GlycineMine: Keyword Search

SO Term

SO:0002007 | MNV

Description:

An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence.

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SO Term

SO:0001013 | MNP

Description:

A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT.

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SO Term

SO:0001014 | intron_domain

Description:

An intronic region that has an attribute.

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SO Term

SO:0001015 | wobble_base_pair

Description:

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.

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SO Term

SO:0001016 | internal_guide_sequence

Description:

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.

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SO Term

SO:0001878 | feature_variant

Description:

A sequence variant that falls entirely or partially within a genomic feature.

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SO Term

SO:0001017 | silent_mutation

Description:

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.

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SO Term

SO:0001060 | sequence_variant

Description:

A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration.

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SO Term

SO:0001537 | structural_variant

Description:

A sequence variant that changes one or more structural features.

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SO Term

SO:0001018 | epitope

Description:

A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.

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SO Term

SO:0001019 | copy_number_variation

Description:

A variation that increases or decreases the copy number of a given region.

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SO Term

SO:0001021 | chromosome_breakpoint

Description:

A chromosomal region that may sustain a double-strand break, resulting in a recombination event.

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SO Term

SO:0001022 | inversion_breakpoint

Description:

The point within a chromosome where an inversion begins or ends.

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SO Term

SO:0001023 | allele

Description:

An allele is one of a set of coexisting sequence variants of a gene.

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SO Term

SO:0001024 | haplotype

Description:

A haplotype is one of a set of coexisting sequence variants of a haplotype block.

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SO Term

SO:0001025 | polymorphic_sequence_variant

Description:

A sequence variant that is segregating in one or more natural populations of a species.

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SO Term

SO:0001027 | genotype

Description:

A genotype is a variant genome, complete or incomplete.

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SO Term

SO:0001028 | diplotype

Description:

A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.

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SO Term

SO:0001032 | mitochondrial_DNA

Description:

DNA belonging to the genome of a mitochondria.

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SO Term

SO:0001033 | chloroplast_DNA

Description:

DNA belonging to the genome of a chloroplast, a photosynthetic plastid.

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SO Term

SO:0001034 | miRtron

Description:

A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.

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SO Term

SO:0001035 | piRNA

Description:

A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.

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SO Term

SO:0001036 | arginyl_tRNA

Description:

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

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SO Term

SO:0001040 | integrated_plasmid

Description:

A plasmid sequence that is integrated within the host chromosome.

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SO Term

SO:0001043 | attCtn_site

Description:

An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.

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SO Term

SO:0001044 | nuclear_mt_pseudogene

Description:

A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.

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SO Term

SO:0001045 | cointegrated_plasmid

Description:

A MGE region consisting of two fused plasmids resulting from a replicative transposition event.

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SO Term

SO:0001048 | inversion_site_part

Description:

A region located within an inversion site.

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SO Term

SO:0001046 | IRLinv_site

Description:

Component of the inversion site located at the left of a region susceptible to site-specific inversion.

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SO Term

SO:0001047 | IRRinv_site

Description:

Component of the inversion site located at the right of a region susceptible to site-specific inversion.

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SO Term

SO:0001049 | defective_conjugative_transposon

Description:

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.

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SO Term

SO:0001649 | nested_repeat

Description:

A repeat that is disrupted by the insertion of another element.

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SO Term

SO:0001050 | repeat_fragment

Description:

A portion of a repeat, interrupted by the insertion of another element.

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SO Term

SO:0001648 | nested_transposon

Description:

A transposon that is disrupted by the insertion of another element.

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SO Term

SO:0001054 | transposon_fragment

Description:

A portion of a transposon, interrupted by the insertion of another element.

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SO Term

SO:0001061 | propeptide_cleavage_site

Description:

The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.

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SO Term

SO:0002250 | propeptide_region_of_CDS

Description:

A CDS region corresponding to a propeptide of a polypeptide.

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SO Term

SO:0001064 | active_peptide

Description:

Active peptides are proteins which are biologically active, released from a precursor molecule.

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SO Term

SO:0001066 | compositionally_biased_region_of_peptide

Description:

Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.

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SO Term

SO:0001067 | polypeptide_motif

Description:

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.).

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SO Term

SO:0001068 | polypeptide_repeat

Description:

A polypeptide_repeat is a single copy of an internal sequence repetition.

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SO Term

SO:0001071 | membrane_structure

Description:

Arrangement of the polypeptide with respect to the lipid bilayer.

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SO Term

SO:0001072 | extramembrane_polypeptide_region

Description:

Polypeptide region that is localized outside of a lipid bilayer.

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SO Term

SO:0001073 | cytoplasmic_polypeptide_region

Description:

Polypeptide region that is localized inside the cytoplasm.

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SO Term

SO:0001074 | non_cytoplasmic_polypeptide_region

Description:

Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.

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SO Term

SO:0001075 | intramembrane_polypeptide_region

Description:

Polypeptide region present in the lipid bilayer.

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SO Term

SO:0001076 | membrane_peptide_loop

Description:

Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane.

