U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon.
Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
Any substituent group or skeleton containing carbon.
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups.
Note that although at some level almost all cellular components can be thought of as protein complexes, this term is intended to exclude structures composed of the same repeating subunit or subunits, for example microtubules. Protein complexes encompassed by this term are generally not structural, and usually have a defined set of subunits.
A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
A protein that is a translation product of the human CD28 gene or a 1:1 ortholog thereof.
T-cell-specific surface glycoprotein CD28
A protein that is a component of collagen. Collagens are trimeric molecules in which each chain comprises a repeating Gly-X-Y triplet, in which X and Y can be any residue but are usually proline and hydroxyproline, respectively. This results in a left-handed helix that combines with other two to form a triple-helical structure.
A collagen type V alpha chain that is a translation product of the human COL5A1 gene or a 1:1 ortholog thereof.
A collagen alpha chain that is a translation product of the human COL5A1, COL5A2, or COL5A3 genes, 1:1 orthologs thereof, or a semi-ortholog thereof.
A protein that is a translation product of the human JCHAIN gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human PIGR gene or a 1:1 ortholog thereof.
hepatocellular carcinoma-associated protein TB6
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
A protein that is produced as the result of proteolytic processing of a longer protein.
A T-cell-specific surface glycoprotein CD28 that has had the signal peptide removed.
T-cell-specific surface glycoprotein CD28, signal peptide removed form
A collagen alpha-1(V) chain that has been processed by proteolytic cleavage.
collagen alpha-1(V) chain proteolytic cleavage product
An immunoglobulin J chain that has had the signal peptide removed.
immunoglobulin J chain, signal peptide removed form
A polymeric immunoglobulin receptor that has had the signal peptide removed.
polymeric immunoglobulin receptor, signal peptide removed form
A polymeric immunoglobulin receptor that has been processed by proteolytic cleavage.
polymeric immunoglobulin receptor proteolytic cleavage product
A part of a protein that is removed during the protein maturation process.
An osteocalcin that has not been proteolytically processed.
An osteocalcin that has had the signal peptide removed but retains the propeptide.
An osteocalcin pro-protein that has been carboxylated on all three eligible residues, corresponding to Glu-17, Glu-21, and Glu-24 of the human mature peptide UniProtKB:P02818. Example: UniProtKB:P02818, 24-100, Glu-68/Glu-72/Glu-75, MOD:00041.
osteocalcin pro-protein, fully carboyxylated form
An osteocalcin pro-protein that has been carboxylated on 1-2 of the three eligible residues, corresponding to Glu-17, Glu-21, and Glu-24 of the human mature peptide UniProtKB:P02818.
osteocalcin pro-protein, undercarboyxylated form
An osteocalcin pro-protein that has not been carboxylated on any of the three eligible residues, corresponding to Glu-17, Glu-21, and Glu-24 of the human mature peptide UniProtKB:P02818. Example: UniProtKB:P02818, 24-100, Glu-68/Glu-72/Glu-75, PR:000026291.
osteocalcin pro-protein, uncarboyxylated form
An osteocalcin that has had both the signal peptide and the propeptide removed.
An osteocalcin peptide that has been carboxylated on all three eligible residues, corresponding to Glu-17, Glu-21, and Glu-24 of the human mature peptide UniProtKB:P02818. Example: UniProtKB:P02818, 52-100, Glu-68/Glu-72/Glu-75, MOD:00041.
osteocalcin peptide, fully carboyxylated form
An osteocalcin peptide that has been carboxylated on 1-2 of the three eligible residues, corresponding to Glu-17, Glu-21, and Glu-24 of the human mature peptide UniProtKB:P02818.
osteocalcin peptide, undercarboyxylated form
An osteocalcin peptide that has not been carboxylated on any of the three eligible residues, corresponding to Glu-17, Glu-21, and Glu-24 of the human mature peptide UniProtKB:P02818. Example: UniProtKB:P02818, 52-100, Glu-68/Glu-72/Glu-75, PR:000026291.
osteocalcin peptide, uncarboyxylated form
An organic group that results from covalent modification or chemical alteration to the side chain or backbone atoms of an amino acid residue or derivative thereof, where such alteration maintains the integrity of the amino acid chain containing the residue.
Category=external. Note: This entity is distinct from MOD:00000 "protein modification" in that the latter includes proteolytic cleavages. [PRO:DAN, PRO:JSG]
A T-cell-specific surface glycoprotein CD28 that is a translation product of some mRNA giving rise to a protein with the amino acid sequence represented by UniProtKB:P10747-1 or a 1:1 ortholog thereof.
T-cell-specific surface glycoprotein CD28 isoform 1
A T-cell-specific surface glycoprotein CD28 isoform 1 that has had the signal peptide removed and has been phosphorylated on the Tyr residue within the C-terminal YMNM motif by LCK. Example: UniProtKB:P10747-1, 19-220, Tyr-191, MOD:00048.
