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    Igsf5 immunoglobulin superfamily, member 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304000, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Igsf5provided by RGD
    Official Full Name
    immunoglobulin superfamily, member 5provided by RGD
    Primary source
    RGD:1359642
    See related
    EnsemblRapid:ENSRNOG00000028216 AllianceGenome:RGD:1359642
    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
    Jam4
    Summary
    Predicted to enable PDZ domain binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be located in apical plasma membrane. Predicted to be active in bicellular tight junction and cell surface. Orthologous to human IGSF5 (immunoglobulin superfamily member 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Liver (RPKM 167.2), Kidney (RPKM 145.7) and 2 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Igsf5 in Genome Data Viewer
    Location:
    11q11
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (49155990..49198872)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (35686513..35729396)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (36736580..36779614)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene Beta-1,3-galactosyltransferase 5 Neighboring gene microRNA 6325 Neighboring gene integrin beta-2-like, pseudogene 1 Neighboring gene Purkinje cell protein 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Altered expression of junctional adhesion molecule 4 in injured podocytes. Harita Y, et al. Am J Physiol Renal Physiol, 2006 Feb. PMID 16118391
    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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The subcellular localization of JAM4 was altered in puromycin aminonucleoside (PAN) nephropathy.
      Title: Altered expression of junctional adhesion molecule 4 in injured podocytes.
    Submit: New GeneRIF Correction

    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 RGD

    Function Evidence Code Pubs
    enables PDZ domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in 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
    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_001006990.2 → NP_001006991.1  immunoglobulin superfamily member 5 precursor

      See identical proteins and their annotated locations for NP_001006991.1

      Status: PROVISIONAL

      Source sequence(s)
      BC097947
      UniProtKB/Swiss-Prot
      Q5VJ70
      UniProtKB/TrEMBL
      A0A8L2R0R2
      Related
      ENSRNOP00000032595.4, ENSRNOT00000032566.8
      Conserved Domains (4) summary
      smart00410
      Location:31 → 126
      IG_like; Immunoglobulin like
      pfam07679
      Location:132 → 220
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:132 → 204
      Ig_3; Immunoglobulin domain
      cl11960
      Location:27 → 114
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086029.1 Reference GRCr8

      Range
      49155990..49198872
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006248156.5 → XP_006248218.1  immunoglobulin superfamily member 5 isoform X2

      Conserved Domains (2) summary
      smart00410
      Location:31 → 124
      IG_like; Immunoglobulin like
      cl11960
      Location:27 → 114
      Ig; Immunoglobulin domain

    2. XM_039088368.2 → XP_038944296.1  immunoglobulin superfamily member 5 isoform X3

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

    3. XM_006248155.5 → XP_006248217.1  immunoglobulin superfamily member 5 isoform X1

      See identical proteins and their annotated locations for XP_006248217.1

      UniProtKB/Swiss-Prot
      Q5VJ70
      UniProtKB/TrEMBL
      A0A8L2R0R2
      Conserved Domains (4) summary
      smart00410
      Location:31 → 126
      IG_like; Immunoglobulin like
      pfam07679
      Location:132 → 220
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:132 → 204
      Ig_3; Immunoglobulin domain
      cl11960
      Location:27 → 114
      Ig; Immunoglobulin domain

    4. XM_063270559.1 → XP_063126629.1  immunoglobulin superfamily member 5 isoform X2

      Related
      ENSRNOP00000084327.2, ENSRNOT00000100325.2

    5. XM_063270560.1 → XP_063126630.1  immunoglobulin superfamily member 5 isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VJ70.1 GenPept UniProtKB/Swiss-Prot:Q5VJ70

    Gene LinkOut

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