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    CD5 CD5 molecule [ Homo sapiens (human) ]

    Gene ID: 921, updated on 15-Sep-2017
    Official Symbol
    CD5provided by HGNC
    Official Full Name
    CD5 moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:1685
    See related
    Ensembl:ENSG00000110448 MIM:153340; Vega:OTTHUMG00000167825
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    T1; LEU1
    Summary
    This gene encodes a member of the scavenger receptor cysteine-rich (SRCR) superfamily. Members of this family are secreted or membrane-anchored proteins mainly found in cells associated with the immune system. This protein is a type-I transmembrane glycoprotein found on the surface of thymocytes, T lymphocytes and a subset of B lymphocytes. The encoded protein contains three SRCR domains and may act as a receptor to regulate T-cell proliferation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2016]
    Orthologs
    Location:
    11q12.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 11 NC_000011.10 (61102458..61127852)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (60869930..60895324)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene CD6 molecule Neighboring gene uncharacterized LOC105369326 Neighboring gene uncharacterized LOC105369325 Neighboring gene VPS37C, ESCRT-I subunit Neighboring gene pepsinogen 3, group I (pepsinogen A)

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
    NHGRI GWA Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    NHGRI GWA Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    NHGRI GWA Catalog

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of CD5 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef HIV-1 Nef impairs the generation of a CD3epsilon(+)CD5(+) CD1a(+) T cell differentiation precursor stage that initiates a D-J rearrangement of the TCRbeta locus PubMed

    Go to the HIV-1, Human Interaction Database

    • Hematopoietic cell lineage, organism-specific biosystem (from KEGG)
      Hematopoietic cell lineage, organism-specific biosystemBlood-cell development progresses from a hematopoietic stem cell (HSC), which can undergo either self-renewal or differentiation into a multilineage committed progenitor cell: a common lymphoid proge...
    • Hematopoietic cell lineage, conserved biosystem (from KEGG)
      Hematopoietic cell lineage, conserved biosystemBlood-cell development progresses from a hematopoietic stem cell (HSC), which can undergo either self-renewal or differentiation into a multilineage committed progenitor cell: a common lymphoid proge...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    scavenger receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    transmembrane signaling receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    T cell costimulation IEA
    Inferred from Electronic Annotation
    more info
     
    apoptotic signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    cell proliferation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cell recognition NAS
    Non-traceable Author Statement
    more info
    PubMed 
    receptor-mediated endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    T-cell surface glycoprotein CD5
    Names
    CD5 antigen (p56-62)
    lymphocyte antigen T1/Leu-1

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001346456.1NP_001333385.1  T-cell surface glycoprotein CD5 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1. This variant contains long terminal repeat (LTR) sequence and uses an alternate LTR promoter. The protein encoded lacks the leader peptide, compared to isoform 1 and represents an intracellular isoform found in a subset of B lymphocytes. (PMID: 15998834)
      Source sequence(s)
      AP000437, BC027901
      UniProtKB/Swiss-Prot
      P06127
    2. NM_014207.3NP_055022.2  T-cell surface glycoprotein CD5 isoform 1 precursor

      See identical proteins and their annotated locations for NP_055022.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). The protein encoded represents an isoform found on the surface of T lymphocytes, B lymphocytes and thymocytes.
      Source sequence(s)
      AK292698, AP000437, BC027901, DB143341, X04391
      Consensus CDS
      CCDS8000.1
      UniProtKB/Swiss-Prot
      P06127
      Related
      ENSP00000342681.3, OTTHUMP00000236973, ENST00000347785.7, OTTHUMT00000396465
      Conserved Domains (2) summary
      smart00202
      Location:36133
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:40132
      SRCR; Scavenger receptor cysteine-rich domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p7 Primary Assembly

      Range
      61102458..61127852
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018922.2 Alternate CHM1_1.1

      Range
      60734232..60759595
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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