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Aliases for PDZD4 Gene

Aliases for PDZD4 Gene

  • PDZ Domain Containing 4 2 3 5
  • PDZ Domain-Containing RING Finger Protein 4-Like Protein 3 4
  • PDZRN4L 3 4
  • PDZK4 3 4
  • PDZ Domain-Containing Protein 4 3
  • KIAA1444 4
  • LNX5 3
  • LU1 3

External Ids for PDZD4 Gene

Previous HGNC Symbols for PDZD4 Gene

  • PDZK4

Previous GeneCards Identifiers for PDZD4 Gene

  • GC0XM152589
  • GC0XM152720
  • GC0XM153067
  • GC0XM141724

Summaries for PDZD4 Gene

GeneCards Summary for PDZD4 Gene

PDZD4 (PDZ Domain Containing 4) is a Protein Coding gene. GO annotations related to this gene include ubiquitin protein ligase activity. An important paralog of this gene is PDZRN3.

Gene Wiki entry for PDZD4 Gene

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDZD4 Gene

Genomics for PDZD4 Gene

Regulatory Elements for PDZD4 Gene

Enhancers for PDZD4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around PDZD4 on UCSC Golden Path with GeneCards custom track

Promoters for PDZD4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for PDZD4 Gene

Chromosome:
X
Start:
153,802,166 bp from pter
End:
153,830,567 bp from pter
Size:
28,402 bases
Orientation:
Minus strand

Genomic View for PDZD4 Gene

Genes around PDZD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDZD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDZD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDZD4 Gene

Proteins for PDZD4 Gene

  • Protein details for PDZD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q76G19-PDZD4_HUMAN
    Recommended name:
    PDZ domain-containing protein 4
    Protein Accession:
    Q76G19
    Secondary Accessions:
    • B3KXB1
    • B7ZKY3
    • Q8NB75
    • Q9BUH9
    • Q9P284

    Protein attributes for PDZD4 Gene

    Size:
    769 amino acids
    Molecular mass:
    86171 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC03666.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PDZD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDZD4 Gene

Post-translational modifications for PDZD4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDZD4 Gene

Domains & Families for PDZD4 Gene

Gene Families for PDZD4 Gene

Protein Domains for PDZD4 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q76G19

UniProtKB/Swiss-Prot:

PDZD4_HUMAN :
  • Contains 1 PDZ (DHR) domain.
Domain:
  • Contains 1 PDZ (DHR) domain.
genes like me logo Genes that share domains with PDZD4: view

Function for PDZD4 Gene

genes like me logo Genes that share phenotypes with PDZD4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDZD4 Gene

Localization for PDZD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDZD4 Gene

Cytoplasm, cell cortex. Note=Mainly localized under the plasma membrane.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDZD4 Gene COMPARTMENTS Subcellular localization image for PDZD4 gene
Compartment Confidence
cytosol 2
nucleus 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PDZD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005938 cell cortex IEA --
genes like me logo Genes that share ontologies with PDZD4: view

Pathways & Interactions for PDZD4 Gene

SuperPathways for PDZD4 Gene

No Data Available

Interacting Proteins for PDZD4 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000164640%0d%0a9606.ENSP00000344782%0d%0a
Selected Interacting proteins: Q76G19-PDZD4_HUMAN ENSP00000164640 for PDZD4 Gene via MINT STRING IID

Gene Ontology (GO) - Biological Process for PDZD4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for PDZD4 Gene

Drugs & Compounds for PDZD4 Gene

No Compound Related Data Available

Transcripts for PDZD4 Gene

Unigene Clusters for PDZD4 Gene

PDZ domain containing 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDZD4 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d · 4e ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b
SP1: - - - - - - - - - - - - - -
SP2: - - - - - - - - - -
SP3: - - - - - - - - - - -
SP4:
SP5: - -
SP6: - - - - - - - - - - - - -
SP7: -
SP8: - - - - - - - - -
SP9: - - - - -
SP10: - - -
SP11: - - - - - -
SP12: - - -
SP13:

Relevant External Links for PDZD4 Gene

GeneLoc Exon Structure for
PDZD4
ECgene alternative splicing isoforms for
PDZD4

Expression for PDZD4 Gene

mRNA expression in normal human tissues for PDZD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDZD4 Gene

This gene is overexpressed in Brain - Cortex (x5.4), Brain - Frontal Cortex (BA9) (x4.7), Brain - Hippocampus (x4.4), Brain - Anterior cingulate cortex (BA24) (x4.3), and Brain - Amygdala (x4.1).

