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    Cd6 CD6 antigen [ Mus musculus (house mouse) ]

    Gene ID: 12511, updated on 23-Jun-2021

    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
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    Genomic context

    See Cd6 in Genome Data Viewer
    Location:
    19 A; 19 7.16 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (10766703..10807427, complement)
    108.20200622 previous assembly 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_000085.7Genomic 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)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables lipopolysaccharide binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables lipoteichoic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables scavenger receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of T cell receptor complex ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in immunological synapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in intrinsic component of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in 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)

    NEW Try the new Transcript table

    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
      ENSMUSP00000046861.9, ENSMUST00000039043.15
      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
      ENSMUSP00000079172.6, ENSMUST00000080292.12
      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 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000085.7 Reference GRCm39 C57BL/6J

      Range
      10766703..10807427 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036161415.1XP_036017308.1  T-cell differentiation antigen CD6 isoform X2

      Conserved Domains (1) summary
      smart00202
      Location:160259
      SR; Scavenger receptor Cys-rich
    2. XM_006526622.3XP_006526685.1  T-cell differentiation antigen CD6 isoform X1

      Conserved Domains (1) summary
      smart00202
      Location:160259
      SR; Scavenger receptor Cys-rich
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