Aliases for PDZRN4 Gene

Aliases for PDZRN4 Gene

  • PDZ Domain Containing Ring Finger 4 2 3 5
  • LNX4 2 3 4
  • PDZ Domain-Containing RING Finger Protein 4 3 4
  • Ligand Of Numb Protein X 4 3 4
  • SEMACAP3-Like Protein 3 4
  • IMAGE5767589 2 3
  • Similar To SemaF Cytoplasmic Domain Associated Protein 3 2
  • DKFZp434B0417 2
  • SAMCAP3L 3
  • FLJ33777 2
  • SEMCAP3L 4
  • PDZRN4 5

External Ids for PDZRN4 Gene

Previous GeneCards Identifiers for PDZRN4 Gene

  • GC12P040117
  • GC12P039868
  • GC12P041582
  • GC12P038608

Summaries for PDZRN4 Gene

GeneCards Summary for PDZRN4 Gene

PDZRN4 (PDZ Domain Containing Ring Finger 4) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include ubiquitin-protein transferase activity and ubiquitin protein ligase activity. An important paralog of this gene is PDZRN3.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PDZRN4 Gene

Genomics for PDZRN4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PDZRN4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J041189 Promoter/Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas 610.1 +1.0 981 2.2 PRDM1 CTCF EZH2 ZNF341 SCRT2 ZBTB26 SCRT1 ZNF335 SIN3A PDZRN4 HSALNG0090507 GXYLT1
GH12J041509 Promoter/Enhancer 0.8 EPDnew Ensembl 600.1 +323.6 323629 5.9 POLR2A ESR1 CTCF KLF1 PDZRN4 ENSG00000257225 piR-30306-004 ENSG00000257228 GXYLT1
GH12J041437 Promoter 0.6 EPDnew 600.1 +249.4 249401 0.1 POLR2A RAD21 TRIM28 CREB1 PDZRN4 piR-37811 LOC107984499 ENSG00000257228 GXYLT1
GH12J041221 Enhancer 0.6 Ensembl ENCODE 18.3 +33.1 33075 1.2 FEZF1 PRDM6 TRIM28 PDZRN4 HSALNG0090507 HSALNG0090508 GXYLT1
GH12J041212 Enhancer 0.4 ENCODE 17.5 +25.0 24977 1 ZNF692 NR2F2 ZFP69B RXRA HSALNG0090507 PDZRN4 GXYLT1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDZRN4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDZRN4

Top Transcription factor binding sites by QIAGEN in the PDZRN4 gene promoter:
  • aMEF-2
  • FOXD3
  • FOXO4
  • HNF-1
  • MEF-2A
  • NF-kappaB
  • NF-kappaB1
  • Nkx2-5
  • RelA

Genomic Locations for PDZRN4 Gene

Genomic Locations for PDZRN4 Gene
chr12:41,188,320-41,574,745
(GRCh38/hg38)
Size:
386,426 bases
Orientation:
Plus strand
chr12:41,582,250-41,968,392
(GRCh37/hg19)
Size:
386,143 bases
Orientation:
Plus strand

Genomic View for PDZRN4 Gene

Genes around PDZRN4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDZRN4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDZRN4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDZRN4 Gene

Proteins for PDZRN4 Gene

  • Protein details for PDZRN4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZMN7-PZRN4_HUMAN
    Recommended name:
    PDZ domain-containing RING finger protein 4
    Protein Accession:
    Q6ZMN7
    Secondary Accessions:
    • Q52LY3
    • Q52LY4
    • Q6N052
    • Q8IUU1
    • Q9NTP7

    Protein attributes for PDZRN4 Gene

    Size:
    1036 amino acids
    Molecular mass:
    117103 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PDZRN4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDZRN4 Gene

Post-translational modifications for PDZRN4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDZRN4 Gene

No data available for DME Specific Peptides for PDZRN4 Gene

Domains & Families for PDZRN4 Gene

Gene Families for PDZRN4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PDZRN4 Gene

InterPro:
Blocks:
  • PDZ/DHR/GLGF domain
ProtoNet:

Suggested Antigen Peptide Sequences for PDZRN4 Gene

GenScript: Design optimal peptide antigens:
  • SEMACAP3-like protein (PZRN4_HUMAN)
genes like me logo Genes that share domains with PDZRN4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PDZRN4 Gene

Function for PDZRN4 Gene

Phenotypes From GWAS Catalog for PDZRN4 Gene

Gene Ontology (GO) - Molecular Function for PDZRN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDZRN4: view
genes like me logo Genes that share phenotypes with PDZRN4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDZRN4

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDZRN4 Gene

Localization for PDZRN4 Gene

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 PDZRN4 gene
Compartment Confidence
nucleus 2
cytosol 2
plasma membrane 1
extracellular 1
peroxisome 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for PDZRN4 Gene

Pathways & Interactions for PDZRN4 Gene

PathCards logo

SuperPathways for PDZRN4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDZRN4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for PDZRN4 Gene

Drugs & Compounds for PDZRN4 Gene

No Compound Related Data Available

Transcripts for PDZRN4 Gene

mRNA/cDNA for PDZRN4 Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDZRN4

Alternative Splicing Database (ASD) splice patterns (SP) for PDZRN4 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b
SP1:
SP2: - -

Relevant External Links for PDZRN4 Gene

GeneLoc Exon Structure for
PDZRN4

Expression for PDZRN4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PDZRN4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDZRN4 Gene

This gene is overexpressed in Colon - Sigmoid (x6.2), Artery - Tibial (x5.9), and Nerve - Tibial (x4.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PDZRN4 Gene



Protein tissue co-expression partners for PDZRN4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PDZRN4

