GlycineMine: Keyword Search

SO Term

SO:0002090 | 3_prime_UTR_intron_variant

Description:

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

•

SO Term

SO:0002091 | 5_prime_UTR_intron_variant

Description:

A UTR variant of intronic sequence of the 5' UTR.

•

SO Term

SO:0002092 | 5_prime_UTR_exon_variant

Description:

A UTR variant of exonic sequence of the 5' UTR.

•

SO Term

SO:0002093 | structural_interaction_variant

Description:

A variant that impacts the internal interactions of the resulting polypeptide structure.

•

SO Term

SO:0002094 | non_allelic_homologous_recombination_region

Description:

A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination.

•

SO Term

SO:0002095 | scaRNA

Description:

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).

•

SO Term

SO:0002096 | short_tandem_repeat_variation

Description:

A variation that expands or contracts a tandem repeat with regard to a reference.

•

SO Term

SO:0002097 | vertebrate_immune_system_pseudogene

Description:

A pseudogene derived from a vertebrate immune system gene.

•

SO Term

SO:0002098 | immunoglobulin_pseudogene

Description:

A pseudogene derived from an immunoglobulin gene.

•

SO Term

SO:0002099 | T_cell_receptor_pseudogene

Description:

A pseudogene derived from a T-cell receptor gene.

•

SO Term

SO:0002100 | IG_C_pseudogene

Description:

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.

•

SO Term

SO:0002101 | IG_J_pseudogene

Description:

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.

•

SO Term

SO:0002102 | IG_V_pseudogene

Description:

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.

•

SO Term

SO:0002103 | TR_V_pseudogene

Description:

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.

•

SO Term

SO:0002104 | TR_J_pseudogene

Description:

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.

•

SO Term

SO:0002105 | translated_processed_pseudogene

Description:

A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated.

•

SO Term

SO:0002106 | translated_unprocessed_pseudogene

Description:

A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated.

•

SO Term

SO:0002107 | transcribed_unprocessed_pseudogene

Description:

A unprocessed pseudogene supported by locus-specific evidence of transcription.

•

SO Term

SO:0002108 | transcribed_unitary_pseudogene

Description:

A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species.

•

SO Term

SO:0002109 | transcribed_processed_pseudogene

Description:

A processed_pseudogene overlapped by locus-specific evidence of transcription.

•

SO Term

SO:0002110 | polymorphic_pseudogene_with_retained_intron

Description:

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.

•

SO Term

SO:0002111 | pseudogene_processed_transcript

Description:

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).

•

SO Term

SO:0002112 | coding_transcript_with_retained_intron

Description:

A protein coding transcript containing a retained intron.

•

SO Term

SO:0002113 | lncRNA_with_retained_intron

Description:

A lncRNA transcript containing a retained intron.

•

SO Term

SO:0002114 | NMD_transcript

Description:

A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay.

•

SO Term

SO:0002115 | pseudogenic_transcript_with_retained_intron

Description:

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.

•

SO Term

SO:0002116 | polymorphic_pseudogene_processed_transcript

Description:

A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding.

•

SO Term

SO:0002118 | NMD_polymorphic_pseudogene_transcript

Description:

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.

•

SO Term

SO:0002119 | allelic_frequency

Description:

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 Term

SO:0002120 | three_prime_overlapping_ncrna

Description:

Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR.

•

SO Term

SO:0002121 | vertebrate_immune_system_gene

Description:

The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci).

•

SO Term

SO:0002122 | immunoglobulin_gene

Description:

A germline immunoglobulin gene.

•

SO Term

SO:0002123 | IG_C_gene

Description:

A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain.

•

SO Term

SO:0002124 | IG_D_gene

Description:

A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene.

•

SO Term

SO:0002125 | IG_J_gene

Description:

A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.

•

SO Term

SO:0002126 | IG_V_gene

Description:

A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain.

•

SO Term

SO:0002128 | mt_rRNA

Description:

Mitochondrial rRNA is an RNA component of the small or large subunits of mitochondrial ribosomes.

