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    Cd247 CD247 antigen [ Mus musculus (house mouse) ]

    Gene ID: 12503, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Cd247provided by MGI
    Official Full Name
    CD247 antigenprovided by MGI
    Primary source
    MGI:MGI:88334
    See related
    Ensembl:ENSMUSG00000005763 AllianceGenome:MGI:88334
    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
    Also known as
    Cd3; T3z; Cd3h; Cd3z; Tcrk; Tcrz; Cd3-eta; Cd3zeta; Cd3-zeta; 4930549J05Rik; A430104F18Rik
    Summary
    Predicted to enable identical protein binding activity and protein tyrosine kinase binding activity. Acts upstream of or within T cell receptor signaling pathway and positive regulation of protein localization to cell surface. Located in Golgi apparatus and plasma membrane. Part of alpha-beta T cell receptor complex. Is expressed in several structures, including alimentary system; brain; genitourinary system; hemolymphoid system gland; and liver and biliary system. Human ortholog(s) of this gene implicated in immunodeficiency 25. Orthologous to human CD247 (CD247 molecule). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in thymus adult (RPKM 43.2), spleen adult (RPKM 5.1) and 2 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Cd247 in Genome Data Viewer
    Location:
    1 H2.3; 1 73.14 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (165607514..165698722)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (165779952..165871153)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E11104 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:167648574-167648683 Neighboring gene STARR-positive B cell enhancer ABC_E1572 Neighboring gene predicted gene, 51752 Neighboring gene STARR-positive B cell enhancer ABC_E4374 Neighboring gene STARR-positive B cell enhancer ABC_E7771 Neighboring gene STARR-positive B cell enhancer ABC_E9064 Neighboring gene cellular repressor of E1A-stimulated genes 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:167732146-167732347 Neighboring gene predicted gene, 23402 Neighboring gene STARR-seq mESC enhancer starr_02912 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:167775596-167775783 Neighboring gene predicted gene, 32999 Neighboring gene POU domain, class 2, transcription factor 1 Neighboring gene STARR-seq mESC enhancer starr_02913 Neighboring gene STARR-positive B cell enhancer ABC_E3324 Neighboring gene STARR-positive B cell enhancer ABC_E9065 Neighboring gene STARR-positive B cell enhancer ABC_E2581 Neighboring gene STARR-positive B cell enhancer ABC_E4375 Neighboring gene STARR-positive B cell enhancer ABC_E4376 Neighboring gene STARR-positive B cell enhancer mm9_chr1:167878460-167878761 Neighboring gene heat shock protein 8 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E2582 Neighboring gene STARR-seq mESC enhancer starr_02914 Neighboring gene STARR-positive B cell enhancer ABC_E798 Neighboring gene STARR-seq mESC enhancer starr_02915 Neighboring gene STARR-seq mESC enhancer starr_02916 Neighboring gene predicted gene, 53642

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Nanoclusters of the resting T cell antigen receptor (TCR) localize to non-raft domains. Beck-García K, et al. Biochim Biophys Acta, 2015 Apr. PMID 25535948
    2. Impaired spatial memory in mice lacking CD3ζ is associated with altered NMDA and AMPA receptors signaling independent of T-cell deficiency. Louveau A, et al. J Neurosci, 2013 Nov 20. PMID 24259588, Free PMC Article
    3. Unique ζ-chain motifs mediate a direct TCR-actin linkage critical for immunological synapse formation and T-cell activation. Klieger Y, et al. Eur J Immunol, 2014 Jan. PMID 24185712
    4. T cell CD3ζ deficiency enables multiorgan tissue inflammation. Deng GM, et al. J Immunol, 2013 Oct 1. PMID 23980209, Free PMC Article
    5. Basic residues in the T-cell receptor ζ cytoplasmic domain mediate membrane association and modulate signaling. Zhang H, et al. Proc Natl Acad Sci U S A, 2011 Nov 29. PMID 22084078, Free PMC Article

    See all (172) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Alternatively Spliced Variants of Murine CD247 Influence T Cell Development and Activation, Revealing the Importance of the CD3zeta C-Terminal Region.
      Title: Alternatively Spliced Variants of Murine CD247 Influence T Cell Development and Activation, Revealing the Importance of the CD3ζ C-Terminal Region.
    2. CD3zeta ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides.
      Title: CD3ζ ITAMs enable ligand discrimination and antagonism by inhibiting TCR signaling in response to low-affinity peptides.
    3. The CD3zeta adaptor structure determines functional differences between human and mouse CD16 Fc receptor signaling.
      Title: The CD3ζ adaptor structure determines functional differences between human and mouse CD16 Fc receptor signaling.
    4. Study findings underline the important roles of p38 and STAT3 in the regulation of PD-L1 expression and prove that IFNalpha induces STAT3/p38-mediated expression of PD-L1 and thereby a reduced stimulatory ability of dendritic cells.
      Title: Interferon-α Up-Regulates the Expression of PD-L1 Molecules on Immune Cells Through STAT3 and p38 Signaling.
    5. ITAM sequence diversity is required for optimal TCR signal transduction and subsequent T cell maturation
      Title: Cutting Edge: CD3 ITAM Diversity Is Required for Optimal TCR Signaling and Thymocyte Development.
    6. Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice
      Title: Comprehensive Survey of miRNA-mRNA Interactions Reveals That Ccr7 and Cd247 (CD3 zeta) are Posttranscriptionally Controlled in Pancreas Infiltrating T Lymphocytes of Non-Obese Diabetic (NOD) Mice.
    7. There is an early (within seconds) interaction between CD3zeta and the coreceptor CD8 that is independent of the binding of CD8 to MHC.
      Title: Ligand-engaged TCR is triggered by Lck not associated with CD8 coreceptor.
    8. The resting TCR localized in the disordered domain of giant plasma membrane (PM) vesicles (GPMVs) and PM spheres (PMSs) and single and nanoclustered TCRs are found in the high-density fractions in sucrose gradients.
      Title: Nanoclusters of the resting T cell antigen receptor (TCR) localize to non-raft domains.
    9. When Ly108 is engaged in trans during cell-cell interactions, Ly108-CD3zeta interactions are promoted in a manner that uniquely depends on Ly108 TM domain, leading to more efficient CD3zeta dephosphorylation.
      Title: SAP-regulated T Cell-APC adhesion and ligation-dependent and -independent Ly108-CD3ζ interactions.
    10. Two transcription factor binding sites and a long non-coding RNA are identified within the Cd247 gene.
      Title: Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (7)  1 citation
    • Chemically induced (ENU) (1) 
    • Endonuclease-mediated (1) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein tyrosine kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transmembrane signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in Fc-gamma receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in T cell receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within T cell receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell surface receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within immune system process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within interleukin-2 production IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of protein localization to cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein complex oligomerization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein-containing complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of Fc-gamma receptor III complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of T cell receptor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of alpha-beta T cell receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of alpha-beta T cell receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of alpha-beta T cell receptor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    CD247 antigen
    Names
    CD3 antigen, zeta polypeptide
    CD3-zeta/eta
    T-cell receptor T3 eta chain
    T-cell surface glycoprotein CD3 zeta chain