T-cell-specific surface glycoprotein CD28 isoform 1, signal peptide removed phosphorylated 1
A T-cell-specific surface glycoprotein CD28 isoform 1, signal peptide removed phosphorylated 1 in human. UniProtKB:P10747-1, 19-220, Tyr-191, MOD:00048.
T-cell-specific surface glycoprotein CD28 isoform 1, signal peptide removed phosphorylated 1 (human)
A protein complex that is composed of two copies of phosphorylated CD28.
A phospho CD28 homodimer whose components are encoded in the genome of human.
A T-cell-specific surface glycoprotein CD28 isoform 1 that has had the signal peptide removed.
T-cell-specific surface glycoprotein CD28 isoform 1, signal peptide removed form
A T-cell-specific surface glycoprotein CD28, signal peptide removed form in human. Example: UniProtKB:P10747-1, 19-220.
T-cell-specific surface glycoprotein CD28, signal peptide removed form (human)
A protein that is encoded in the genome of Homo sapiens.
A protein that is a translation product of the human BGLAP gene or a 1:1 ortholog thereof.
gamma-carboxyglutamic acid-containing protein
A protein that is encoded in the genome of some Eukaryota.
A protein that includes at least one phosphorylated residue.
A protein that includes at least one carboxylated residue.
An osteocalcin (human) that has had the signal peptide removed. UniProtKB:P02818, 24-100.
osteocalcin, signal peptide removed form (human)
A collagen alpha-1(V) chain (human) that includes at least one 3-hydroxy-proline and at least one 4-hydroxy-proline. UniProtKB:P20908, MOD:00038|MOD:00039.
collagen alpha-1(V) chain 3-hydroxy-proline and 4-hydroxy-proline form (human)
A collagen alpha-1(V) chain (human) that includes at least one 4-hydroxy-proline. UniProtKB:P20908, MOD:00039.
collagen alpha-1(V) chain 4-hydroxy-proline form (human)
A collagen alpha-1(V) chain (human) that has had the signal peptide removed. UniProtKB:P20908, 38-1838.
collagen alpha-1(V) chain, signal peptide removed form (human)
A collagen alpha-1(V) chain (human) that has had the signal peptide removed and that includes at least one 3-hydroxy-proline and at least three 4-hydroxy-prolines. UniProtKB:P20908, 38-1838, MOD:00038|MOD:00039(3+).
collagen alpha-1(V) chain, signal peptide removed 3-hydroxy-proline and 4-hydroxy-proline form (human)
A collagen alpha-1(V) chain (human) that has had the signal peptide removed and that includes at least one 4-hydroxy-proline. UniProtKB:P20908, 38-1838, MOD:00039.
collagen alpha-1(V) chain, signal peptide removed 4-hydroxy-proline form (human)
An amino-acid residue that is either a modified or unmodified L-glutamic acid residue.
amino-acid residue related to L-glutamic acid
An amino-acid residue that is either a modified or unmodified L-proline residue.
An amino-acid residue that is either a modified or unmodified L-tyrosine residue.
amino-acid residue related to L-tyrosine
An IgA immunoglobulin complex, circulating that in monomeric form is composed of two identical immunoglobulin heavy chains of the secretory isoform of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
Category=organism-complex. Requested by=HIPC. Requested by=CL.
IgA1 immunoglobulin complex, circulating (human)
An IgA1 immunoglobulin complex, circulating (human) that is composed of two identical immunoglobulin heavy chains of the secretory isoform of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
monomeric IgA1 immunoglobulin complex (human)
An IgA1 immunoglobulin complex, circulating (human) that is composed of two, three, or four monomeric IgA1 immunoglobulin complexes linked through both direct disulfide bonds and through disulfide binded monomers of J chain acting as a bridge. Each IgA1 monomer consists of two identical immunoglobulin heavy chains of the secretory isoform of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds. Dimeric IgA1 is sometimes complexed additionally with secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
Category=organism-complex. Requested by=HIPC. Requested by=CL. Dimeric IgA1 is by far the most common form of polymeric IgA1. In human only the IgA1 isotype is capable of a polymeric forms.
polymeric IgA1 immunoglobulin complex (human)
A polymeric IgA1 immunoglobulin complex (human) that is composed of two monomeric IgA immunoglobulin complexes linked through both direct disulfide bonds and through a disulfide binded monomer of J chain acting as a bridge. Each IgA1 monomer consists of two identical immunoglobulin heavy chains of the secretory isoform of the IgA isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds. Dimeric IgA1 is sometimes complexed additionally with secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
Category=organism-complex. Requested by=HIPC. Requested by=CL. Dimeric IgA1 is by far the most common form of polymeric IgA1. In human only the IgA1 isotype is capable of a dimeric form.
dimeric IgA1 immunoglobulin complex (human)
A polymeric IgA1 immunoglobulin complex (human) that is complexed with one chain of secretory component (SC). Polymeric IgA1 is present in mucosal areas, having been transported via a transcytosis mechanism in mucosal epithelial cells relying on the polymeric Ig receptor, a portion of which then remains bound to the polymeric IgA as secretory component.
