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    CD6 CD6 molecule [ Homo sapiens (human) ]

    Gene ID: 923, updated on 29-Oct-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See CD6 in Genome Data Viewer
    Location:
    11q12.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (60971680..61020377)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60922811..60971572)
    RS_2024_09 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 BRD4-independent group 4 enhancer GRCh37_chr11:60686309-60687508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3379 Neighboring gene transmembrane protein 109 Neighboring gene transmembrane protein 132A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4786 Neighboring gene solute carrier family 15 member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4788 Neighboring gene RNA, U6 small nuclear 933, pseudogene Neighboring gene tRNA-Ala (TGC) 10-1 Neighboring gene uncharacterized LOC105369326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:60774736-60775444 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:60779887-60780476 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:60780477-60781066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:60793655-60794220 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3384 Neighboring gene uncharacterized LOC105369325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:60824202-60824702 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:60828388-60829587 Neighboring gene long intergenic non-protein coding RNA 2954 Neighboring gene uncharacterized LOC124902677

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. The CD6 multiple sclerosis susceptibility allele is associated with alterations in CD4+ T cell proliferation. Kofler DM, et al. J Immunol, 2011 Sep 15. PMID 21849685
    2. The lymphocyte glycoprotein CD6 contains a repeated domain structure characteristic of a new family of cell surface and secreted proteins. Aruffo A, et al. J Exp Med, 1991 Oct 1. PMID 1919444, Free PMC Article
    3. Biosynthesis and post-translational modification of CD6, a T cell signal-transducing molecule. Swack JA, et al. J Biol Chem, 1991 Apr 15. PMID 2016320
    4. Assignment of gene coding human T-cell differentiation antigen, Tp120, to chromosome 11. Tsuge I, et al. Somat Cell Mol Genet, 1985 May. PMID 3923629
    5. Human CD6 possesses a large, alternatively spliced cytoplasmic domain. Robinson WH, et al. Eur J Immunol, 1995 Oct. PMID 7589069

    See all (71) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The CD318/CD6 axis limits type 1 diabetes islet autoantigen-specific human T cell activation.
      Title: The CD318/CD6 axis limits type 1 diabetes islet autoantigen-specific human T cell activation.
    2. Polymorphisms in the CD6-ALCAM axis may modulate psoriasis risk and outcomes.
      Title: Polymorphisms in the CD6-ALCAM axis may modulate psoriasis risk and outcomes.
    3. Activation of cytotoxic lymphocytes through CD6 enhances killing of cancer cells.
      Title: Activation of cytotoxic lymphocytes through CD6 enhances killing of cancer cells.
    4. CD6 and Its Interacting Partners: Newcomers to the Block of Cancer Immunotherapies.
      Title: CD6 and Its Interacting Partners: Newcomers to the Block of Cancer Immunotherapies.
    5. Gene variation impact on prostate cancer progression: Lymphocyte modulator, activation, and cell adhesion gene variant contribution.
      Title: Gene variation impact on prostate cancer progression: Lymphocyte modulator, activation, and cell adhesion gene variant contribution.
    6. Th1 and Th17 cells are resistant towards T cell activation-induced downregulation of CD6.
      Title: Th1 and Th17 cells are resistant towards T cell activation-induced downregulation of CD6.
    7. The CD6/ALCAM pathway promotes lupus nephritis via T cell-mediated responses.
      Title: The CD6/ALCAM pathway promotes lupus nephritis via T cell-mediated responses.
    8. Compromised levels of CD6 and reduced T cell activation in the aged immune system.
      Title: Compromised levels of CD6 and reduced T cell activation in the aged immune system.
    9. Contribution of Evolutionary Selected Immune Gene Polymorphism to Immune-Related Disorders: The Case of Lymphocyte Scavenger Receptors CD5 and CD6.
      Title: Contribution of Evolutionary Selected Immune Gene Polymorphism to Immune-Related Disorders: The Case of Lymphocyte Scavenger Receptors CD5 and CD6.
    10. Attenuation of Murine Collagen-Induced Arthritis by Targeting CD6.
      Title: Attenuation of Murine Collagen-Induced Arthritis by Targeting CD6.
    Submit: New GeneRIF Correction See all GeneRIFs (47)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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
    		  
    Process Evidence Code Pubs
    involved_in acute inflammatory response to antigenic stimulus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in immunological synapse formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lipopolysaccharide-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cytokine production involved in inflammatory response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to lipopolysaccharide IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of T cell receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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

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    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_001254750.2 → NP_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/TrEMBL
      Q8N4Q7
      Related
      ENSP00000340628.5, ENST00000352009.9
      Conserved Domains (2) summary
      smart00202
      Location:161 → 260
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:166 → 260
      SRCR; Scavenger receptor cysteine-rich domain

    2. NM_001254751.2 → NP_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/TrEMBL
      Q8N4Q7
      Related
      ENSP00000390676.2, ENST00000452451.6
      Conserved Domains (2) summary
      smart00202
      Location:161 → 260
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:166 → 260
      SRCR; Scavenger receptor cysteine-rich domain

    3. NM_006725.5 → NP_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
      A4KAD4, A4KAD5, P30203, Q8WWJ3, Q8WWJ4, Q8WWJ5, Q8WWJ6, Q8WWJ7, Q9UMF2, Q9Y4K7, Q9Y4K8, Q9Y4K9, Q9Y4L0
      UniProtKB/TrEMBL
      A8K9I9
      Related
      ENSP00000323280.7, ENST00000313421.11
      Conserved Domains (2) summary
      smart00202
      Location:161 → 260
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:166 → 260
      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_2024_08

    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_047427881.1 → XP_047283837.1  T-cell differentiation antigen CD6 isoform X13

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

      UniProtKB/TrEMBL
      A8K9I9
      Conserved Domains (2) summary
      smart00202
      Location:161 → 260
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:166 → 260
      SRCR; Scavenger receptor cysteine-rich domain

    3. XM_047427875.1 → XP_047283831.1  T-cell differentiation antigen CD6 isoform X4

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

      UniProtKB/TrEMBL
      A8K9I9
      Conserved Domains (2) summary
      smart00202
      Location:161 → 260
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:166 → 260
      SRCR; Scavenger receptor cysteine-rich domain

    5. XM_006718740.3 → XP_006718803.1  T-cell differentiation antigen CD6 isoform X6

      UniProtKB/TrEMBL
      A8K9I9
      Conserved Domains (2) summary
      smart00202
      Location:161 → 260
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:166 → 260
      SRCR; Scavenger receptor cysteine-rich domain

    6. XM_006718738.3 → XP_006718801.1  T-cell differentiation antigen CD6 isoform X2

      UniProtKB/TrEMBL
      A8K9I9
      Conserved Domains (2) summary
      smart00202
      Location:161 → 260
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:166 → 260
      SRCR; Scavenger receptor cysteine-rich domain

    7. XM_047427874.1 → XP_047283830.1  T-cell differentiation antigen CD6 isoform X3

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

      UniProtKB/TrEMBL
      A8K9I9
      Conserved Domains (2) summary
      smart00202
      Location:161 → 260
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:166 → 260
      SRCR; Scavenger receptor cysteine-rich domain

    9. XM_047427876.1 → XP_047283832.1  T-cell differentiation antigen CD6 isoform X8

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

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

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

    13. XM_047427878.1 → XP_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_054370518.1 → XP_054226493.1  T-cell differentiation antigen CD6 isoform X1

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

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

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

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

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

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

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

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

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

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

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

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P30203.3 GenPept UniProtKB/Swiss-Prot:P30203

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