    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_001113391.2 → NP_001106862.1  CD247 antigen isoform zeta precursor

      See identical proteins and their annotated locations for NP_001106862.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (zeta) encodes the shortest isoform (zeta).
      Source sequence(s)
      AC093371, AK138774, BC052824, BM240376
      Consensus CDS
      CCDS48427.1
      UniProtKB/Swiss-Prot
      P24161, P29020, Q9D3G3
      Related
      ENSMUSP00000005907.6, ENSMUST00000005907.12
      Conserved Domains (3) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam02189
      Location:139 → 158
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    2. NM_001113392.2 → NP_001106863.1  CD247 antigen isoform iota precursor

      See identical proteins and their annotated locations for NP_001106863.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (iota) has alternate exon structure in the 3' coding region and 3' UTR, compared to variant zeta. The resulting isoform (iota) has a distinct C-terminus and is longer than isoform zeta.
      Source sequence(s)
      AC093371, AK138774
      Consensus CDS
      CCDS48429.1
      UniProtKB/TrEMBL
      Q3UU54
      Related
      ENSMUSP00000124297.2, ENSMUST00000161971.8
      Conserved Domains (2) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    3. NM_001113393.2 → NP_001106864.2  CD247 antigen isoform theta precursor

      See identical proteins and their annotated locations for NP_001106864.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (theta) uses an alternate in-frame splice site in the central coding region, and has alternate exon structure in the 3' coding region and 3' UTR, compared to variant zeta. The resulting isoform (theta) has a distinct C-terminus and is longer than isoform zeta.
      Source sequence(s)
      AC093371, AC124587
      Consensus CDS
      CCDS48428.2
      UniProtKB/TrEMBL
      A2MZG6, E7EXC2, J3QMU3
      Related
      ENSMUSP00000124299.3, ENSMUST00000161559.3
      Conserved Domains (2) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    4. NM_031162.4 → NP_112439.1  CD247 antigen isoform eta precursor

      See identical proteins and their annotated locations for NP_112439.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (eta) has alternate exon structure in the 3' coding region and 3' UTR, compared to variant zeta. The resulting isoform (eta) has a distinct C-terminus and is longer than isoform zeta. Variants eta and kappa encode the same isoform.
      Source sequence(s)
      AC093371, AC124587, BF020526
      Consensus CDS
      CCDS15443.1
      UniProtKB/TrEMBL
      J3QMU3
      Related
      ENSMUSP00000027849.5, ENSMUST00000027849.11
      Conserved Domains (2) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    RNA

    1. NR_103716.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (kappa) differs at the 3' end compared to variant zeta. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant zeta, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC093371, AC124587

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000067.7 Reference GRCm39 C57BL/6J

      Range
      165607514..165698722
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011238745.4 → XP_011237047.1  CD247 antigen isoform X1

      See identical proteins and their annotated locations for XP_011237047.1

      UniProtKB/Swiss-Prot
      P24161, P29020, Q9D3G3
      Conserved Domains (3) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam02189
      Location:139 → 158
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    2. XM_011238746.2 → XP_011237048.1  CD247 antigen isoform X2

      Conserved Domains (2) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    3. XM_036156509.1 → XP_036012402.1  CD247 antigen isoform X1

      UniProtKB/Swiss-Prot
      P24161, P29020, Q9D3G3
      Conserved Domains (3) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam02189
      Location:139 → 158
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    4. XM_017313285.2 → XP_017168774.1  CD247 antigen isoform X1

      UniProtKB/Swiss-Prot
      P24161, P29020, Q9D3G3
      Conserved Domains (3) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam02189
      Location:139 → 158
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    5. XM_036156498.1 → XP_036012391.1  CD247 antigen isoform X1

      UniProtKB/Swiss-Prot
      P24161, P29020, Q9D3G3
      Conserved Domains (3) summary
      smart00077
      Location:69 → 89
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam02189
      Location:139 → 158
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam11628
      Location:28 → 58
      TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001113394.2: Suppressed sequence

      Description
      NM_001113394.2: This RefSeq was permanently suppressed because the transcript is a nonsense-mediated mRNA decay (NMD) candidate when it uses a supported upstream start codon.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P24161.1 GenPept UniProtKB/Swiss-Prot:P24161

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