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PDZRN4 PDZ domain containing ring finger 4 [ Homo sapiens (human) ]

Gene ID: 29951, updated on 21-Dec-2019

Summary

Official Symbol
PDZRN4provided by HGNC
Official Full Name
PDZ domain containing ring finger 4provided by HGNC
Primary source
HGNC:HGNC:30552
See related
Ensembl:ENSG00000165966 MIM:609730
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LNX4; SAMCAP3L
Expression
Broad expression in prostate (RPKM 5.3), urinary bladder (RPKM 3.3) and 15 other tissues See more
Orthologs

Genomic context

See PDZRN4 in Genome Data Viewer
Location:
12q12
Exon count:
11
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (41188320..41574745)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (41582250..41968392)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene methionyl aminopeptidase 1 pseudogene Neighboring gene contactin 1 Neighboring gene uncharacterized LOC107984496 Neighboring gene uncharacterized LOC107984499 Neighboring gene uncharacterized LOC107984498 Neighboring gene RNA, 5S ribosomal pseudogene 360 Neighboring gene MT-ND2 pseudogene 17

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study identifies protein quantitative trait loci (pQTLs).
NHGRI GWA Catalog
A genome-wide association study identifies susceptibility loci of silica related pneumoconiosis in Han Chinese.
NHGRI GWA Catalog
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
PDZ domain-containing RING finger protein 4
Names
IMAGE5767589
SEMACAP3-like protein
ligand of Numb protein X 4

NCBI Reference Sequences (RefSeq)

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_001164595.2NP_001158067.1  PDZ domain-containing RING finger protein 4 isoform 1

    See identical proteins and their annotated locations for NP_001158067.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC021651, AC090531, AK294535, AW297403, BX640695
    Consensus CDS
    CCDS53777.1
    UniProtKB/Swiss-Prot
    Q6ZMN7
    UniProtKB/TrEMBL
    B4DGD1
    Related
    ENSP00000384197.2, ENST00000402685.7
    Conserved Domains (4) summary
    smart00228
    Location:221313
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00162
    Location:1754
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cd00992
    Location:402484
    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) ...
    cl19105
    Location:66108
    Sina; Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins ...
  2. NM_013377.4NP_037509.3  PDZ domain-containing RING finger protein 4 isoform 2

    See identical proteins and their annotated locations for NP_037509.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses a distinct start codon, compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC090531, AK131554, BC093744, BX640695
    Consensus CDS
    CCDS8739.1
    UniProtKB/Swiss-Prot
    Q6ZMN7
    Related
    ENSP00000439990.2, ENST00000539469.6
    Conserved Domains (2) summary
    smart00228
    Location:2455
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
    cd00992
    Location:144226
    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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    41188320..41574745
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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