GlycineMine: Keyword Search

SO Term

SO:0002307 | DNA_loop

Description:

A region of DNA between two loop anchor positions that are held in close physical proximity.

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SO Term

SO:0002308 | DNA_loop_anchor

Description:

The ends of a DNA loop where the two strands of DNA are held in close physical proximity. During interphase the anchors of DNA loops are convergently oriented CTCF binding sites.

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SO Term

SO:0002310 | cryptic_promoter

Description:

The promoter of a cryptic gene.

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SO Term

SO:0002312 | core_prokaryotic_promoter_element

Description:

An element that always exists within the promoter region of a prokaryotic gene.

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SO Term

SO:0002313 | core_viral_promoter_element

Description:

An element that always exists within the promoter region of a viral gene.

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SO Term

SO:0002314 | altered_gene_product_level

Description:

A sequence variant that alters the level of transcription of a gene.

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SO Term

SO:0002315 | increased_gene_product_level

Description:

A sequence variant that increases the level of transcription of a gene.

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SO Term

SO:0002316 | decreased_gene_product_level

Description:

A sequence variant that decreases the level of transcription of a gene.

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SO Term

SO:0002317 | absent_gene_product

Description:

A sequence variant that entirely stops the transcription of a gene.

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SO Term

SO:0002318 | altered_gene_product_structure

Description:

A sequence variant that alters the structure of a gene product.

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SO Term

SO:0002319 | NMD_triggering_variant

Description:

A sequence variant that leads to a change in the location of a termination codon in a transcript that leads to nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants.

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SO Term

SO:0002320 | NMD_escaping_variant

Description:

A sequence variant that leads to a change in the location of a termination codon in a transcript but allows the transcript to escape nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants.

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SO Term

SO:0002321 | stop_gained_NMD_triggering

Description:

A stop_gained (SO:0001587) variant that is degraded by nonsense-mediated decay (NMD).

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SO Term

SO:0002322 | stop_gained_NMD_escaping

Description:

A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD).

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SO Term

SO:0002323 | frameshift_variant_NMD_triggering

Description:

A frameshift_variant (SO:0001589) that is degraded by nonsense-mediated decay (NMD).

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SO Term

SO:0002324 | frameshift_variant_NMD_escaping

Description:

A frameshift_variant (SO:0001589) that allows the transcript to escape nonsense-mediated decay (NMD).

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SO Term

SO:0002325 | splice_donor_variant_NMD_triggering

Description:

A splice_donor_variant (SO:0001575) that is degraded by nonsense-mediated decay (NMD).

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SO Term

SO:0002326 | splice_donor_variant_NMD_escaping

Description:

A splice_donor_variant (SO:0001575) that allows the transcript to escape nonsense-mediated decay (NMD).

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SO Term

SO:0002327 | splice_acceptor_variant_NMD_triggering

Description:

A splice_acceptor_variant (SO:0001574) that is degraded by nonsense-mediated decay (NMD).

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SO Term

SO:0002328 | splice_acceptor_variant_NMD_escaping

Description:

A splice_acceptor_variant (SO:0001574) that allows the transcript to escape nonsense-mediated decay (NMD).

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SO Term

SO:0002329 | minus_1_translational_frameshift

Description:

The region of mRNA 1 base long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.

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SO Term

SO:0002330 | minus_2_translational_frameshift

Description:

The region of mRNA 2 bases long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.

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SO Term

SO:0002332 | epigenomically_modified_region

Description:

A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.

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SO Term

SO:0002333 | amber_stop_codon

Description:

A stop codon with the DNA sequence TAG.

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SO Term

SO:0002334 | ochre_stop_codon

Description:

A stop codon with the DNA sequence TAA.

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SO Term

SO:0002335 | opal_stop_codon

Description:

A stop codon with the DNA sequence TGA.

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SO Term

SO:0002336 | cytosolic_rRNA_2S_gene

Description:

A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera.

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SO Term

SO:0002337 | cytosolic_2S_rRNA

Description:

Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules.

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SO Term

SO:0002338 | U7_snRNA

Description:

A 57 to 71 nucleotide RNA that is a component of the U7 small nuclear ribonucleoprotein complex (U7 snRNP). The U7 snRNP is required for histone pre-mRNA processing.

