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    Igsf5 immunoglobulin superfamily, member 5 [ Mus musculus (house mouse) ]

    Gene ID: 72058, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Igsf5provided by MGI
    Official Full Name
    immunoglobulin superfamily, member 5provided by MGI
    Primary source
    MGI:MGI:1919308
    See related
    Ensembl:ENSMUSG00000000159 AllianceGenome:MGI:1919308
    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
    JCAM; Jam4; 2010003D20Rik
    Summary
    Enables PDZ domain binding activity. Acts upstream of or within cell-cell adhesion. Located in bicellular tight junction and cell surface. Is expressed in several structures, including alimentary system; brain; genitourinary system; liver; and respiratory system. Orthologous to human IGSF5 (immunoglobulin superfamily member 5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in large intestine adult (RPKM 11.1), kidney adult (RPKM 8.5) and 11 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Igsf5 in Genome Data Viewer
    Location:
    16 C4; 16 56.93 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (96162676..96266772)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (96361479..96465572)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_41616 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:96495129-96495238 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:96514185-96514338 Neighboring gene UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5 Neighboring gene STARR-positive B cell enhancer mm9_chr16:96562962-96563262 Neighboring gene predicted gene, 41510 Neighboring gene STARR-seq mESC enhancer starr_41621 Neighboring gene integrin beta 2-like Neighboring gene STARR-positive B cell enhancer ABC_E8916 Neighboring gene Purkinje cell protein 4 Neighboring gene DS cell adhesion molecule Neighboring gene STARR-seq mESC enhancer starr_41622 Neighboring gene predicted gene, 32509

    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. A CTX family cell adhesion molecule, JAM4, is expressed in stem cell and progenitor cell populations of both male germ cell and hematopoietic cell lineages. Nagamatsu G, et al. Mol Cell Biol, 2006 Nov. PMID 16982697, Free PMC Article
    2. JAM4, a junctional cell adhesion molecule interacting with a tight junction protein, MAGI-1. Hirabayashi S, et al. Mol Cell Biol, 2003 Jun. PMID 12773569, Free PMC Article
    3. Ligand-of-Numb protein X is an endocytic scaffold for junctional adhesion molecule 4. Kansaku A, et al. Oncogene, 2006 Aug 24. PMID 16832352
    4. Spatially heterogeneous choroid plexus transcriptomes encode positional identity and contribute to regional CSF production. Lun MP, et al. J Neurosci, 2015 Mar 25. PMID 25810521, Free PMC Article
    5. A gene expression map of human chromosome 21 orthologues in the mouse. Gitton Y, et al. Nature, 2002 Dec 5. PMID 12466855

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LNX1 provides an endocytic scaffold for JAM4 that is implicated in the reorganization of cell junctions.
      Title: Ligand-of-Numb protein X is an endocytic scaffold for junctional adhesion molecule 4.
    2. JAM4 together with MAGI-1 provides an adhesion machinery at tight junctions, which may regulate the permeability of kidney glomerulus and small intestinal epithelial cells
      Title: JAM4, a junctional cell adhesion molecule interacting with a tight junction protein, MAGI-1.
    3. These results suggest that JAM4 is expressed in stem cells and progenitor cells but that other cell adhesion molecules may substitute for JAM4 function in JAM4-deficient mice both in male germ cell and hematopoietic lineages.
      Title: A CTX family cell adhesion molecule, JAM4, is expressed in stem cell and progenitor cell populations of both male germ cell and hematopoietic cell lineages.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    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 PDZ domain binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell-cell adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in apical plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in bicellular tight junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in bicellular tight junction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    immunoglobulin superfamily member 5
    Names
    JAM-4
    cell adhesion molecule JCAM
    junction adhesion molecule 4
    junctional adhesion molecule 4

    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_001177886.1 → NP_001171357.1  immunoglobulin superfamily member 5 isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK086973
      Consensus CDS
      CCDS49925.1
      UniProtKB/Swiss-Prot
      Q7TSN7, Q9D8G2
      UniProtKB/TrEMBL
      D3YXH1
      Related
      ENSMUSP00000109425.2, ENSMUST00000113794.8
      Conserved Domains (4) summary
      smart00410
      Location:31 → 126
      IG_like; Immunoglobulin like
      pfam07679
      Location:132 → 216
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:132 → 204
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 124
      Ig; Immunoglobulin domain

    2. NM_001177887.1 → NP_001171358.1  immunoglobulin superfamily member 5 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001171358.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate 3' exon, as compared to variant 1. The resulting isoform (2) is 2 aa shorter and has a different C-terminus, as compared to isoform 1.
      Source sequence(s)
      AK078934, AK086973, BP772151, BX511978
      Consensus CDS
      CCDS49924.1
      UniProtKB/Swiss-Prot
      Q7TSN7, Q9D8G2
      UniProtKB/TrEMBL
      A0A0B4J1E1
      Related
      ENSMUSP00000000163.7, ENSMUST00000000163.13
      Conserved Domains (4) summary
      smart00410
      Location:31 → 126
      IG_like; Immunoglobulin like
      pfam07679
      Location:132 → 216
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:132 → 204
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 124
      Ig; Immunoglobulin domain

    3. NM_028078.3 → NP_082354.1  immunoglobulin superfamily member 5 isoform 3 precursor

      See identical proteins and their annotated locations for NP_082354.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an internal in-frame coding exon and has an alternate 3' exon, as compared to variant 1. The resulting isoform (2) is shorter; it lacks an internal segment and has a different C-terminus, as compared to isoform 1.
      Source sequence(s)
      AK008060, BP772151, BY033616
      Consensus CDS
      CCDS28357.1
      UniProtKB/TrEMBL
      A0A0R4J105, D3YXH0
      Related
      ENSMUSP00000079874.4, ENSMUST00000081093.10
      Conserved Domains (2) summary
      smart00410
      Location:31 → 124
      IG_like; Immunoglobulin like
      cl11960
      Location:31 → 124
      Ig; Immunoglobulin domain

    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_000082.7 Reference GRCm39 C57BL/6J

      Range
      96162676..96266772
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011246151.4 → XP_011244453.1  immunoglobulin superfamily member 5 isoform X1

      UniProtKB/Swiss-Prot
      Q7TSN7, Q9D8G2
      Conserved Domains (2) summary
      smart00409
      Location:31 → 126
      IG; Immunoglobulin
      cl11960
      Location:137 → 206
      Ig; Immunoglobulin domain

    2. XM_006523095.5 → XP_006523158.1  immunoglobulin superfamily member 5 isoform X2

      UniProtKB/Swiss-Prot
      Q7TSN7, Q9D8G2
      Conserved Domains (2) summary
      smart00409
      Location:31 → 126
      IG; Immunoglobulin
      cl11960
      Location:137 → 206
      Ig; Immunoglobulin domain

    3. XM_011246152.4 → XP_011244454.1  immunoglobulin superfamily member 5 isoform X3

      Conserved Domains (1) summary
      smart00409
      Location:31 → 124
      IG; Immunoglobulin

    4. XM_011246153.4 → XP_011244455.1  immunoglobulin superfamily member 5 isoform X4

      See identical proteins and their annotated locations for XP_011244455.1

      UniProtKB/TrEMBL
      D3YXH0
      Conserved Domains (1) summary
      smart00410
      Location:31 → 124
      IG_like; Immunoglobulin like

    RNA

    1. XR_004939222.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7TSN7.1 GenPept UniProtKB/Swiss-Prot:Q7TSN7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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