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    Nphs2 nephrosis 2, podocin [ Mus musculus (house mouse) ]

    Gene ID: 170484, updated on 9-Dec-2024

    Summary

    Official Symbol
    Nphs2provided by MGI
    Official Full Name
    nephrosis 2, podocinprovided by MGI
    Primary source
    MGI:MGI:2157018
    See related
    Ensembl:ENSMUSG00000026602 AllianceGenome:MGI:2157018
    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
    PDCN; SRN1
    Summary
    Acts upstream of or within gene expression. Located in cytoplasmic side of plasma membrane. Is active in cell periphery. Colocalizes with slit diaphragm. Is expressed in liver; metanephros; and ureter. Used to study nephrotic syndrome. Human ortholog(s) of this gene implicated in nephrotic syndrome type 2. Orthologous to human NPHS2 (NPHS2 stomatin family member, podocin). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Restricted expression toward kidney adult (RPKM 17.5) See more
    Orthologs
    NEW
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    Genomic context

    See Nphs2 in Genome Data Viewer
    Location:
    1 G3; 1 67.71 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (156138105..156155605)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (156310535..156328035)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 30472 Neighboring gene STARR-seq mESC enhancer starr_02734 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:158194711-158194894 Neighboring gene STARR-seq mESC enhancer starr_02735 Neighboring gene tudor domain containing 5 Neighboring gene axonemal dynein light chain domain containing 1 Neighboring gene ribosomal protein L35, retrotransposed Neighboring gene STARR-seq mESC enhancer starr_02736 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:158338195-158338508 Neighboring gene STARR-positive B cell enhancer ABC_E3317 Neighboring gene STARR-positive B cell enhancer ABC_E9485 Neighboring gene sterol O-acyltransferase 1 Neighboring gene STARR-positive B cell enhancer ABC_E2571 Neighboring gene STARR-positive B cell enhancer mm9_chr1:158404407-158404707

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (5) 
    • Targeted (6)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in actin cytoskeleton organization ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in metanephric podocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in cell periphery IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell-cell junction ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic side of plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane raft ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
     
    colocalizes_with slit diaphragm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with slit diaphragm ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    podocin
    Names
    nephrosis 2 homolog, podocin

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_130456.4NP_569723.1  podocin

      See identical proteins and their annotated locations for NP_569723.1

      Status: VALIDATED

      Source sequence(s)
      AC161414, FJ715770
      Consensus CDS
      CCDS15391.1
      UniProtKB/Swiss-Prot
      Q8BWE6, Q91X05, Q91Z95
      UniProtKB/TrEMBL
      C0LL94, C0LL95
      Related
      ENSMUSP00000027896.5, ENSMUST00000027896.10
      Conserved Domains (1) summary
      cd08827
      Location:124346
      SPFH_podocin; Podocin, a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

    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
      156138105..156155605
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011238765.2XP_011237067.1  podocin isoform X3

      Conserved Domains (1) summary
      cl19107
      Location:124179
      SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
    2. XM_006496683.4XP_006496746.1  podocin isoform X1

      Conserved Domains (1) summary
      cl19107
      Location:124267
      SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
    3. XM_006496684.3XP_006496747.1  podocin isoform X2

      Conserved Domains (1) summary
      cl19107
      Location:2203
      SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily