GlycineMine: Keyword Search

SO Term

SO:0001989 | 5_prime_UTR_premature_start_codon_loss_variant

Description:

A 5' UTR variant where a premature start codon is lost.

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SO Term

SO:0001990 | five_prime_UTR_premature_start_codon_location_variant

Description:

A 5' UTR variant where a premature start codon is moved.

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SO Term

SO:0001991 | consensus_AFLP_fragment

Description:

A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input.

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SO Term

SO:0001993 | extended_cis_splice_site

Description:

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.

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SO Term

SO:0001994 | intron_base_5

Description:

Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron.

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SO Term

SO:0001995 | extended_intronic_splice_region_variant

Description:

A sequence variant occurring in the intron, within 10 bases of exon.

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SO Term

SO:0001996 | extended_intronic_splice_region

Description:

Region of intronic sequence within 10 bases of an exon.

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SO Term

SO:0001997 | subtelomere

Description:

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.

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SO Term

SO:0001998 | sgRNA

Description:

A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method.

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SO Term

SO:0001999 | mating_type_region_motif

Description:

DNA motif that is a component of a mating type region.

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SO Term

SO:0002001 | Y_region

Description:

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).

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SO Term

SO:0002002 | Z1_region

Description:

A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR).

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SO Term

SO:0002003 | Z2_region

Description:

A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR).

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SO Term

SO:0002004 | ARS_consensus_sequence

Description:

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.

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SO Term

SO:0002005 | DSR_motif

Description:

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.

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SO Term

SO:0002006 | zinc_repressed_element

Description:

A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc.

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SO Term

SO:0002008 | rare_amino_acid_variant

Description:

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.

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SO Term

SO:0002009 | selenocysteine_loss

Description:

A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid.

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SO Term

SO:0002010 | pyrrolysine_loss

Description:

A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid.

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SO Term

SO:0002011 | intragenic_variant

Description:

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.

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SO Term

SO:0002012 | start_lost

Description:

A codon variant that changes at least one base of the canonical start codon.

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SO Term

SO:0002013 | 5_prime_UTR_truncation

Description:

A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence.

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SO Term

SO:0002014 | 5_prime_UTR_elongation

Description:

A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence.

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SO Term

SO:0002015 | 3_prime_UTR_truncation

Description:

A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence.

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SO Term

SO:0002016 | 3_prime_UTR_elongation

Description:

A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence.

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SO Term

SO:0002017 | conserved_intergenic_variant

Description:

A sequence variant located in a conserved intergenic region, between genes.

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SO Term

SO:0002018 | conserved_intron_variant

Description:

A transcript variant occurring within a conserved region of an intron.

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SO Term

SO:0002019 | start_retained_variant

Description:

A sequence variant where at least one base in the start codon is changed, but the start remains.

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SO Term

SO:0002020 | boundary_element

Description:

Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions.

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SO Term

SO:0002021 | mating_type_region_replication_fork_barrier

Description:

A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.

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SO Term

SO:0002022 | priRNA

Description:

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.

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SO Term

SO:0002023 | multiplexing_sequence_identifier

Description:

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.

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SO Term

SO:0002024 | W_region

Description:

The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR.

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SO Term

SO:0002025 | cis_acting_homologous_chromosome_pairing_region

Description:

A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I.

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SO Term

SO:0002026 | intein_encoding_region

Description:

The nucleotide sequence which encodes the intein portion of the precursor gene.

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SO Term

SO:0002027 | uORF

Description:

A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation.

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SO Term

SO:0002028 | sORF

Description:

An open reading frame that encodes a peptide of less than 100 amino acids.

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SO Term

SO:0002029 | tnaORF

Description:

A translated ORF encoded entirely within the antisense strand of a known protein coding gene.

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SO Term

SO:0002030 | X_region

Description:

One of two segments of homology found at all three mating loci (HML, MAT and HMR).

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SO Term

SO:0002031 | shRNA

Description:

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.

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SO Term

SO:0002032 | moR

Description:

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.

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SO Term

SO:0002033 | loR

Description:

A short, non coding transcript of loop-derived sequences encoded in precursor miRNA.

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SO Term

SO:0002034 | miR_encoding_snoRNA_primary_transcript

Description:

A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.

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SO Term

SO:0002035 | lncRNA_primary_transcript

Description:

A primary transcript encoding a lncRNA.

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SO Term

SO:0002036 | miR_encoding_lncRNA_primary_transcript

Description:

A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.

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SO Term

SO:0002037 | miR_encoding_tRNA_primary_transcript

Description:

A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.

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SO Term

SO:0002038 | shRNA_primary_transcript

Description:

A primary transcript encoding an shRNA.

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SO Term

SO:0002039 | miR_encoding_shRNA_primary_transcript

Description:

A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.

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SO Term

SO:0002040 | vaultRNA_primary_transcript

Description:

A primary transcript encoding a vaultRNA.

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SO Term

SO:0002041 | miR_encoding_vaultRNA_primary_transcript

Description:

A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.

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SO Term

SO:0002042 | Y_RNA_primary_transcript

Description:

A primary transcript encoding a Y-RNA.

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SO Term

SO:0002043 | miR_encoding_Y_RNA_primary_transcript

Description:

A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.

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SO Term

SO:0002044 | TCS_element

Description:

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.

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SO Term

SO:0002045 | pheromone_response_element

Description:

A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)].

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SO Term

SO:0002046 | FRE

Description:

A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae.

