SO:1000031 interchromosomal_mutation "A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke] 0 0 47275 5 NULL SO:1000032 indel "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http\\://www.hgvs.org/mutnomen/recs-DNA.html#indel] 0 0 47276 5 NULL SO:1000035 duplication "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th] 0 0 47277 5 DBVAR,SOFA SO:1000036 inversion "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 0 47278 5 NULL SO:1000037 chromosomal_duplication "An extra chromosome." [SO:ke] 0 0 47279 5 NULL SO:1000038 intrachromosomal_duplication "A duplication that occurred within a chromosome." [SO:ke] 0 0 47280 5 NULL SO:1000039 direct_tandem_duplication "A tandem duplication where the individual regions are in the same orientation." [SO:ke] 0 0 47281 5 NULL SO:1000040 inverted_tandem_duplication "A tandem duplication where the individual regions are not in the same orientation." [SO:ke] 0 0 47282 5 NULL SO:1000041 intrachromosomal_transposition "A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke] 0 0 47283 5 NULL SO:1000042 compound_chromosome "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke] 0 0 47284 5 NULL SO:1000043 Robertsonian_fusion "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation] 0 0 47285 5 NULL SO:1000044 chromosomal_translocation "A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual] 0 0 47286 5 NULL SO:1000045 ring_chromosome "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome] 0 0 47287 5 NULL SO:1000046 pericentric_inversion "A chromosomal inversion that includes the centromere." [FB:reference_manual] 0 0 47288 5 NULL SO:1000047 paracentric_inversion "A chromosomal inversion that does not include the centromere." [FB:reference_manual] 0 0 47289 5 NULL SO:1000048 reciprocal_chromosomal_translocation "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual] 0 0 47290 5 NULL SO:1000049 sequence_variation_affecting_transcript "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47291 5 NULL SO:1000050 sequence_variant_causing_no_change_in_transcript "No effect on the state of the RNA." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47292 5 NULL SO:1000054 sequence_variation_affecting_coding_sequence "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47293 5 NULL SO:1000055 sequence_variant_causing_initiator_codon_change_in_transcript "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47294 5 NULL SO:1000056 sequence_variant_causing_amino_acid_coding_codon_change_in_transcript "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47295 5 NULL SO:1000057 sequence_variant_causing_synonymous_codon_change_in_transcript "The changed codon has the same translation product as the original codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47296 5 NULL SO:1000058 sequence_variant_causing_non_synonymous_codon_change_in_transcript "A DNA point mutation that causes a substitution of an amino acid by an other." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47297 5 NULL SO:1000059 sequence_variant_causing_missense_codon_change_in_transcript "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47298 5 NULL SO:1000060 sequence_variant_causing_conservative_missense_codon_change_in_transcript "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47299 5 NULL SO:1000061 sequence_variant_causing_nonconservative_missense_codon_change_in_transcript "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47300 5 NULL SO:1000062 sequence_variant_causing_nonsense_codon_change_in_transcript "The nucleotide change in the codon triplet creates a terminator codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47301 5 NULL SO:1000063 sequence_variant_causing_terminator_codon_change_in_transcript "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke] 0 1 47302 5 NULL SO:1000064 sequence_variation_affecting_reading_frame "An umbrella term for terms describing an effect of a sequence variation on the frame of translation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47303 5 NULL SO:1000065 frameshift_sequence_variation "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] 0 1 47304 5 NULL SO:1000066 sequence_variant_causing_plus_1_frameshift_mutation "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke] 0 1 47305 5 NULL SO:1000067 sequence_variant_causing_minus_1_frameshift "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke] 0 1 47306 5 NULL SO:1000068 sequence_variant_causing_plus_2_frameshift "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke] 0 1 47307 5 NULL SO:1000069 sequence_variant_causing_minus_2_frameshift "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke] 0 1 47308 5 NULL SO:1000070 sequence_variant_affecting_transcript_processing "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47309 5 NULL SO:1000071 sequence_variant_affecting_splicing "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47310 5 NULL SO:1000072 sequence_variant_affecting_splice_donor "A sequence_variant_effect that changes the splice donor sequence." [SO:ke] 0 1 47311 5 NULL SO:1000073 sequence_variant_affecting_splice_acceptor "A sequence_variant_effect that changes the splice acceptor sequence." [SO:ke] 0 1 47312 5 NULL SO:1000074 sequence_variant_causing_cryptic_splice_activation "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47313 5 NULL SO:1000075 sequence_variant_affecting_editing "Sequence variant affects the editing of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47314 5 NULL SO:1000076 sequence_variant_affecting_transcription "Mutation affects the process of transcription, its initiation, progression or termination." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47315 5 NULL SO:1000078 sequence_variant_decreasing_rate_of_transcription "A sequence variation that decreases the rate a which transcription of the sequence occurs." [SO:ke] 0 1 47316 5 NULL SO:1000079 sequence_variation_affecting_transcript_sequence "" [] 0 1 47317 5 NULL SO:1000080 sequence_variant_increasing_rate_of_transcription "" [] 0 1 47318 5 NULL SO:1000081 sequence_variant_affecting_rate_of_transcription "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke] 0 1 47319 5 NULL SO:1000082 sequence variant_affecting_transcript_stability "Sequence variant affects the stability of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47320 5 NULL SO:1000083 sequence_variant_increasing_transcript_stability "Sequence variant increases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47321 5 NULL SO:1000084 sequence_variant_decreasing_transcript_stability "Sequence variant decreases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47322 5 NULL SO:1000085 sequence_variation_affecting_level_of_transcript "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] 0 1 47323 5 NULL SO:1000086 sequence_variation_decreasing_level_of_transcript "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] 0 1 47324 5 NULL SO:1000087 sequence_variation_increasing_level_of_transcript "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke] 0 1 47325 5 NULL SO:1000088 sequence_variant_affecting_translational_product "A sequence variant causing a change in primary translation product of a transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47326 5 NULL SO:1000089 sequence_variant_causing_no_change_of_translational_product "The sequence variant at RNA level does not lead to any change in polypeptide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47327 5 NULL SO:1000092 sequence_variant_causing_complex_change_of_translational_product "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47328 5 NULL SO:1000093 sequence_variant_causing_amino_acid_substitution "The replacement of a single amino acid by another." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47329 5 NULL SO:1000094 sequence_variant_causing_conservative_amino_acid_substitution "" [] 0 1 47330 5 NULL SO:1000095 sequence_variant_causing_nonconservative_amino_acid_substitution "" [] 0 1 47331 5 NULL SO:1000096 sequence_variant_causing_amino_acid_insertion "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47332 5 NULL SO:1000097 sequence_variant_causing_amino_acid_deletion "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47333 5 NULL SO:1000098 sequence_variant_causing_polypeptide_truncation "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47334 5 NULL SO:1000099 sequence_variant_causing_polypeptide_elongation "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47335 5 NULL SO:1000100 mutation_causing_polypeptide_N_terminal_elongation "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47336 5 NULL SO:1000101 mutation_causing_polypeptide_C_terminal_elongation "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47337 5 NULL SO:1000102 sequence_variant_affecting_level_of_translational_product "" [] 0 1 47338 5 NULL SO:1000103 sequence_variant_decreasing_level_of_translation_product "" [] 0 1 47339 5 NULL SO:1000104 sequence_variant_increasing_level_of_translation_product "" [] 0 1 47340 5 NULL SO:1000105 sequence_variant_affecting_polypeptide_amino_acid_sequence "" [] 0 1 47341 5 NULL SO:1000106 mutation_causing_inframe_polypeptide_N_terminal_elongation "" [] 0 1 47342 5 NULL SO:1000107 mutation_causing_out_of_frame_polypeptide_N_terminal_elongation "" [] 0 1 47343 5 NULL SO:1000108 mutaton_causing_inframe_polypeptide_C_terminal_elongation "" [] 0 1 47344 5 NULL SO:1000109 mutation_causing_out_of_frame_polypeptide_C_terminal_elongation "" [] 0 1 47345 5 NULL SO:1000110 frame_restoring_sequence_variant "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] 0 1 47346 5 NULL SO:1000111 sequence_variant_affecting_3D_structure_of_polypeptide "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." [SO:ke] 0 1 47347 5 NULL SO:1000112 sequence_variant_causing_no_3D_structural_change "" [] 0 1 47348 5 NULL SO:1000115 sequence_variant_causing_complex_3D_structural_change "" [] 0 1 47349 5 NULL SO:1000116 sequence_variant_causing_conformational_change "" [] 0 1 47350 5 NULL SO:1000117 sequence_variant_affecting_polypeptide_function "" [] 0 1 47351 5 NULL SO:1000118 sequence_variant_causing_loss_of_function_of_polypeptide "" [] 0 1 47352 5 NULL SO:1000119 sequence_variant_causing_inactive_ligand_binding_site "" [] 0 1 47353 5 NULL SO:1000120 sequence_variant_causing_inactive_catalytic_site "" [] 0 1 47354 5 NULL SO:1000121 