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SO Term

SO:0002339 | scaRNA_gene

Description:

A gene that encodes for a scaRNA (small Cajal body-specific RNA).

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SO Term

SO:0002340 | RNA_7SK

Description:

An abundant small nuclear RNA that, together with associated cellular proteins, regulates the activity of the positive transcription elongation factor b (P-TEFb). It is often described in literature as similar to a snRNA, except of longer length.

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SO Term

SO:0002341 | RNA_7SK_gene

Description:

A gene encoding a 7SK RNA (SO:0002340).

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SO Term

SO:0002344 | mt_SSU_rRNA

Description:

Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes.

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SO Term

SO:0002345 | mt_LSU_rRNA

Description:

Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes.

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SO Term

SO:0002346 | plastid_rRNA

Description:

Plastid rRNA is an RNA component of the small or large subunits of plastid (such as chloroplast) ribosomes.

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SO Term

SO:0002347 | plastid_SSU_rRNA

Description:

Plastid SSU rRNA is an RNA component of the small subunit of plastid (such as chloroplast) ribosomes.

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SO Term

SO:0002348 | plastid_LSU_rRNA

Description:

Plastid LSU rRNA is an RNA component of the large subunit of plastid (such as chloroplast) ribosomes.

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SO Term

SO:0002349 | fragile_site

Description:

A heritable locus on a chromosome that is prone to DNA breakage.

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SO Term

SO:0002350 | common_fragile_site

Description:

A fragile site considered part of the normal chromosomal structure.

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SO Term

SO:0002351 | rare_fragile_site

Description:

A fragile site found in the chromosomes of less than five percent of the human population.

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SO Term

SO:0002352 | sisRNA

Description:

A non-coding RNA typically derived from intronic sequence of the sense strand of a cognate host gene, that is not rapidly degraded. It may contain exonic sequences, 5′ caps, and/or polyA tails.

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SO Term

SO:0002353 | sbRNA_gene

Description:

A gene encoding a stem-bulge RNA.

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SO Term

SO:0002354 | sbRNA

Description:

A small non-coding stem-loop RNA present in nematodes and insects, functionally and structurally related to vertebrate Y RNA.

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SO Term

SO:0002355 | hpRNA_gene

Description:

A gene encoding a hpRNA.

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SO Term

SO:0002356 | hpRNA

Description:

An RNA comprising an extended inverted repeat, the stem of which is typically much longer than that of miRNA precursors and can be up to 400 base pairs in length. hpRNAs are processed by Dicer-2 to generate endogenous short interfering RNAs (siRNAs).

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SO Term

SO:0002357 | biosynthetic_gene_cluster

Description:

A physically clustered group of two or more genes in a particular genome that together encode a biosynthetic pathway for the production of a specialized metabolite (including its chemical variants).

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SO Term

SO:0002358 | vault_RNA_gene

Description:

A gene that encodes a vault RNA.

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SO Term

SO:0002359 | Y_RNA_gene

Description:

A gene that encodes a Y RNA.

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SO Term

SO:0002363 | mt_rRNA_gene

Description:

A gene that codes for mitochondrial rRNA.

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SO Term

SO:0002364 | mt_LSU_rRNA_gene

Description:

A gene that codes for mitochondrial LSU rRNA.

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SO Term

SO:0002365 | mt_SSU_rRNA_gene

Description:

A gene that codes for mitochondrial SSU rRNA.

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SO Term

SO:0002366 | plastid_rRNA_gene

Description:

A gene that codes for plastid rRNA.

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SO Term

SO:0002367 | plastid_LSU_rRNA_gene

Description:

A gene that codes for plastid LSU rRNA.

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SO Term

SO:0002368 | plastid_SSU_rRNA_gene

Description:

A gene that codes for plastid SSU rRNA.

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SO Term

SO:0002369 | C_D_box_scaRNA

Description:

A scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs.

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SO Term

SO:0002370 | H_ACA_box_scaRNA

Description:

A scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs.

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SO Term

SO:0002371 | C-D_H_ACA_box_scaRNA

Description:

A scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs.

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SO Term

SO:0002372 | C_D_box_scaRNA_gene

Description:

A gene that codes for scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs.

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SO Term

SO:0002373 | H_ACA_box_scaRNA_gene

Description:

A gene that codes for scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs.

