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

Gene ID: 72058, updated on 5-Mar-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; genitourinary system; liver; nervous system; and respiratory system. Orthologous to human IGSF5 (immunoglobulin superfamily member 5). [provided by Alliance of Genome Resources, Apr 2022]
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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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)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (1) 

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 anchoring junction 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 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

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

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