sequence_variant_causing_polypeptide_localization_change "" [] 0 1 47355 5 NULL SO:1000122 sequence_variant_causing_polypeptide_post_translational_processing_change "" [] 0 1 47356 5 NULL SO:1000123 polypeptide_post_translational_processing_affected "" [] 0 1 47357 5 NULL SO:1000124 sequence_variant_causing_partial_loss_of_function_of_polypeptide "" [] 0 1 47358 5 NULL SO:1000125 sequence_variant_causing_gain_of_function_of_polypeptide "" [] 0 1 47359 5 NULL SO:1000126 sequence_variant_affecting_transcript_secondary_structure "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke] 0 1 47360 5 NULL SO:1000127 sequence_variant_causing_compensatory_transcript_secondary_structure_mutation "" [] 0 1 47361 5 NULL SO:1000132 sequence_variant_effect "The effect of a change in nucleotide sequence." [SO:ke] 0 1 47362 5 NULL SO:1000134 sequence_variant_causing_polypeptide_fusion "" [] 0 1 47363 5 NULL SO:1000136 autosynaptic_chromosome "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304] 0 0 47364 5 NULL SO:1000138 homo_compound_chromosome "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke] 0 0 47365 5 NULL SO:1000140 hetero_compound_chromosome "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke] 0 0 47366 5 NULL SO:1000141 chromosome_fission "A chromosome that occurred by the division of a larger chromosome." [SO:ke] 0 0 47367 5 NULL SO:1000142 dexstrosynaptic_chromosome "An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual] 0 0 47368 5 NULL SO:1000143 laevosynaptic_chromosome "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual] 0 0 47369 5 NULL SO:1000144 free_duplication "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual] 0 0 47370 5 NULL SO:1000145 free_ring_duplication "A ring chromosome which is a copy of another chromosome." [SO:ke] 0 0 47371 5 NULL SO:1000147 deficient_translocation "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual] 0 0 47372 5 NULL SO:1000148 inversion_cum_translocation "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual] 0 0 47373 5 NULL SO:1000149 bipartite_duplication "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual] 0 0 47374 5 NULL SO:1000150 cyclic_translocation "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual] 0 0 47375 5 NULL SO:1000151 bipartite_inversion "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual] 0 0 47376 5 NULL SO:1000152 uninverted_insertional_duplication "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] 0 0 47377 5 NULL SO:1000153 inverted_insertional_duplication "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual] 0 0 47378 5 NULL SO:1000154 insertional_duplication "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke] 0 0 47379 5 NULL SO:1000155 interchromosomal_transposition "A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke] 0 0 47380 5 NULL SO:1000156 inverted_interchromosomal_transposition "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual] 0 0 47381 5 NULL SO:1000157 uninverted_interchromosomal_transposition "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] 0 0 47382 5 NULL SO:1000158 inverted_intrachromosomal_transposition "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual] 0 0 47383 5 NULL SO:1000159 uninverted_intrachromosomal_transposition "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual] 0 0 47384 5 NULL SO:1000160 unoriented_insertional_duplication "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] 0 0 47385 5 NULL SO:1000161 unoriented_interchromosomal_transposition "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] 0 0 47386 5 NULL SO:1000162 unoriented_intrachromosomal_transposition "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual] 0 0 47387 5 NULL SO:1000170 uncharacterized_chromosomal_mutation "" [] 0 0 47388 5 NULL SO:1000171 deficient_inversion "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke] 0 0 47389 5 DBVAR SO:1000173 tandem_duplication "A duplication consisting of 2 identical adjacent regions." [SO:ke] 0 0 47390 5 NULL SO:1000175 partially_characterized_chromosomal_mutation "" [] 0 0 47391 5 NULL SO:1000180 sequence_variant_affecting_gene_structure "A sequence_variant_effect that changes the gene structure." [SO:ke] 0 1 47392 5 NULL SO:1000181 sequence_variant_causing_gene_fusion "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene." [SO:ke] 0 1 47393 5 NULL SO:1000182 chromosome_number_variation "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke] 0 0 47394 5 NULL SO:1000183 chromosome_structure_variation "" [] 0 0 47395 5 NULL SO:1000184 sequence_variant_causes_exon_loss "A sequence variant affecting splicing and causes an exon loss." [SO:ke] 0 1 47396 5 NULL SO:1000185 sequence_variant_causes_intron_gain "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] 0 1 47397 5 NULL SO:1000186 sequence_variant_causing_cryptic_splice_donor_activation "" [] 0 1 47398 5 NULL SO:1001186 sequence_variant_causing_cryptic_splice_acceptor_activation "" [] 0 1 47399 5 NULL SO:1001187 alternatively_spliced_transcript "A transcript that is alternatively spliced." [SO:xp] 0 0 47400 5 NULL SO:1001188 encodes_1_polypeptide "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke] 0 0 