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CD6 CD6 molecule [ Homo sapiens (human) ]

Gene ID: 923, updated on 21-Mar-2023

Summary

Official Symbol
CD6provided by HGNC
Official Full Name
CD6 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1691
See related
Ensembl:ENSG00000013725 MIM:186720; AllianceGenome:HGNC:1691
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TP120
Summary
This gene encodes a protein found on the outer membrane of T-lymphocytes as well as some other immune cells. The encoded protein contains three scavenger receptor cysteine-rich (SRCR) domains and a binding site for an activated leukocyte cell adhesion molecule. The gene product is important for continuation of T cell activation. This gene may be associated with susceptibility to multiple sclerosis (PMID: 19525953, 21849685). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Expression
Biased expression in lymph node (RPKM 22.7), appendix (RPKM 13.7) and 9 other tissues See more
Orthologs
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Genomic context

See CD6 in Genome Data Viewer
Location:
11q12.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (60971680..61020377)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60922811..60971572)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (60739152..60787849)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902676 Neighboring gene transmembrane protein 109 Neighboring gene transmembrane protein 132A Neighboring gene solute carrier family 15 member 3 Neighboring gene RNA, U6 small nuclear 933, pseudogene Neighboring gene tRNA-Ala (TGC) 10-1 Neighboring gene uncharacterized LOC105369326 Neighboring gene uncharacterized LOC105369325 Neighboring gene uncharacterized LOC124902677 Neighboring gene CD5 molecule

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 Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci.
EBI GWAS Catalog
Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ44171

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables lipopolysaccharide binding IDA
Inferred from Direct Assay
more info
PubMed 
enables lipoteichoic acid binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein kinase binding IEA
Inferred from Electronic Annotation
more info
 
enables scavenger receptor activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cell surface IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in immunological synapse IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
T-cell differentiation antigen CD6
Names
CD6 antigen
T12

NCBI Reference Sequences (RefSeq)

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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_001254750.2NP_001241679.1  T-cell differentiation antigen CD6 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001241679.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
    Source sequence(s)
    AI657093, AP003721, U66145
    Consensus CDS
    CCDS58138.1
    UniProtKB/Swiss-Prot
    P30203
    Related
    ENSP00000340628.5, ENST00000352009.9
    Conserved Domains (2) summary
    smart00202
    Location:161260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166260
    SRCR; Scavenger receptor cysteine-rich domain
  2. NM_001254751.2NP_001241680.1  T-cell differentiation antigen CD6 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001241680.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.
    Source sequence(s)
    AI657093, AP003721, U66146
    Consensus CDS
    CCDS58137.1
    UniProtKB/Swiss-Prot
    P30203
    Related
    ENSP00000390676.2, ENST00000452451.6
    Conserved Domains (2) summary
    smart00202
    Location:161260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166260
    SRCR; Scavenger receptor cysteine-rich domain
  3. NM_006725.5NP_006716.3  T-cell differentiation antigen CD6 isoform 1 precursor

    See identical proteins and their annotated locations for NP_006716.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
    Source sequence(s)
    BC033755, BC078669, DB155411
    Consensus CDS
    CCDS7999.1
    UniProtKB/Swiss-Prot
    P30203, Q9Y4L0
    UniProtKB/TrEMBL
    Q6AZ88, Q8N4Q7
    Related
    ENSP00000323280.7, ENST00000313421.11
    Conserved Domains (2) summary
    smart00202
    Location:161260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166260
    SRCR; Scavenger receptor cysteine-rich domain

RNA

  1. NR_045638.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in an internal exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI657093, AP003721, DB155411, X60992
    Related
    ENST00000344931.9

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    60971680..61020377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427881.1XP_047283837.1  T-cell differentiation antigen CD6 isoform X13

  2. XM_011545360.3XP_011543662.1  T-cell differentiation antigen CD6 isoform X1

    Conserved Domains (2) summary
    smart00202
    Location:161260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166260
    SRCR; Scavenger receptor cysteine-rich domain
  3. XM_047427875.1XP_047283831.1  T-cell differentiation antigen CD6 isoform X4

  4. XM_006718739.3XP_006718802.1  T-cell differentiation antigen CD6 isoform X5

    Conserved Domains (2) summary
    smart00202
    Location:161260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166260
    SRCR; Scavenger receptor cysteine-rich domain
  5. XM_006718740.3XP_006718803.1  T-cell differentiation antigen CD6 isoform X6

    Conserved Domains (2) summary
    smart00202
    Location:161260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166260
    SRCR; Scavenger receptor cysteine-rich domain
  6. XM_006718738.3XP_006718801.1  T-cell differentiation antigen CD6 isoform X2

    UniProtKB/Swiss-Prot
    P30203
    Conserved Domains (2) summary
    smart00202
    Location:161260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166260
    SRCR; Scavenger receptor cysteine-rich domain
  7. XM_047427874.1XP_047283830.1  T-cell differentiation antigen CD6 isoform X3

  8. XM_011545362.3XP_011543664.1  T-cell differentiation antigen CD6 isoform X7

    UniProtKB/Swiss-Prot
    P30203
    Conserved Domains (2) summary
    smart00202
    Location:161260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166260
    SRCR; Scavenger receptor cysteine-rich domain
  9. XM_047427876.1XP_047283832.1  T-cell differentiation antigen CD6 isoform X8

  10. XM_047427879.1XP_047283835.1  T-cell differentiation antigen CD6 isoform X11

  11. XM_047427880.1XP_047283836.1  T-cell differentiation antigen CD6 isoform X12

  12. XM_047427877.1XP_047283833.1  T-cell differentiation antigen CD6 isoform X9

  13. XM_047427878.1XP_047283834.1  T-cell differentiation antigen CD6 isoform X10

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    60922811..60971572
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370518.1XP_054226493.1  T-cell differentiation antigen CD6 isoform X1

  2. XM_054370521.1XP_054226496.1  T-cell differentiation antigen CD6 isoform X4

  3. XM_054370522.1XP_054226497.1  T-cell differentiation antigen CD6 isoform X5

  4. XM_054370523.1XP_054226498.1  T-cell differentiation antigen CD6 isoform X6

  5. XM_054370519.1XP_054226494.1  T-cell differentiation antigen CD6 isoform X2

  6. XM_054370520.1XP_054226495.1  T-cell differentiation antigen CD6 isoform X3

  7. XM_054370524.1XP_054226499.1  T-cell differentiation antigen CD6 isoform X7

  8. XM_054370525.1XP_054226500.1  T-cell differentiation antigen CD6 isoform X8

  9. XM_054370528.1XP_054226503.1  T-cell differentiation antigen CD6 isoform X11

  10. XM_054370529.1XP_054226504.1  T-cell differentiation antigen CD6 isoform X12

  11. XM_054370526.1XP_054226501.1  T-cell differentiation antigen CD6 isoform X9

  12. XM_054370527.1XP_054226502.1  T-cell differentiation antigen CD6 isoform X10