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SO Term

SO:0001077 | transmembrane_polypeptide_region

Description:

Polypeptide region traversing the lipid bilayer.

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SO Term

SO:0001079 | polypeptide_structural_motif

Description:

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.

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SO Term

SO:0001080 | coiled_coil

Description:

A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.

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SO Term

SO:0001081 | helix_turn_helix

Description:

A motif comprising two helices separated by a turn.

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SO Term

SO:0001114 | peptide_helix

Description:

A helix is a secondary_structure conformation where the peptide backbone forms a coil.

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SO Term

SO:0001082 | polypeptide_sequencing_information

Description:

Incompatibility in the sequence due to some experimental problem.

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SO Term

SO:0001083 | non_adjacent_residues

Description:

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.

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SO Term

SO:0001084 | non_terminal_residue

Description:

The residue at an extremity of the sequence is not the terminal residue.

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SO Term

SO:0001085 | sequence_conflict

Description:

Different sources report differing sequences.

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SO Term

SO:0001086 | sequence_uncertainty

Description:

Describes the positions in a sequence where the authors are unsure about the sequence assignment.

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SO Term

SO:0100001 | biochemical_region_of_peptide

Description:

A region of a peptide that is involved in a biochemical function.

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SO Term

SO:0001089 | post_translationally_modified_region

Description:

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.

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SO Term

SO:0100002 | molecular_contact_region

Description:

A region that is involved a contact with another molecule.

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SO Term

SO:0001092 | polypeptide_metal_contact

Description:

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

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SO Term

SO:0001656 | metal_binding_site

Description:

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

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SO Term

SO:0001093 | protein_protein_contact

Description:

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

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SO Term

SO:0001094 | polypeptide_calcium_ion_contact_site

Description:

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

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SO Term

SO:0001095 | polypeptide_cobalt_ion_contact_site

Description:

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

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SO Term

SO:0001096 | polypeptide_copper_ion_contact_site

Description:

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

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SO Term

SO:0001097 | polypeptide_iron_ion_contact_site

Description:

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

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SO Term

SO:0001098 | polypeptide_magnesium_ion_contact_site

Description:

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

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SO Term

SO:0001099 | polypeptide_manganese_ion_contact_site

Description:

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

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SO Term

SO:0001100 | polypeptide_molybdenum_ion_contact_site

Description:

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

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SO Term

SO:0001101 | polypeptide_nickel_ion_contact_site

Description:

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

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SO Term

SO:0001102 | polypeptide_tungsten_ion_contact_site

Description:

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

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SO Term

SO:0001103 | polypeptide_zinc_ion_contact_site

Description:

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

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SO Term

SO:0001237 | amino_acid

Description:

A sequence feature that corresponds to a single amino acid residue in a polypeptide.

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SO Term

SO:0001104 | catalytic_residue

Description:

Amino acid involved in the activity of an enzyme.

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SO Term

SO:0100019 | polypeptide_catalytic_motif

Description:

A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues.

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SO Term

SO:0001657 | ligand_binding_site

Description:

A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.

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SO Term

SO:0001105 | polypeptide_ligand_contact

Description:

Residues which interact with a ligand.

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SO Term

SO:0001106 | asx_motif

Description:

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).

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SO Term

SO:0001107 | beta_bulge

Description:

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.

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SO Term

SO:0001108 | beta_bulge_loop

Description:

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.

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SO Term

SO:0001109 | beta_bulge_loop_five

Description:

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.

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SO Term

SO:0001110 | beta_bulge_loop_six

Description:

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.

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SO Term

SO:0001111 | beta_strand

Description:

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.

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SO Term

SO:0001112 | antiparallel_beta_strand

Description:

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.

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SO Term

SO:0001113 | parallel_beta_strand

Description:

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.

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SO Term

SO:0001115 | left_handed_peptide_helix

Description:

A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.

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SO Term

SO:0001116 | right_handed_peptide_helix

Description:

A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.

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SO Term

SO:0001117 | alpha_helix

Description:

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.

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SO Term

SO:0001118 | pi_helix

Description:

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.

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SO Term

SO:0001119 | three_ten_helix

Description:

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.

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SO Term

SO:0001120 | polypeptide_nest_motif

Description:

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.

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SO Term

SO:0001121 | polypeptide_nest_left_right_motif

Description:

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.

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SO Term

SO:0001122 | polypeptide_nest_right_left_motif

Description:

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.

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SO Term

SO:0001123 | schellmann_loop

Description:

A motif of six or seven consecutive residues that contains two H-bonds.

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SO Term

SO:0001124 | schellmann_loop_seven

Description:

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).

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SO Term

SO:0001125 | schellmann_loop_six

Description:

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).

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SO Term

SO:0001126 | serine_threonine_motif

Description:

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).

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SO Term

SO:0001127 | serine_threonine_staple_motif

Description:

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.

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SO Term

SO:0001129 | asx_turn_left_handed_type_one

Description:

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.

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