Category=organism-complex. Requested by=HIPC. Requested by=CL. In human only the IgA1 isotype in the polymeric form is capable of becoming secretory IgA.
secretory polymeric IgA1 immunoglobulin complex (human)
A dimeric form of secretory IgA1 immunoglobulin complex.
Category=organism-complex. Requested by=HIPC. Requested by=CL. Note that an IgA1 immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Dimeric IgA1 is by far the most common form of polymeric IgA. In human only the IgA1 isotype is capable of a dimeric form.
secretory dimeric IgA1 immunoglobulin complex (human)
A polymeric immunoglobulin receptor secretory component in human. UniProtKB:P01833, 19-603.
Category=organism-modification. Requested by=HIPC. Requested by=CL.
polymeric immunoglobulin receptor secretory component (human)
A protein that is a translation product of some mRNA produced by a somatically recombined immunoglobulin heavy chain locus.
Category=family. Requested by=IEDB. Note: In human, the IgH locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/349. In mouse, the locus is described by MGI:96442.
A protein that is a translation product of some mRNA produced by a somatically recombined immunoglobulin light chain locus.
Category=family. Note: In human, the kappa light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/351, and the lambda light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/353. In mouse, the kappa locus is described by MGI:96494, and the lambda locus is described by MGI:96526.
An immunoglobulin heavy chain protein in which the constant region is encoded either by the IgA1 gene segment or the IgA2 gene segment.
An IgA heavy chain protein in which the constant region is encoded by the IgA1 gene segment.
An IgA1 heavy chain protein that is encoded in the genome of human.
immunoglobulin alpha 1 heavy chain (human)
immunoglobulin heavy chain alpha 1 (human)
An immunoglobulin light chain protein that is produced from the immunoglobulin kappa locus.
Category=gene. Note: In human, the kappa light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/351. In mouse, the kappa locus is described by MGI:96494.
An immunoglobulin light chain protein that is produced from the immunoglobulin lambda locus.
Category=gene. Note: In human, the lambda light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/353. In mouse, the lambda locus is described by MGI:96526.
An immunoglobulin light chain protein that is encoded in the genome of human.
Category=organism-family. Note: The kappa light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/351, and the lambda light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/353.
immunoglobulin light chain protein (human)
An Ig kappa light chain protein that is encoded in the genome of human.
Category=organism-gene. Note: The kappa light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/351.
An Ig lambda light chain protein that is encoded in the genome of human.
Category=organism-gene. Note: The lambda light chain locus is described by https://www.genenames.org/cgi-bin/genefamilies/set/353.
A polymeric immunoglobulin receptor, signal peptide removed form that has been processed by proteolytic cleavage to separate the extracellular domain (represented here) from the transmembrane domain. Example: UniProtKB:P01833, 19-603.
Category=modification. Requested by=HIPC. Requested by=CL.
polymeric immunoglobulin receptor secretory component
An IgA1 heavy chain protein that is a translation product of some mRNA polyadenylated at a site 5' to the membrane exons, thus preventing their incorporation the final spliced mRNA.
immunoglobulin A1 heavy chain, secretory isoform
immunoglobulin alpha 1 heavy chain, secretory isoform
immunoglobulin heavy chain alpha 1, secretory isoform
Category=seqgroup. Requested by=HIPC. Requested by=CL.
IgA1 heavy chain protein, secretory isoform
An IgA1 heavy chain protein, secretory isoform that is encoded in the genome of human. This is a translation product of an IgA1 mRNA polyadenylated at a site 5' to the membrane exons, thus preventing their incorporation the final spliced mRNA.
immunoglobulin A1 heavy chain, secretory isoform (human)
immunoglobulin alpha 1 heavy chain, secretory isoform (human)
immunoglobulin heavy chain alpha 1, secretory isoform (human)
Category=organism-seqgroup. Requested by=HIPC. Requested by=CL.
IgA1 heavy chain protein, secretory isoform (human)
An immunoglobulin J chain that is encoded in the genome of human.
joining chain of multimeric IgA and IgM (human)
A polymeric immunoglobulin receptor that is encoded in the genome of human.
hepatocellular carcinoma-associated protein TB6 (human)
polymeric immunoglobulin receptor (human)
An osteocalcin that is encoded in the genome of human.
gamma-carboxyglutamic acid-containing protein (human)
A T-cell-specific surface glycoprotein CD28 that is encoded in the genome of human.
T-cell-specific surface glycoprotein CD28 (human)
A T-cell-specific surface glycoprotein CD28 isoform 1 that is encoded in the genome of human.
T-cell-specific surface glycoprotein CD28 isoform 1 (human)
A collagen alpha-1(V) chain that is encoded in the genome of human.
The signal peptide can be cleaved either co- or post-translationally. For this reason, we do not use the derives_from relation when defining protein forms lacking the signal peptide (because the precursor form might not yet exist at the time of removal).
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.