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

    Gene ID: 57595, updated on 28-Oct-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, Oct 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153802166..153830544, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152075829..152104208, complement)
    RS_2024_09 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 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 (17) 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_2024_08

    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

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

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