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    Pdzd4 PDZ domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 245469, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Pdzd4provided by MGI
    Official Full Name
    PDZ domain containing 4provided by MGI
    Primary source
    MGI:MGI:2443483
    See related
    Ensembl:ENSMUSG00000002006 AllianceGenome:MGI:2443483
    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
    LU1; Xlu; Pdzk4; PDZRN4L; Pdzrnk4l; B230341P03; Kiaa1444-hp; D130075J17Rik
    Summary
    Predicted to be located in cell cortex. Is expressed in nervous system; neural retina; and seminiferous cord. Orthologous to human PDZD4 (PDZ domain containing 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in CNS E18 (RPKM 41.7), whole brain E14.5 (RPKM 32.0) and 10 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pdzd4 in Genome Data Viewer
    Location:
    X A7.3; X 37.41 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (72836963..72868649, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (73793357..73825043, complement)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E11049 Neighboring gene isocitrate dehydrogenase 3 (NAD+), gamma Neighboring gene STARR-seq mESC enhancer starr_47355 Neighboring gene signal sequence receptor, delta Neighboring gene STARR-seq mESC enhancer starr_47357 Neighboring gene predicted gene, 23615 Neighboring gene STARR-seq mESC enhancer starr_47358 Neighboring gene STARR-seq mESC enhancer starr_47359 Neighboring gene L1 cell adhesion molecule Neighboring gene Rho GTPase activating protein 4 Neighboring gene arginine vasopressin receptor 2

    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 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. Identification and characterization of human PDZRN4L gene and mouse Pdzrn4l gene in silico. Katoh M, et al. Int J Mol Med, 2004 Jun. PMID 15138636
    2. Phenotypic annotation of the mouse X chromosome. Cox BJ, et al. Genome Res, 2010 Aug. PMID 20548051, Free PMC Article
    3. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808
    4. Cell-Type-Specific Gene Expression in Developing Mouse Neocortex: Intermediate Progenitors Implicated in Axon Development. Bedogni F, et al. Front Mol Neurosci, 2021. PMID 34321999, Free PMC Article
    5. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, et al. Nucleic Acids Res, 2003 Jan 1. PMID 12520002, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Gene trapped (1) 

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Component Evidence Code Pubs
    located_in cell cortex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PDZ domain-containing protein 4
    Names
    PDZ domain-containing RING finger protein 4-like protein

    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_001029868.2 → NP_001025039.1  PDZ domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_001025039.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL672094, BC056462
      Consensus CDS
      CCDS30214.1
      UniProtKB/Swiss-Prot
      A2AFG4, Q6PHP2, Q9QY39
      Related
      ENSMUSP00000002080.6, ENSMUST00000002080.12
      Conserved Domains (1) summary
      cd00992
      Location:136 → 218
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    2. NM_001290540.1 → NP_001277469.1  PDZ domain-containing protein 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK046101, AL672094, BC056462
      Consensus CDS
      CCDS72393.1
      UniProtKB/TrEMBL
      A2AFG3
      Related
      ENSMUSP00000110081.3, ENSMUST00000114438.3
      Conserved Domains (1) summary
      cd00992
      Location:19 → 103
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    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_000086.8 Reference GRCm39 C57BL/6J

      Range
      72836963..72868649 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006528017.4 → XP_006528080.1  PDZ domain-containing protein 4 isoform X1

    2. XM_036161954.1 → XP_036017847.1  PDZ domain-containing protein 4 isoform X3

    3. XM_006528022.5 → XP_006528085.1  PDZ domain-containing protein 4 isoform X5

    4. XM_006528021.5 → XP_006528084.1  PDZ domain-containing protein 4 isoform X4

      Conserved Domains (1) summary
      pfam17820
      Location:20 → 71
      PDZ_6; PDZ domain

    5. XM_006528020.2 → XP_006528083.1  PDZ domain-containing protein 4 isoform X2

      Conserved Domains (1) summary
      cd00992
      Location:18 → 100
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9QY39.2 GenPept UniProtKB/Swiss-Prot:Q9QY39

    Gene LinkOut

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

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