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    Pdzrn4 PDZ domain containing RING finger 4 [ Mus musculus (house mouse) ]

    Gene ID: 239618, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Pdzrn4provided by MGI
    Official Full Name
    PDZ domain containing RING finger 4provided by MGI
    Primary source
    MGI:MGI:3056996
    See related
    Ensembl:ENSMUSG00000036218 AllianceGenome:MGI:3056996
    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
    LNX4; SAMCAP3L; mKIAA3027; 1110017D07Rik
    Summary
    Is expressed in brain and skeleton. Orthologous to human PDZRN4 (PDZ domain containing ring finger 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in CNS E14 (RPKM 3.1), whole brain E14.5 (RPKM 2.7) and 10 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    15 E3; 15 46.53 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (92294691..92669700)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (92396810..92771827)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene contactin 1 Neighboring gene predicted gene, 36901 Neighboring gene STARR-positive B cell enhancer mm9_chr15:92171487-92171788 Neighboring gene STARR-seq mESC enhancer starr_39511 Neighboring gene predicted gene, 26760 Neighboring gene predicted gene, 53194 Neighboring gene STARR-seq mESC enhancer starr_39512 Neighboring gene STARR-seq mESC enhancer starr_39513 Neighboring gene predicted gene, 52207 Neighboring gene RIKEN cDNA 4930588J15 gene Neighboring gene STARR-seq mESC enhancer starr_39514 Neighboring gene STARR-seq mESC enhancer starr_39515 Neighboring gene STARR-seq mESC enhancer starr_39516 Neighboring gene STARR-seq mESC enhancer starr_39518 Neighboring gene STARR-seq mESC enhancer starr_39519 Neighboring gene STARR-seq mESC enhancer starr_39520 Neighboring gene predicted gene, 18815 Neighboring gene predicted gene, 30085

    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. Laminar organization of the early developing anterior hypothalamus. Caqueret A, et al. Dev Biol, 2006 Oct 1. PMID 16860307
    2. Developmental gene expression profiling along the tonotopic axis of the mouse cochlea. Son EJ, et al. PLoS One, 2012. PMID 22808246, Free PMC Article
    3. Prediction of the coding sequences of mouse homologues of KIAA gene: IV. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2004 Jun 30. PMID 15368895
    4. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. Diez-Roux G, et al. PLoS Biol, 2011 Jan 18. PMID 21267068, Free PMC Article
    5. Antisense transcription in the mammalian transcriptome. Katayama S, et al. Science, 2005 Sep 2. PMID 16141073

    See all (13) 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)
    • Endonuclease-mediated (2) 

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA3027

    Gene Ontology Provided by MGI

    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  

    General protein information

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    Preferred Names
    PDZ domain-containing RING finger protein 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_001164593.1 → NP_001158065.1  PDZ domain-containing RING finger protein 4 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK003741, AK135524, BC151034, BY708733
      Consensus CDS
      CCDS49709.1
      UniProtKB/TrEMBL
      B9EKP7, E9PUZ9
      Related
      ENSMUSP00000133159.3, ENSMUST00000169942.10
      Conserved Domains (3) summary
      smart00184
      Location:18 → 55
      RING; Ring finger
      smart00228
      Location:202 → 294
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:383 → 465
      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_001164594.1 → NP_001158066.1  PDZ domain-containing RING finger protein 4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses an alternate start codon, compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK003741, AK135524, AK173342, BY127298
      Consensus CDS
      CCDS49710.1
      UniProtKB/TrEMBL
      E9Q5P6, Q3UXJ7
      Related
      ENSMUSP00000040456.9, ENSMUST00000035399.10
      Conserved Domains (2) summary
      cd00992
      Location:144 → 226
      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) ...
      cl00117
      Location:20 → 53
      PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      92294691..92669700
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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