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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

Additional gene information for PDZD4 Gene

No data available for Entrez Gene Summary , CIViC 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
GH0XH153826 1.3 Ensembl ENCODE dbSUPER 16.2 +2.0 1969 3 KLF1 ZIC2 HIC1 ZFHX2 GLIS2 EGR1 PATZ1 ZNF600 PRDM10 ZBTB20 PDZD4 IDH3G
GH0XH153900 1.6 FANTOM5 Ensembl ENCODE 10.5 -71.9 -71938 4 HDGF GLI4 TCF12 ZNF766 GLIS2 GATA2 ZNF143 FOS REST ZNF658 SNORA70 HCFC1 EMD DKC1 TMEM187 SNORA56 LOC105373383 SLC10A3 PLXNA3 PLXNB3
GH0XH153886 0.9 FANTOM5 ENCODE 13.4 -56.4 -56401 1 MAZ KLF1 GATA3 GATA2 ZBTB48 IKZF1 ZIC2 EZH2 EGR2 RENBP TMEM187 PDZD4 SSR4 IDH3G SRPK3 PLXNB3 ARHGAP4 NAA10 BCAP31
GH0XH153884 0.8 ENCODE 13.4 -54.6 -54568 1 CTCF KLF1 MAX KLF17 RAD21 ZIC2 HIC1 ZFHX2 GLIS2 SMC3 TMEM187 PDZD4 PLXNB3 LCA10 AVPR2
GH0XH154595 0.9 Ensembl ENCODE 10.3 -766.0 -766010 1 CTCF MAX CEBPB FEZF1 SALL2 RAD21 EP300 JUND SMC3 POU5F1 LOC105373383 GDI1 GAB3 PDZD4 L1CAM FAM3A ENSG00000232155 CTAG1A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000249604 266 1400 MAZ ZBTB8A ZNF398 ZIC2 HIC1 ZFHX2 GLIS2 EGR1 PATZ1 ZBTB26

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

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for PDZD4 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for PDZD4 Gene

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

  • Applied Biological Materials Clones for PDZD4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDZD4 gene
Compartment Confidence
nucleus 2
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PDZD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005938 cell cortex IEA --
genes like me logo Genes that share ontologies with PDZD4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDZD4 Gene

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://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000164640%0d%0a9606.ENSP00000379133%0d%0a
Selected Interacting proteins: Q76G19-PDZD4_HUMAN ENSP00000164640 for PDZD4 Gene via IID STRING

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

  • Applied Biological Materials Clones for PDZD4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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.

Evidence on tissue expression from TISSUES for PDZD4 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with PDZD4: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PDZD4 Gene

Orthologs for PDZD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDZD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDZD4 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDZD4 33 34
  • 90.95 (n)
cow
(Bos Taurus)
Mammalia PDZD4 33 34
  • 88.95 (n)
mouse
(Mus musculus)
Mammalia Pdzd4 33 16 34
  • 86.68 (n)
rat
(Rattus norvegicus)
Mammalia Pdzd4 33
  • 86.55 (n)
oppossum
(Monodelphis domestica)
Mammalia PDZD4 34
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDZD4 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdzd4 33
  • 68.76 (n)
zebrafish
(Danio rerio)
Actinopterygii pdzd4 33 34
  • 59.39 (n)
PDZD4 (2 of 2) 34
  • 51 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Slip1 34
  • 18 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea C50F7.6 34
  • 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
rs1000424478 -- 153,806,194(+) GGGGG(A/C)AGGCT intron-variant
rs1000643431 -- 153,814,331(+) TAGCC(A/G)GGCAT intron-variant
rs1000796004 -- 153,832,469(+) AGGGC(C/T)TCAGT upstream-variant-2KB
rs1000912027 -- 153,832,054(+) TTGCC(C/G)TTGGG upstream-variant-2KB

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 and characterization of human PDZRN4L gene and mouse Pdzrn4l gene in silico. (PMID: 15138636) Katoh M … Katoh M (International journal of molecular medicine 2004) 3 4 22 60
  2. 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 60
  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 research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 60
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for PDZD4 Gene

Sources for PDZD4 Gene

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