SOURCE GeneReport for Unigene cluster for PDZRN4 Gene:

Hs.380044

Evidence on tissue expression from TISSUES for PDZRN4 Gene

  • Nervous system(4.6)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with PDZRN4: view

Primer Products

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDZRN4 Gene

Orthologs for PDZRN4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDZRN4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PDZRN4 30 31
  • 99.36 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PDZRN4 31
  • 91 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia PDZRN4 30 31
  • 88.15 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pdzrn4 30
  • 85.1 (n)
Mouse
(Mus musculus)
Mammalia Pdzrn4 30 17 31
  • 84.41 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PDZRN4 31
  • 83 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PDZRN4 30 31
  • 81.13 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PDZRN4 31
  • 81 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pdzrn4 30
  • 73.47 (n)
Zebrafish
(Danio rerio)
Actinopterygii pdzrn4 30 31
  • 59.63 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Slip1 31
  • 17 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea C50F7.6 31
  • 26 (a)
OneToMany
Species where no ortholog for PDZRN4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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 PDZRN4 Gene

ENSEMBL:
Gene Tree for PDZRN4 (if available)
TreeFam:
Gene Tree for PDZRN4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDZRN4: view image

Paralogs for PDZRN4 Gene

Paralogs for PDZRN4 Gene

(7) SIMAP similar genes for PDZRN4 Gene using alignment to 1 proteins:

  • PZRN4_HUMAN
genes like me logo Genes that share paralogs with PDZRN4: view

Variants for PDZRN4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDZRN4 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
VAR_035951 A colorectal cancer sample p.Gly784Arg
rs285584 - p.Gly429Ser

Additional dbSNP identifiers (rs#s) for PDZRN4 Gene

Structural Variations from Database of Genomic Variants (DGV) for PDZRN4 Gene

Variant ID Type Subtype PubMed ID
dgv484e212 CNV loss 25503493
esv1009674 CNV deletion 20482838
esv1158500 CNV deletion 17803354
esv1471392 CNV insertion 17803354
esv1562276 CNV deletion 17803354
esv2012474 CNV deletion 18987734
esv2204947 CNV deletion 18987734
esv2487088 CNV insertion 19546169
esv2627708 CNV deletion 19546169
esv2648805 CNV deletion 19546169
esv2657522 CNV deletion 23128226
esv2661468 CNV deletion 23128226
esv2677208 CNV deletion 23128226
esv2745809 CNV deletion 23290073
esv2745810 CNV deletion 23290073
esv2745811 CNV deletion 23290073
esv2745812 CNV deletion 23290073
esv2745813 CNV deletion 23290073
esv2745814 CNV deletion 23290073
esv2745815 CNV deletion 23290073
esv2759896 CNV gain 17122850
esv2761735 CNV gain 21179565
esv29365 CNV loss 19812545
esv3252718 CNV deletion 24192839
esv3549104 CNV deletion 23714750
esv3549105 CNV deletion 23714750
esv3629308 CNV loss 21293372
esv3629309 CNV loss 21293372
esv3629310 CNV loss 21293372
esv3629311 CNV gain 21293372
esv3629315 CNV loss 21293372
esv3629316 CNV loss 21293372
esv3892195 CNV gain 25118596
esv3999 CNV loss 18987735
esv5085 CNV loss 18987735
esv5502 CNV loss 19470904
esv991188 CNV deletion 20482838
esv994358 CNV insertion 20482838
nsv1037987 CNV gain 25217958
nsv1048124 CNV loss 25217958
nsv1048258 CNV gain 25217958
nsv1050627 CNV loss 25217958
nsv1070526 CNV deletion 25765185
nsv1076388 CNV duplication 25765185
nsv1113478 CNV deletion 24896259
nsv1118233 CNV deletion 24896259
nsv1122143 CNV deletion 24896259
nsv1122727 CNV deletion 24896259
nsv1134219 CNV deletion 24896259
nsv472568 CNV novel sequence insertion 20440878
nsv474485 CNV novel sequence insertion 20440878
nsv517338 CNV loss 19592680
nsv52593 CNV deletion 16902084
nsv558699 CNV loss 21841781
nsv558700 CNV loss 21841781
nsv818915 CNV gain 17921354
nsv826348 CNV loss 20364138
nsv826349 CNV loss 20364138
nsv832383 CNV gain 17160897
nsv832384 CNV gain 17160897
nsv832385 CNV loss 17160897
nsv957927 CNV deletion 24416366
nsv958652 CNV deletion 24416366
nsv983313 CNV duplication 23825009
nsv983384 CNV duplication 23825009

Variation tolerance for PDZRN4 Gene

Residual Variation Intolerance Score: 51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.07; 95.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDZRN4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDZRN4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDZRN4 Gene

Disorders for PDZRN4 Gene

Additional Disease Information for PDZRN4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

No disorders were found for PDZRN4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDZRN4 Gene

Publications for PDZRN4 Gene

  1. Identification and characterization of PDZRN3 and PDZRN4 genes in silico. (PMID: 15010864) Katoh M … Katoh M (International journal of molecular medicine 2004) 2 3 4 23
  2. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4
  3. Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (PMID: 19010793) Baranzini SE … Oksenberg JR (Human molecular genetics 2009) 3 41
  4. A genome-wide association study identifies protein quantitative trait loci (pQTLs). (PMID: 18464913) Melzer D … Ferrucci L (PLoS genetics 2008) 3 41
  5. The finished DNA sequence of human chromosome 12. (PMID: 16541075) Scherer SE … Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team (Nature 2006) 3 4

Products for PDZRN4 Gene

Sources for PDZRN4 Gene