Format

Send to:

Choose Destination

CD5 CD5 molecule [ Homo sapiens (human) ]

Gene ID: 921, updated on 7-Dec-2018

Summary

Official Symbol
CD5provided by HGNC
Official Full Name
CD5 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1685
See related
Ensembl:ENSG00000110448 MIM:153340
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]
Expression
Biased expression in lymph node (RPKM 19.1), appendix (RPKM 11.9) and 10 other tissues See more
Orthologs

Genomic context

See CD5 in Genome Data Viewer
Location:
11q12.2
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (61093963..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 Sharpr-MPRA regulatory region 3147/8872 Neighboring gene VPS37C, ESCRT-I subunit

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
scavenger receptor activity IEA
Inferred from Electronic Annotation
more info
 
signaling receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
transmembrane signaling receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
T cell costimulation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
T-cell surface glycoprotein CD5
Names
CD5 antigen (p56-62)
epididymis secretory sperm binding protein
lymphocyte antigen T1/Leu-1

NCBI Reference Sequences (RefSeq)

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_014207.4NP_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, ENST00000347785.7
    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 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    61093963..61127852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center