•

SO Term

SO:0002129 | mt_tRNA

Description:

Mitochondrial transfer RNA.

•

SO Term

SO:0002130 | NSD_transcript

Description:

A transcript that contains a CDS but has no stop codon before the polyA site is reached.

•

SO Term

SO:0002131 | sense_intronic_ncRNA

Description:

A long non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence.

•

SO Term

SO:0002132 | sense_overlap_ncRNA

Description:

A long non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence.

•

SO Term

SO:0002133 | T_cell_receptor_gene

Description:

A T-cell receptor germline gene.

•

SO Term

SO:0002134 | TR_C_Gene

Description:

A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain.

•

SO Term

SO:0002135 | TR_D_Gene

Description:

A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene.

•

SO Term

SO:0002136 | TR_J_Gene

Description:

A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain.

•

SO Term

SO:0002137 | TR_V_Gene

Description:

A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain.

•

SO Term

SO:0002138 | predicted_transcript

Description:

A transcript feature that has been predicted but is not yet validated.

•

SO Term

SO:0002139 | unconfirmed_transcript

Description:

This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies.

•

SO Term

SO:0002140 | early_origin_of_replication

Description:

An origin of replication that initiates early in S phase.

•

SO Term

SO:0002141 | late_origin_of_replication

Description:

An origin of replication that initiates late in S phase.

•

SO Term

SO:0002144 | histone_2AZ_acetylation_site

Description:

A histone 2AZ modification where the modification is the acetylation of the residue.

•

SO Term

SO:0002145 | H2AZK4_acetylation_site

Description:

A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated.

•

SO Term

SO:0002146 | H2AZK7_acetylation_site

Description:

A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated.

•

SO Term

SO:0002147 | H2AZK11_acetylation_site

Description:

A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated.

•

SO Term

SO:0002148 | H2AZK13_acetylation_site

Description:

A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated.

•

SO Term

SO:0002149 | H2AZK15_acetylation_site

Description:

A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated.

•

SO Term

SO:0002150 | AUG_initiated_uORF

Description:

A uORF beginning with the canonical start codon AUG.

•

SO Term

SO:0002151 | non_AUG_initiated_uORF

Description:

A uORF beginning with a codon other than AUG.

•

SO Term

SO:0002152 | genic_downstream_transcript_variant

Description:

A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms.

•

SO Term

SO:0002153 | genic_upstream_transcript_variant

Description:

A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms.

•

SO Term

SO:0002154 | mitotic_recombination_region

Description:

A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells.

•

SO Term

SO:0002155 | meiotic_recombination_region

Description:

A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase.

•

SO Term

SO:0002156 | CArG_box

Description:

A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'.

•

SO Term

SO:0002157 | Mat2P

Description:

A gene cassette array containing H+ mating type specific information.

•

SO Term

SO:0002158 | Mat3M

Description:

A gene cassette array containing H- mating type specific information.

•

SO Term

SO:0002159 | SHP_box

Description:

A conserved Cdc48/p97 interaction motif with strict consensus sequence F[PI]GKG[TK][RK]LG[GT] and relaxed consensus sequence FXGKGX[RK]LG.

•

SO Term

SO:0002161 | short_tandem_repeat_change

Description:

A sequence variant where the copies of a short tandem repeat (STR) feature are either contracted or expanded.

•

SO Term

SO:0002162 | short_tandem_repeat_expansion

Description:

A short tandem repeat variant containing more repeat units than the reference sequence.

•

SO Term

SO:0002163 | short_tandem_repeat_contraction

Description:

A short tandem repeat variant containing fewer repeat units than the reference sequence.

•

SO Term

SO:0002164 | H2BK5_acetylation_site

Description:

A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B histone protein is acetylated.

•

SO Term

SO:0002165 | trinucleotide_repeat_expansion

Description:

A short tandem repeat expansion with an increase in a sequence of three nucleotide units repeated in tandem compared to a reference sequence.