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SO Term

SO:0002047 | transcription_pause_site

Description:

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.

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SO Term

SO:0002048 | disabled_reading_frame

Description:

A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons).

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SO Term

SO:0002049 | H3K27_acetylation_site

Description:

A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated.

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SO Term

SO:0002050 | constitutive_promoter

Description:

A promoter that allows for continual transcription of gene.

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SO Term

SO:0002051 | inducible_promoter

Description:

A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors.

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SO Term

SO:0002052 | dominant_negative_variant

Description:

A variant where the mutated gene product adversely affects the other (wild type) gene product.

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SO Term

SO:0002053 | gain_of_function_variant

Description:

A sequence variant whereby new or enhanced function is conferred on the gene product.

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SO Term

SO:0002054 | loss_of_function_variant

Description:

A sequence variant whereby the gene product has diminished or abolished function.

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SO Term

SO:0002055 | null_mutation

Description:

A variant whereby the gene product is not functional or the gene product is not produced.

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SO Term

SO:0002056 | intronic_splicing_silencer

Description:

An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.

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SO Term

SO:0002058 | exonic_splicing_silencer

Description:

An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.

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SO Term

SO:0002059 | recombination_enhancer

Description:

A regulatory_region that promotes or induces the process of recombination.

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SO Term

SO:0002060 | interchromosomal_translocation

Description:

A translocation where the regions involved are from different chromosomes.

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SO Term

SO:0002061 | intrachromosomal_translocation

Description:

A translocation where the regions involved are from the same chromosome.

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SO Term

SO:0002062 | complex_chromosomal_rearrangement

Description:

A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis.

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SO Term

SO:0002063 | Alu_insertion

Description:

An insertion of sequence from the Alu family of mobile elements.

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SO Term

SO:0002272 | L1_LINE_retrotransposon

Description:

Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs.

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SO Term

SO:0002064 | LINE1_insertion

Description:

An insertion from the Line1 family of mobile elements.

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SO Term

SO:0002065 | SVA_insertion

Description:

An insertion of sequence from the SVA family of mobile elements.

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SO Term

SO:0002066 | mobile_element_deletion

Description:

A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element).

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SO Term

SO:0002268 | Endogenous_Retrovirus_LTR_retrotransposon

Description:

Endogenous retrovirus (ERV) retrotransposons are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses (Type D). F-Class III families are similar to foamy viruses.

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SO Term

SO:0002067 | HERV_deletion

Description:

A deletion of the HERV mobile element with respect to a reference.

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SO Term

SO:0002068 | SVA_deletion

Description:

A deletion of an SVA mobile element.

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SO Term

SO:0002069 | LINE1_deletion

Description:

A deletion of a LINE1 mobile element with respect to a reference.

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SO Term

SO:0002070 | Alu_deletion

Description:

A deletion of an Alu mobile element with respect to a reference.

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SO Term

SO:1001251 | CDS_supported_by_sequence_similarity_data

Description:

A CDS that is supported by sequence similarity data.

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SO Term

SO:0002071 | CDS_supported_by_peptide_spectrum_match

Description:

A CDS that is supported by proteomics data.

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SO Term

SO:1001254 | CDS_predicted

Description:

A CDS that is predicted.

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SO Term

SO:0002073 | no_sequence_alteration

Description:

A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence.

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SO Term

SO:0002074 | intergenic_1kb_variant

Description:

A variant that falls in an intergenic region that is 1 kb or less between 2 genes.

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SO Term

SO:0002075 | incomplete_transcript_variant

Description:

A sequence variant that intersects an incompletely annotated transcript.

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SO Term

SO:0002076 | incomplete_transcript_3UTR_variant

Description:

A sequence variant that intersects the 3' UTR of an incompletely annotated transcript.

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SO Term

SO:0002077 | incomplete_transcript_5UTR_variant

Description:

A sequence variant that intersects the 5' UTR of an incompletely annotated transcript.

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SO Term

SO:0002078 | incomplete_transcript_intronic_variant

Description:

A sequence variant that intersects the intron of an incompletely annotated transcript.

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SO Term

SO:0002079 | incomplete_transcript_splice_region_variant

Description:

A sequence variant that intersects the splice region of an incompletely annotated transcript.

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SO Term

SO:0002080 | incomplete_transcript_exonic_variant

Description:

A sequence variant that intersects the exon of an incompletely annotated transcript.

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SO Term

SO:0002081 | incomplete_transcript_CDS

Description:

A sequence variant that intersects the coding regions of an incompletely annotated transcript.

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SO Term

SO:0002082 | incomplete_transcript_coding_splice_variant

Description:

A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript.

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SO Term

SO:0002083 | 2KB_downstream_variant

Description:

A sequence variant located within 2KB 3' of a gene.

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SO Term

SO:0002084 | exonic_splice_region_variant

Description:

A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary.

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SO Term

SO:0002085 | unidirectional_gene_fusion

Description:

A sequence variant whereby two genes, on the same strand have become joined.

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SO Term

SO:0002086 | bidirectional_gene_fusion

Description:

A sequence variant whereby two genes, on alternate strands have become joined.

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SO Term

SO:0002087 | pseudogenic_CDS

Description:

A non functional descendant of the coding portion of a coding transcript, part of a pseudogene.

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SO Term

SO:0002088 | non_coding_transcript_splice_region_variant

Description:

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.

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SO Term

SO:0002089 | 3_prime_UTR_exon_variant

Description:

A UTR variant of exonic sequence of the 3' UTR.

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