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    Cd6 CD6 antigen [ Mus musculus (house mouse) ]

    Gene ID: 12511, updated on 12-Nov-2019

    Summary

    Official Symbol
    Cd6provided by MGI
    Official Full Name
    CD6 antigenprovided by MGI
    Primary source
    MGI:MGI:103566
    See related
    Ensembl:ENSMUSG00000024670
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Expression
    Biased expression in thymus adult (RPKM 87.0), spleen adult (RPKM 18.0) and 1 other tissue See more
    Orthologs

    Genomic context

    See Cd6 in Genome Data Viewer
    Location:
    19 A; 19 7.16 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    108 current GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (10789339..10830062, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 19 NC_000085.5 (10863829..10904548, complement)

    Chromosome 19 - NC_000085.6Genomic Context describing neighboring genes Neighboring gene CD5 antigen Neighboring gene RIKEN cDNA A430093F15 gene Neighboring gene solute carrier family 15, member 3 Neighboring gene transmembrane protein 132A Neighboring gene transmembrane protein 109

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    lipopolysaccharide binding ISO
    Inferred from Sequence Orthology
    more info
     
    lipoteichoic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
     
    scavenger receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    acute inflammatory response to antigenic stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ISO
    Inferred from Sequence Orthology
    more info
     
    immunological synapse formation ISO
    Inferred from Sequence Orthology
    more info
     
    lipopolysaccharide-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of T cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of cytokine production involved in inflammatory response ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of protein phosphorylation ISO
    Inferred from Sequence Orthology
    more info
     
    response to lipopolysaccharide ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    colocalizes_with T cell receptor complex ISO
    Inferred from Sequence Orthology
    more info
     
    immunological synapse ISO
    Inferred from Sequence Orthology
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    intrinsic component of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    spanning component of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    T-cell differentiation antigen CD6

    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_001037801.2NP_001032890.1  T-cell differentiation antigen CD6 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001032890.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an in-frame segment in the coding region, compared to variant 2. The resulting protein (isoform 1) is shorter when it is compared to isoform 2.
      Source sequence(s)
      AK030823, BQ553341
      Consensus CDS
      CCDS50391.1
      UniProtKB/Swiss-Prot
      Q61003
      Related
      ENSMUSP00000046861.8, ENSMUST00000039043.14
      Conserved Domains (2) summary
      smart00202
      Location:160259
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:165259
      SRCR; Scavenger receptor cysteine-rich domain
    2. NM_009852.3NP_033982.3  T-cell differentiation antigen CD6 isoform 2 precursor

      See identical proteins and their annotated locations for NP_033982.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longer transcript and encodes the longer protein (isoform 2).
      Source sequence(s)
      AK030823, BQ553341
      Consensus CDS
      CCDS37917.1
      UniProtKB/Swiss-Prot
      Q61003
      Related
      ENSMUSP00000079172.5, ENSMUST00000080292.11
      Conserved Domains (2) summary
      smart00202
      Location:160259
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:165259
      SRCR; Scavenger receptor cysteine-rich domain

    RefSeqs of Annotated Genomes: Mus musculus 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 GRCm38.p6 C57BL/6J

    Genomic

    1. NC_000085.6 Reference GRCm38.p6 C57BL/6J

      Range
      10789339..10830062 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006526622.3XP_006526685.1  T-cell differentiation antigen CD6 isoform X1

      Conserved Domains (2) summary
      smart00202
      Location:160259
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:165259
      SRCR; Scavenger receptor cysteine-rich domain
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