47401 5 NULL SO:1001189 encodes_greater_than_1_polypeptide "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke] 0 0 47402 5 NULL SO:1001190 encodes_different_polypeptides_different_stop "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke] 0 0 47403 5 NULL SO:1001191 encodes_overlapping_peptides_different_start "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke] 0 0 47404 5 NULL SO:1001192 encodes_disjoint_polypeptides "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke] 0 0 47405 5 NULL SO:1001193 encodes_overlapping_polypeptides_different_start_and_stop "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke] 0 0 47406 5 NULL SO:1001194 alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping "" [] 0 1 47407 5 NULL SO:1001195 encodes_overlapping_peptides "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke] 0 0 47408 5 NULL SO:1001196 cryptogene "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma] 0 0 47409 5 NULL SO:1001197 dicistronic_primary_transcript "A primary transcript that has the quality dicistronic." [SO:xp] 0 0 47410 5 NULL SO:1001217 member_of_regulon "" [] 0 0 47411 5 NULL SO:1001244 alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping "" [] 0 1 47412 5 NULL SO:1001246 CDS_independently_known "A CDS with the evidence status of being independently known." [SO:xp] 0 0 47413 5 NULL SO:1001247 orphan_CDS "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma] 0 0 47414 5 NULL SO:1001249 CDS_supported_by_domain_match_data "A CDS that is supported by domain similarity." [SO:xp] 0 0 47415 5 NULL SO:1001251 CDS_supported_by_sequence_similarity_data "A CDS that is supported by sequence similarity data." [SO:xp] 0 0 47416 5 NULL SO:1001254 CDS_predicted "A CDS that is predicted." [SO:ke] 0 0 47417 5 NULL SO:1001255 status_of_coding_sequence "" [] 0 1 47418 5 NULL SO:1001259 CDS_supported_by_EST_or_cDNA_data "A CDS that is supported by similarity to EST or cDNA data." [SO:xp] 0 0 47419 5 NULL SO:1001260 internal_Shine_Dalgarno_sequence "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke] 0 0 47420 5 NULL SO:1001261 recoded_mRNA "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] 0 0 47421 5 NULL SO:1001262 minus_1_translationally_frameshifted "An attribute describing a translational frameshift of -1." [SO:ke] 0 0 47422 5 NULL SO:1001263 plus_1_translationally_frameshifted "An attribute describing a translational frameshift of +1." [SO:ke] 0 0 47423 5 NULL SO:1001264 mRNA_recoded_by_translational_bypass "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract] 0 0 47424 5 NULL SO:1001265 mRNA_recoded_by_codon_redefinition "A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma] 0 0 47425 5 NULL SO:1001266 stop_codon_redefinition_as_selenocysteine "" [] 0 1 47426 5 NULL SO:1001267 stop_codon_readthrough "" [] 0 1 47427 5 NULL SO:1001268 recoding_stimulatory_region "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract] 0 0 47428 5 NULL SO:1001269 four_bp_start_codon "A non-canonical start codon with 4 base pairs." [SO:ke] 0 0 47429 5 NULL SO:1001270 stop_codon_redefinition_as_pyrrolysine "" [] 0 1 47430 5 NULL SO:1001271 archaeal_intron "An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma] 0 0 47431 5 NULL SO:1001272 tRNA_intron "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke] 0 0 47432 5 NULL SO:1001273 CTG_start_codon "A non-canonical start codon of sequence CTG." [SO:ke] 0 0 47433 5 NULL SO:1001274 SECIS_element "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031] 0 0 47434 5 NULL SO:1001275 retron "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma] 0 0 47435 5 NULL SO:1001277 three_prime_recoding_site "The recoding stimulatory signal located downstream of the recoding site." [SO:ke] 0 0 47436 5 NULL SO:1001279 three_prime_stem_loop_structure "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke] 0 0 47437 5 NULL SO:1001280 five_prime_recoding_site "The recoding stimulatory signal located upstream of the recoding site." [SO:ke] 0 0 47438 5 NULL SO:1001281 flanking_three_prime_quadruplet_recoding_signal "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke] 0 0 47439 5 NULL SO:1001282 UAG_stop_codon_signal "A stop codon signal for a UAG stop codon redefinition." [SO:ke] 0 0 47440 5 NULL SO:1001283 UAA_stop_codon_signal "A stop codon signal for a UAA stop codon redefinition." [SO:ke] 0 0 47441 5 SOFA SO:1001284 regulon "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732] 0 0 47442 5 NULL SO:1001285 UGA_stop_codon_signal "A stop codon signal for a UGA stop codon redefinition." [SO:ke] 0 0 47443 5 NULL SO:1001286 three_prime_repeat_recoding_signal "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke] 0 0 47444 5 NULL SO:1001287 distant_three_prime_recoding_signal "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov\\:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract] 0 0 47445 5 NULL SO:1001288 stop_codon_signal "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke] 0 0 47446 5 SOFA SO:2000061 databank_entry "The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke] 0 0 47447 5 NULL SO:3000000 gene_segment "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add] 0 0