•

SO Term

SO:0002166 | ref_miRNA

Description:

A ref_miRNA (RefSeq-miRNA) sequence is assigned at the creation of a new mature miRNA entry in a database. The ref_miRNA sequence designation remains unchanged even if a different isomiR is later shown to be expressed at a higher level. A ref_miRNA can be produced by one or multiple pre-miRNA.

•

SO Term

SO:0002167 | isomiR

Description:

IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA.

•

SO Term

SO:0002168 | RNA_thermometer

Description:

An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression.

•

SO Term

SO:0002169 | splice_polypyrimidine_tract_variant

Description:

A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17).

•

SO Term

SO:0002170 | splice_donor_region_variant

Description:

A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron).

•

SO Term

SO:0002171 | telomeric_D_loop

Description:

A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus.

•

SO Term

SO:0002172 | sequence_alteration_artifact

Description:

A sequence_alteration where the source of the alteration is due to an artifact in the base-calling or assembly process.

•

SO Term

SO:0002173 | indel_artifact

Description:

An indel that is the result of base-calling or assembly error.

•

SO Term

SO:0002174 | deletion_artifact

Description:

A deletion that is the result of base-calling or assembly error.

•

SO Term

SO:0002175 | insertion_artifact

Description:

An insertion that is the result of base-calling or assembly error.

•

SO Term

SO:0002176 | substitution_artifact

Description:

A substitution that is the result of base-calling or assembly error.

•

SO Term

SO:0002177 | duplication_artifact

Description:

A duplication that is the result of base-calling or assembly error.

•

SO Term

SO:0002178 | SNV_artifact

Description:

An SNV that is the result of base-calling or assembly error.

•

SO Term

SO:0002179 | MNV_artifact

Description:

An MNV that is the result of base-calling or assembly error.

•

SO Term

SO:0002181 | ribozyme_gene

Description:

A gene that encodes a ribozyme.

•

SO Term

SO:0002182 | antisense_lncRNA_gene

Description:

A gene that encodes an antisense long, non-coding RNA.

•

SO Term

SO:0002183 | sense_overlap_ncRNA_gene

Description:

A gene that encodes a sense overlap long non-coding RNA.

•

SO Term

SO:0002184 | sense_intronic_ncRNA_gene

Description:

A gene that encodes a sense intronic long non-coding RNA.

•

SO Term

SO:0002185 | bidirectional_promoter_lncRNA

Description:

A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand.

•

SO Term

SO:0002186 | mutational_hotspot

Description:

A region of genomic sequence known to undergo mutational events with greater frequency than expected by chance.

•

SO Term

SO:0002187 | HERV_insertion

Description:

An insertion of sequence from the HERV family of mobile elements with respect to a reference.

•

SO Term

SO:0002188 | functional_gene_region

Description:

A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product.

•

SO Term

SO:0002189 | allelic_pseudogene

Description:

A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.

•

SO Term

SO:0002190 | enhancer_blocking_element

Description:

A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator.

•

SO Term

SO:0002191 | imprinting_control_region

Description:

A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs.

•

SO Term

SO:0002192 | flanking_repeat

Description:

A repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites).

•

SO Term

SO:0002193 | processed_pseudogenic_rRNA

Description:

The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.

•

SO Term

SO:0002194 | unprocessed_pseudogenic_rRNA

Description:

The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions.

•

SO Term

SO:0002195 | unitary_pseudogenic_rRNA

Description:

The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain.

•

Your name:
Your email address:
Subject:
Message:	---- Current page: ---- /glycinemine/keywordSearchResults.do;jsessionid=9A9D75D79D0C108D5DA815A19809C795?facet_Category=SOTerm&searchOffset=2000&searchTerm=%2A

GlycineMine

Search our database by keyword

Examples

Search results 2001 to 2100 out of 2386 for *

Category restricted to SOTerm

Categories