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    Cd4 Cd4 molecule [ Rattus norvegicus (Norway rat) ]

    Gene ID: 24932, updated on 18-Apr-2019

    Summary

    Official Symbol
    Cd4provided by RGD
    Official Full Name
    Cd4 moleculeprovided by RGD
    Primary source
    RGD:2306
    See related
    Ensembl:ENSRNOG00000016294
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    p55; W3/25
    Summary
    MHC class II binding protein that may be a candidate gene for collagen-induced arthritis; human CD4 is a receptor required for HIV infection [RGD, Feb 2006]
    Expression
    Biased expression in Thymus (RPKM 876.1), Spleen (RPKM 309.4) and 7 other tissues See more
    Orthologs

    Genomic context

    See Cd4 in Genome Data Viewer
    Location:
    4q42
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (157381862..157408357, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 4 NC_005103.3 (224399640..224426134, complement)

    Chromosome 4 - NC_005103.4Genomic Context describing neighboring genes Neighboring gene G protein subunit beta 3 Neighboring gene prolyl 3-hydroxylase 3 Neighboring gene G protein-coupled receptor 162 Neighboring gene lymphocyte activating 3 Neighboring gene uncharacterized LOC102553981 Neighboring gene parathymosin

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    MHC class II protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    MHC class II protein binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    coreceptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    immunoglobulin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    interleukin-16 binding IEA
    Inferred from Electronic Annotation
    more info
     
    interleukin-16 binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    interleukin-16 receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    interleukin-16 receptor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein homodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein tyrosine kinase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein tyrosine kinase binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein tyrosine kinase binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Process Evidence Code Pubs
    T cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    T cell activation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    T cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    T cell selection ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    T cell selection ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    cell surface receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cellular response to granulocyte macrophage colony-stimulating factor stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to granulocyte macrophage colony-stimulating factor stimulus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytokine production ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    defense response to Gram-negative bacterium ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    helper T cell enhancement of adaptive immune response ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    induction by virus of host cell-cell fusion IEA
    Inferred from Electronic Annotation
    more info
     
    induction by virus of host cell-cell fusion ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    interleukin-15-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    interleukin-15-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    macrophage differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    maintenance of protein location in cell IEA
    Inferred from Electronic Annotation
    more info
     
    maintenance of protein location in cell ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of ERK1 and ERK2 cascade IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of ERK1 and ERK2 cascade ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of I-kappaB kinase/NF-kappaB signaling IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of I-kappaB kinase/NF-kappaB signaling ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of MAPK cascade ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of T cell activation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of T cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of calcium ion transport into cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of calcium-mediated signaling ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of kinase activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of monocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of monocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of peptidyl-tyrosine phosphorylation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of protein kinase activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of protein phosphorylation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of viral entry into host cell IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of viral entry into host cell ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of T cell activation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    regulation of calcium ion transport ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    response to estradiol IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to vitamin D IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    cell surface ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    endoplasmic reticulum lumen ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    external side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    external side of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    integral component of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    membrane raft IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    membrane raft ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    T-cell surface glycoprotein CD4
    Names
    CD4 antigen
    T-cell surface antigen T4/Leu-3
    W3/25 antigen

    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_012705.1NP_036837.1  T-cell surface glycoprotein CD4 precursor

      See identical proteins and their annotated locations for NP_036837.1

      Status: PROVISIONAL

      Source sequence(s)
      M15768
      UniProtKB/Swiss-Prot
      P05540
      Related
      ENSRNOP00000021915.1, ENSRNOT00000021915.2
      Conserved Domains (5) summary
      cd07690
      Location:30123
      Ig1_CD4; First immunoglobulin (Ig) domain of CD4
      smart00410
      Location:30121
      IG_like; Immunoglobulin like
      pfam05790
      Location:127206
      C2-set; Immunoglobulin C2-set domain
      pfam09191
      Location:211315
      CD4-extracel; CD4, extracellular
      pfam12104
      Location:425452
      Tcell_CD4_C; T cell CD4 receptor C terminal region

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005103.4 Reference Rnor_6.0 Primary Assembly

      Range
      157381862..157408357 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006237333.3XP_006237395.1  T-cell surface glycoprotein CD4 isoform X2

      Conserved Domains (4) summary
      pfam05790
      Location:74153
      C2-set; Immunoglobulin C2-set domain
      pfam09191
      Location:158262
      CD4-extracel; CD4, extracellular
      pfam12104
      Location:372399
      Tcell_CD4_C; T cell CD4 receptor C terminal region
      cl11960
      Location:3081
      Ig; Immunoglobulin domain
    2. XM_006237331.3XP_006237393.1  T-cell surface glycoprotein CD4 isoform X1

      See identical proteins and their annotated locations for XP_006237393.1

      UniProtKB/Swiss-Prot
      P05540
      Conserved Domains (5) summary
      cd07690
      Location:30123
      Ig1_CD4; First immunoglobulin (Ig) domain of CD4
      smart00410
      Location:30121
      IG_like; Immunoglobulin like
      pfam05790
      Location:127206
      C2-set; Immunoglobulin C2-set domain
      pfam09191
      Location:211315
      CD4-extracel; CD4, extracellular
      pfam12104
      Location:425452
      Tcell_CD4_C; T cell CD4 receptor C terminal region
    3. XM_008763280.2XP_008761502.1  T-cell surface glycoprotein CD4 isoform X1

      See identical proteins and their annotated locations for XP_008761502.1

      UniProtKB/Swiss-Prot
      P05540
      Conserved Domains (5) summary
      cd07690
      Location:30123
      Ig1_CD4; First immunoglobulin (Ig) domain of CD4
      smart00410
      Location:30121
      IG_like; Immunoglobulin like
      pfam05790
      Location:127206
      C2-set; Immunoglobulin C2-set domain
      pfam09191
      Location:211315
      CD4-extracel; CD4, extracellular
      pfam12104
      Location:425452
      Tcell_CD4_C; T cell CD4 receptor C terminal region

    Alternate Rn_Celera

    Genomic

    1. AC_000072.1 Alternate Rn_Celera

      Range
      146407680..146432465 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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