Protein differential expression in normal tissues from HIPED for PDZD4 Gene

This gene is overexpressed in Liver (30.7), Fetal Brain (22.2), and Adipocyte (16.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PDZD4 Gene



Protein tissue co-expression partners for PDZD4 Gene

NURSA nuclear receptor signaling pathways regulating expression of PDZD4 Gene:

PDZD4

SOURCE GeneReport for Unigene cluster for PDZD4 Gene:

Hs.92732

mRNA Expression by UniProt/SwissProt for PDZD4 Gene:

Q76G19-PDZD4_HUMAN
Tissue specificity: Brain-specific. Expressed in fetal and adult brain. Up-regulated in synovial carcinomas.
genes like me logo Genes that share expression patterns with PDZD4: view

Primer Products

Orthologs for PDZD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDZD4 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PDZD4 34
  • 88.95 (n)
  • 92.46 (a)
PDZD4 35
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDZD4 34
  • 90.95 (n)
  • 93.94 (a)
PDZD4 35
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdzd4 34
  • 86.68 (n)
  • 93.34 (a)
Pdzd4 16
Pdzd4 35
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdzd4 34
  • 86.55 (n)
  • 93.34 (a)
oppossum
(Monodelphis domestica)
Mammalia PDZD4 35
  • 84 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDZD4 35
  • 99 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDZD4 35
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdzd4 34
  • 68.76 (n)
  • 73.76 (a)
zebrafish
(Danio rerio)
Actinopterygii pdzd4 34
  • 59.39 (n)
  • 57.94 (a)
pdzd4 35
  • 45 (a)
OneToMany
PDZD4 (2 of 2) 35
  • 51 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Slip1 35
  • 18 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea C50F7.6 35
  • 22 (a)
OneToMany
Species where no ortholog for PDZD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PDZD4 Gene

ENSEMBL:
Gene Tree for PDZD4 (if available)
TreeFam:
Gene Tree for PDZD4 (if available)

Paralogs for PDZD4 Gene

Paralogs for PDZD4 Gene

(3) SIMAP similar genes for PDZD4 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with PDZD4: view

Variants for PDZD4 Gene

Sequence variations from dbSNP and Humsavar for PDZD4 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs782272149 A breast cancer sample 153,808,541(+) GGAGC(A/G)CAGGG intron-variant, reference, missense, utr-variant-5-prime
rs1018766 -- 153,809,953(+) GCAAG(C/G)AGTGC intron-variant
rs1018767 -- 153,810,200(+) GGCTT(A/G)TGGAA intron-variant
rs1894297 -- 153,824,929(+) GGAGG(C/T)GGAGG intron-variant
rs2001007 -- 153,820,937(+) ATATT(G/T)GGAGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDZD4 Gene

Variant ID Type Subtype PubMed ID
dgv4325n106 CNV deletion 24896259
esv33199 CNV gain+loss 17666407
esv3575025 CNV loss 25503493
nsv469867 CNV loss 16826518
nsv7159 CNV deletion 18451855

Variation tolerance for PDZD4 Gene

Residual Variation Intolerance Score: 6.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.48; 28.85% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDZD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDZD4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDZD4 Gene

Disorders for PDZD4 Gene

Relevant External Links for PDZD4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDZD4

No disorders were found for PDZD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDZD4 Gene

Publications for PDZD4 Gene

  1. Identification of PDZK4, a novel human gene with PDZ domains, that is upregulated in synovial sarcomas. (PMID: 15077175) Nagayama S. … Nakamura Y. (Oncogene 2004) 2 3 4 65
  2. Identification and characterization of human PDZRN4L gene and mouse Pdzrn4l gene in silico. (PMID: 15138636) Katoh M. … Katoh M. (Int. J. Mol. Med. 2004) 3 4 22 65
  3. 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. (PMID: 10819331) Nagase T. … Ohara O. (DNA Res. 2000) 2 3 4 65
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 65
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 65

Products for PDZD4 Gene

Sources for PDZD4 Gene

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