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SO Term

SO:0002374 | C-D_H_ACA_box_scaRNA_gene

Description:

A gene that codes for scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs.

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SO Term

SO:0002375 | C_D_box_snoRNA_gene

Description:

A gene that codes a 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'.

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SO Term

SO:0002376 | H_ACA_box_snoRNA_gene

Description:

A gene that codes for 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.

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SO Term

SO:0002377 | U14_snoRNA_gene

Description:

A gene that codes for 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.

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SO Term

SO:0002378 | U3_snoRNA_gene

Description:

A gene that codes for 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.

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SO Term

SO:0002379 | methylation_guide_snoRNA_gene

Description:

A gene that codes for 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.

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SO Term

SO:0002380 | pseudouridylation_guide_snoRNA_gene

Description:

A gene that codes for 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.

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SO Term

SO:0005841 | methylation_guide_snoRNA

Description:

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.

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SO Term

SO:0005843 | rRNA_cleavage_RNA

Description:

An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules.

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SO Term

SO:0005845 | exon_of_single_exon_gene

Description:

An exon that is the only exon in a gene.

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SO Term

SO:0005848 | gene_cassette_member

Description:

A gene that is a member of a gene cassette, which is a mobile genetic element.

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SO Term

SO:0005847 | cassette_array_member

Description:

A gene that is a member of a gene cassette, which is a mobile genetic element.

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SO Term

SO:0005849 | gene_subarray_member

Description:

A gene that is a member of a group of genes that are either regulated or transcribed together within a larger group of genes that are regulated or transcribed together.

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SO Term

SO:0005850 | primer_binding_site

Description:

Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.

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SO Term

SO:0005851 | gene_array

Description:

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.

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SO Term

SO:0005852 | gene_subarray

Description:

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.

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SO Term

SO:0005856 | selenocysteine_tRNA_primary_transcript

Description:

A primary transcript encoding seryl tRNA (SO:000269).

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SO Term

SO:0005857 | selenocysteinyl_tRNA

Description:

A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region.

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SO Term

SO:0005858 | syntenic_region

Description:

A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.

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SO Term

SO:0100003 | intrinsically_unstructured_polypeptide_region

Description:

A region of polypeptide chain with high conformational flexibility.

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SO Term

SO:0100004 | catmat_left_handed_three

Description:

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.

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SO Term

SO:0100005 | catmat_left_handed_four

Description:

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.

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SO Term

SO:0100006 | catmat_right_handed_three

Description:

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.

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SO Term

SO:0100007 | catmat_right_handed_four

Description:

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.

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SO Term

SO:0100008 | alpha_beta_motif

Description:

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.

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SO Term

SO:0100009 | lipoprotein_signal_peptide

Description:

A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.

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SO Term

SO:0100010 | no_output

Description:

An experimental region wherean analysis has been run and not produced any annotation.

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SO Term

SO:0100012 | peptide_coil

Description:

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).

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SO Term

SO:0100013 | hydrophobic_region_of_peptide

Description:

Hydrophobic regions are regions with a low affinity for water.

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SO Term

SO:0100014 | n_terminal_region

Description:

The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa).

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SO Term

SO:0100015 | c_terminal_region

Description:

The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa).

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SO Term

SO:0100016 | central_hydrophobic_region_of_signal_peptide

Description:

The central, hydrophobic region of the signal peptide (approx 7-15 aa).

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SO Term

SO:0100018 | polypeptide_binding_motif

Description:

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.

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SO Term

SO:0100020 | polypeptide_DNA_contact

Description:

A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA.

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SO Term

SO:1000005 | complex_substitution

Description:

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.

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SO Term

SO:1000008 | point_mutation

Description:

A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.

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SO Term

SO:1000009 | transition

Description:

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.

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SO Term

SO:1000010 | pyrimidine_transition

Description:

A substitution of a pyrimidine, C or T, for another pyrimidine.

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SO Term

SO:1000011 | C_to_T_transition

Description:

A transition of a cytidine to a thymine.

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SO Term

SO:1000012 | C_to_T_transition_at_pCpG_site

Description:

The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.

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SO Term

SO:1000013 | T_to_C_transition

Description:

A transition of a thymine to a cytidine.

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