{ "uniprot_canonical_ac": "A0JD32-1", "uniprot_ac": "A0JD32", "uniprot_id": "TV382_HUMAN", "mass": { "chemical_mass": 13278.0, "monoisotopic_mass": 13278.0 }, "refseq": {}, "gene_names": [ { "name": "TRAV38-2DV8", "resource": "UniProtKB", "type": "recommended", "url": "https://www.uniprot.org/uniprot/A0JD32", "id": "A0JD32" } ], "protein_names": [ { "name": "T cell receptor alpha variable 38-2/delta variable 8", "resource": "UniProtKB", "type": "recommended", "url": "", "id": "A0JD32" } ], "function": [ { "annotation": "V region of the variable domain of T cell receptor (TR) alpha chain that participates in the antigen recognition (PubMed:24600447). Alpha-beta T cell receptors are antigen specific receptors which are essential to the immune response and are present on the cell surface of T lymphocytes. Recognize peptide-major histocompatibility (MH) (pMH) complexes that are displayed by antigen presenting cells (APC), a prerequisite for efficient T cell adaptive immunity against pathogens (PubMed:25493333). Binding of alpha-beta TR to pMH complex initiates TR-CD3 clustering on the cell surface and intracellular activation of LCK that phosphorylates the ITAM motifs of CD3G, CD3D, CD3E and CD247 enabling the recruitment of ZAP70. In turn ZAP70 phosphorylates LAT, which recruits numerous signaling molecules to form the LAT signalosome. The LAT signalosome propagates signal branching to three major signaling pathways, the calcium, the mitogen-activated protein kinase (MAPK) kinase and the nuclear factor NF-kappa-B (NF-kB) pathways, leading to the mobilization of transcription factors that are critical for gene expression and essential for T cell growth and differentiation (PubMed:23524462). The T cell repertoire is generated in the thymus, by V-(D)-J rearrangement. This repertoire is then shaped by intrathymic selection events to generate a peripheral T cell pool of self-MH restricted, non-autoaggressive T cells. Post-thymic interaction of alpha-beta TR with the pMH complexes shapes TR structural and functional avidity (PubMed:15040585).", "evidence": [ { "database": "UniProtKB", "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32#function" }, { "database": "PubMed", "id": "23524462", "url": "https://glygen.org/publication/PubMed/23524462" }, { "database": "PubMed", "id": "25493333", "url": "https://glygen.org/publication/PubMed/25493333" }, { "database": "PubMed", "id": "15040585", "url": "https://glygen.org/publication/PubMed/15040585" }, { "database": "PubMed", "id": "24600447", "url": "https://glygen.org/publication/PubMed/24600447" } ] } ], "disease": [], "snv": [ { "evidence": [ { "id": "rs1483553049", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483553049" }, { "id": "rs1483553049", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1483553049" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "start_pos": 80, "end_pos": 80, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NAT->NAI).", "chr_id": "14", "chr_pos": "22281638", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T80", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1294778736", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294778736" }, { "id": "rs1294778736", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1294778736#frequency_tab" }, { "id": "rs1294778736", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294778736" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 98, "end_pos": 98, "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (KIS->NIS).", "chr_id": "14", "chr_pos": "22281693", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K98", "keywords": [ "ebi", "germline" ] } ], "mutagenesis": [], "expression_tissue": [ { "tissue": { "name": "Adult mammalian kidney", "namespace": "UBERON", "id": "0000082", "url": "http://purl.obolibrary.org/obo/UBERON_0000082" }, "score": "49.85", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] }, { "tissue": { "name": "Stomach", "namespace": "UBERON", "id": "0000945", "url": "http://purl.obolibrary.org/obo/UBERON_0000945" }, "score": "56.18", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] }, { "tissue": { "name": "Esophagus", "namespace": "UBERON", "id": "0001043", "url": "http://purl.obolibrary.org/obo/UBERON_0001043" }, "score": "55.31", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] }, { "tissue": { "name": "Rectum", "namespace": "UBERON", "id": "0001052", "url": "http://purl.obolibrary.org/obo/UBERON_0001052" }, "score": "69.44", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] }, { "tissue": { "name": "Urinary