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

Gene ID: 239618, updated on 27-Nov-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, Nov 2024]
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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See Pdzrn4 in Genome Data Viewer
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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