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PDZD4 PDZ domain containing 4 [ Homo sapiens (human) ]

Gene ID: 57595, updated on 5-Mar-2024

Summary

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Official Symbol
PDZD4provided by HGNC
Official Full Name
PDZ domain containing 4provided by HGNC
Primary source
HGNC:HGNC:21167
See related
Ensembl:ENSG00000067840 MIM:300634; AllianceGenome:HGNC:21167
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LU1; LNX5; PDZK4; PDZRN4L
Summary
Predicted to be located in cell cortex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 47.1), spleen (RPKM 4.7) and 4 other tissues See more
Orthologs
mouse all
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Genomic context

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See PDZD4 in Genome Data Viewer
Location:
Xq28
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153802166..153830544, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152075829..152104208, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153067621..153095999, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905227 Neighboring gene SRSF protein kinase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153059193-153059920 Neighboring gene isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma Neighboring gene CRISPRi-validated cis-regulatory element chrX.2654 Neighboring gene signal sequence receptor subunit 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21072 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:153092379-153092957 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153099642-153099888 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:153110079-153110947 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:153110948-153111815 Neighboring gene CYCS pseudogene 45 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153128028-153128886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153128887-153129745 Neighboring gene L1 cell adhesion molecule Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153147023-153148020 Neighboring gene L1CAM antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

Bibliography

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Related articles in PubMed

  1. Identification of PDZK4, a novel human gene with PDZ domains, that is upregulated in synovial sarcomas. Nagayama S, et al. Oncogene, 2004 Jul 15. PMID 15077175
  2. 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
  3. The genomic organization of a human creatine transporter (CRTR) gene located in Xq28. Sandoval N, et al. Genomics, 1996 Jul 15. PMID 8661155
  4. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
  5. RNF43 inhibits WNT5A-driven signaling and suppresses melanoma invasion and resistance to the targeted therapy. Radaszkiewicz T, et al. Elife, 2021 Oct 27. PMID 34702444, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Might play an important role in the proliferation of SS cells and might be a suitable target for SS drugs.
    Title: Identification of PDZK4, a novel human gene with PDZ domains, that is upregulated in synovial sarcomas.
  2. PDZRN4L showed 49.9% total-amino-acid identity with PDZRN4 short isoform (PDZRN4S). PDZ, PR34H1 and PR34H2 domains were conserved between PDZRN4L and PDZRN4S.
    Title: Identification and characterization of human PDZRN4L gene and mouse Pdzrn4l gene in silico.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Potential readthrough

Included gene: IDH3G

Homology

Clone Names

  • FLJ34125, KIAA1444

Gene Ontology Provided by GOA

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_001303512.2 → NP_001290441.1  PDZ domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_001290441.1

    Status: REVIEWED

    Source sequence(s)
    U52111
    Consensus CDS
    CCDS78518.1
    UniProtKB/TrEMBL
    B3KW03, Q17RL8
    Related
    ENSP00000377355.3, ENST00000393758.7
    Conserved Domains (1) summary
    smart00228
    Location:144 → 220
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

  2. NM_001303513.3 → NP_001290442.1  PDZ domain-containing protein 4 isoform 3

    See identical proteins and their annotated locations for NP_001290442.1

    Status: REVIEWED

    Source sequence(s)
    U52111
    UniProtKB/TrEMBL
    B3KVR9, B3KW03
    Conserved Domains (1) summary
    smart00228
    Location:42 → 118
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

  3. NM_001303514.2 → NP_001290443.1  PDZ domain-containing protein 4 isoform 4

    See identical proteins and their annotated locations for NP_001290443.1

    Status: REVIEWED

    Source sequence(s)
    U52111
    Consensus CDS
    CCDS78517.1
    UniProtKB/TrEMBL
    B3KW03
    Related
    ENSP00000442033.1, ENST00000544474.5
    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) ...

  4. NM_001303515.2 → NP_001290444.1  PDZ domain-containing protein 4 isoform 5

    See identical proteins and their annotated locations for NP_001290444.1

    Status: REVIEWED

    Source sequence(s)
    U52111
    UniProtKB/TrEMBL
    B3KW03
    Conserved Domains (1) summary
    smart00228
    Location:63 → 139
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

  5. NM_001303516.2 → NP_001290445.1  PDZ domain-containing protein 4 isoform 6

    Status: REVIEWED

    Source sequence(s)
    U52111
    UniProtKB/TrEMBL
    B3KW03
    Conserved Domains (1) summary
    smart00228
    Location:57 → 133
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

  6. NM_032512.5 → NP_115901.2  PDZ domain-containing protein 4 isoform 2

    See identical proteins and their annotated locations for NP_115901.2

    Status: REVIEWED

    Source sequence(s)
    U52111
    Consensus CDS
    CCDS14732.1
    UniProtKB/Swiss-Prot
    B3KXB1, B7ZKY3, Q76G19, Q8NB75, Q9BUH9, Q9P284
    UniProtKB/TrEMBL
    B3KW03
    Related
    ENSP00000164640.4, ENST00000164640.8
    Conserved Domains (1) summary
    smart00228
    Location:138 → 214
    PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    153802166..153830544 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152075829..152104208 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q76G19.1 GenPept UniProtKB/Swiss-Prot:Q76G19

Gene LinkOut

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