bladder", "namespace": "UBERON", "id": "0001255", "url": "http://purl.obolibrary.org/obo/UBERON_0001255" }, "score": "38.4", "present": "LOW", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] }, { "tissue": { "name": "Thyroid gland", "namespace": "UBERON", "id": "0002046", "url": "http://purl.obolibrary.org/obo/UBERON_0002046" }, "score": "36.46", "present": "LOW", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] }, { "tissue": { "name": "Liver", "namespace": "UBERON", "id": "0002107", "url": "http://purl.obolibrary.org/obo/UBERON_0002107" }, "score": "16.88", "present": "LOW", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] }, { "tissue": { "name": "Prostate gland", "namespace": "UBERON", "id": "0002367", "url": "http://purl.obolibrary.org/obo/UBERON_0002367" }, "score": "38.05", "present": "LOW", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] }, { "tissue": { "name": "Thoracic mammary gland", "namespace": "UBERON", "id": "0005200", "url": "http://purl.obolibrary.org/obo/UBERON_0005200" }, "score": "44.74", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817" } ] } ], "expression_disease": [], "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32" } ], "common_name": "Human" } ], "gene": [ { "name": "TRAV38-2DV8", "url": "https://www.uniprot.org/uniprot/A0JD32", "locus": { "chromosome": "14", "start_pos": 22281748, "end_pos": 22281105, "strand": "-", "evidence": [ { "database": "Ensembl Gene", "id": "ENSG00000211817", "url": "https://www.ensembl.org/id/ENSG00000211817" } ] } } ], "crossref": [ { "id": "ENSG00000211817", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000211817", "database": "Bgee", "categories": [ "Gene Expression" ] }, { "id": "TRAV38-2DV8", "url": "http://www.genecards.org/cgi-bin/carddisp.pl?gene=TRAV38-2DV8", "database": "GeneCards", "categories": [ "Gene Annotation", "Organism-specific" ] }, { "id": "12138", "url": "https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=12138", "database": "HGNC", "categories": [ "Organism-specific" ] }, { "id": "IPR007110", "url": "https://www.ebi.ac.uk/interpro/entry/IPR007110", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "IPR013106", "url": "https://www.ebi.ac.uk/interpro/entry/IPR013106", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "IPR013783", "url": "https://www.ebi.ac.uk/interpro/entry/IPR013783", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "IPR036179", "url": "https://www.ebi.ac.uk/interpro/entry/IPR036179", "database": "InterPro", "categories": [ "Protein Classification" ] }, { "id": "NX_A0JD32", "url": "https://www.nextprot.org/entry/NX_A0JD32", "database": "neXtProt", "categories": [ "Protein", "Organism-specific" ] }, { "id": "TVILHCT", "url": "https://omabrowser.org/oma/group/TVILHCT/", "database": "OMA", "categories": [ "Protein Classification" ] }, { "id": "PTHR19367", "url": "http://www.pantherdb.org/panther/family.do?clsAccession=PTHR19367", "database": "PANTHER", "categories": [ "Protein Classification" ] }, { "id": "PTHR19367:SF40", "url": "http://www.pantherdb.org/panther/family.do?clsAccession=PTHR19367:SF40", "database": "PANTHER", "categories": [ "Protein Classification" ] }, { "id": "PF07686", "url": "http://pfam.xfam.org/family/PF07686", "database": "Pfam", "categories": [ "Protein Classification" ] }, { "id": "PR_A0JD32", "url": "http://purl.obolibrary.org/obo/PR_A0JD32", "database": "PRO", "categories": [ "Protein" ] }, { "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "A0JD32-1", "url": "https://www.uniprot.org/uniprot/A0JD32-1", "database": "UniProtKB", "categories": [ "Protein" ] } ], "sequence": { "sequence": "MACPGFLWALVISTCLEFSMAQTVTQSQPEMSVQEAETVTLSCTYDTSESDYYLFWYKQPPSRQMILVIRQEAYKQQNATENRFSVNFQKAAKSFSLKISDSQLGDAAMYFCAYRS", "length": 116, "header": "sp|A0JD32-1|TV382_HUMAN Isoform 1 of T cell receptor alpha variable 38-2/delta variable 8 OS=Homo sapiens OX=9606 GN=TRAV38-2DV8 PE=3 SV=1 CANONICAL=A0JD32-1" }, "isoforms": [ { "isoform_ac": "A0JD32-1", "url": "", "sequence": { "sequence": "MACPGFLWALVISTCLEFSMAQTVTQSQPEMSVQEAETVTLSCTYDTSESDYYLFWYKQPPSRQMILVIRQEAYKQQNATENRFSVNFQKAAKSFSLKISDSQLGDAAMYFCAYRS", "length": 116, "header": "sp|A0JD32-1|TV382_HUMAN Isoform 1 of T cell receptor alpha variable 38-2/delta variable 8 OS=Homo sapiens OX=9606 GN=TRAV38-2DV8 PE=3 SV=1 CANONICAL=A0JD32-1" }, "locus": { "chromosome": "14", "start_pos": 22281747, "end_pos": 22281151, "strand": "-", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000390465.2", "url": "https://www.ensembl.org/id/ENST00000390465.2" }, { "database": "Ensembl Peptide", "id": "ENSP00000452332.1", "url": "https://www.ensembl.org/id/ENSP00000452332.1" } ] } } ], "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "site_category": "predicted", "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "start_pos": 78, "start_aa": "Asn", "end_pos": 78, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn78", "evidence": [ { "id": "A0JD32", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/A0JD32#ptm_processing" } ] } ], "phosphorylation": [], "glycation": [], "keywords": [ "glycoprotein", "glycoprotein_predicted" ], "publication": [ { "title": "The many important facets of T-cell repertoire diversity.", "journal": "Nature reviews. Immunology", "date": "2004-02", "authors": "Nikolich-Zugich Janko, Slifka Mark K, Messaoudi Ilhem", "evidence": [ { "database": "UniProtKB", "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32" } ], "reference": [ { "type": "PubMed", "id": "15040585", "url": "https://glygen.org/publication/PubMed/15040585" } ] }, { "title": "Structural biology of the T-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling.", "journal": "Cold Spring Harb. Perspect. Biol.", "date": "2010", "authors": "Wucherpfennig Kai W, Gagnon Etienne, Call Melissa J, Huseby Eric S, Call Matthew E", "evidence": [ { "database": "UniProtKB", "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32" } ], "reference": [ { "type": "PubMed", "id": "20452950", "url": "https://glygen.org/publication/PubMed/20452950" } ] }, { "title": "T cell receptor signalling networks: branched, diversified and bounded.", "journal": "Nature reviews. Immunology", "date": "2013-04", "authors": "Brownlie Rebecca J, Zamoyska Rose", "evidence": [ { "database": "UniProtKB", "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32" } ], "reference": [ { "type": "PubMed", "id": "23524462", "url": "https://glygen.org/publication/PubMed/23524462" } ] }, { "title": "Immunoglobulin and T Cell Receptor Genes: IMGT(\u00ae) and the Birth and Rise of Immunoinformatics.", "journal": "Frontiers in immunology", "date": "2014", "authors": "Lefranc Marie-Paule", "evidence": [ { "database": "UniProtKB", "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32" } ], "reference": [ { "type": "PubMed", "id": "24600447", "url": "https://glygen.org/publication/PubMed/24600447" } ] }, { "title": "T cell antigen receptor recognition of antigen-presenting molecules.", "journal": "Annual review of immunology", "date": "2015", "authors": "Rossjohn Jamie, Gras Stephanie, Miles John J, Turner Stephen J, Godfrey Dale I, McCluskey James", "evidence": [ { "database": "UniProtKB", "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32" } ], "reference": [ { "type": "PubMed", "id": "25493333", "url": "https://glygen.org/publication/PubMed/25493333" } ] }, { "title": "Analysis of the 1.1-Mb human alpha/delta T-cell receptor locus with bacterial artificial chromosome clones.", "journal": "Genome Res.", "date": "1997", "authors": "Boysen C, Simon M I, Hood L", "evidence": [ { "database": "UniProtKB", "id": "A0JD32", "url": "https://www.uniprot.org/uniprot/A0JD32" } ], "reference": [ { "type": "PubMed", "id": "9110172", "url": "https://glygen.org/publication/PubMed/9110172" } ] } ], "pathway": [], "orthologs": [ { "uniprot_canonical_ac": "Q5R1A4-1", "protein_name": "T cell receptor delta variable 2-2", "gene_name": "Trdv2-2", "tax_id": 10090, "organism": "Mus musculus", "sequence": { "sequence": "MVRPFFLWVLFLSTSLEASMAQTVSQPQKKKSVQVAESATLDCTYDTSDTNYLLFWYKQQGGQVTLVILQEAYKQYNATLNRFSVNFQKAAKSFSLEISDSQLGDAATYFCALMER", "length": 116 }, 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