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Aliases for PRDM4 Gene

Aliases for PRDM4 Gene

  • PR/SET Domain 4 2 3 5
  • PR Domain-Containing Protein 4 3 4
  • PR Domain Containing 4 2 3
  • PR Domain 4 2 3
  • PFM1 3 4
  • PR-Domain Zinc-Finger Protein PFM1 3
  • PR Domain Zinc Finger Protein 4 3
  • EC 2.1.1.- 4

External Ids for PRDM4 Gene

Previous GeneCards Identifiers for PRDM4 Gene

  • GC12M107237
  • GC12M108007
  • GC12M106629
  • GC12M108126
  • GC12M105186

Summaries for PRDM4 Gene

Entrez Gene Summary for PRDM4 Gene

  • The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. An elevated expression level of this gene has been observed in PC12 cells treated with nerve growth factor, beta polypeptide (NGF). This gene is located in a chromosomal region that is thought to contain tumor suppressor genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for PRDM4 Gene

PRDM4 (PR/SET Domain 4) is a Protein Coding gene. Among its related pathways are p75 NTR receptor-mediated signalling and Development HGF signaling pathway. Gene Ontology (GO) annotations related to this gene include methyltransferase activity. An important paralog of this gene is PRDM14.

UniProtKB/Swiss-Prot for PRDM4 Gene

  • May function as a transcription factor involved in cell differentiation.

Additional gene information for PRDM4 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRDM4 Gene

Genomics for PRDM4 Gene

GeneHancer (GH) Regulatory Elements for PRDM4 Gene

Promoters and enhancers for PRDM4 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
GH12I107758 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 566 +0.8 805 3.7 ARID4B SIN3A FEZF1 YY1 POLR2B ZNF207 ZNF143 FOS SP3 SP5 PRDM4 PWP1 GC12M107739 LOC101929162
GH12I108626 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.4 -877.6 -877592 24.2 HDGF PKNOX1 SMAD1 ARNT FEZF1 IRF4 POLR2B ZNF766 CBX5 ZNF207 SELPLG PWP1 SART3 PRDM4 UBE3B RNU4-32P CORO1C FICD LOC101929162 TMEM119
GH12I106984 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 13.7 +774.7 774744 3.3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B MTERF2 GC12P106984 PWP1 PRDM4 ENSG00000260329 CRY1
GH12I108578 Enhancer 0.7 ENCODE 39.1 -817.8 -817786 0.8 HDGF ESRRA ZNF211 TSC22D4 SALL2 YBX1 ZKSCAN1 ZFHX2 ZNF791 ZNF239 SART3 PWP1 PRDM4 UBE3B WSCD2 ALKBH2 LOC101929162 USP30 KCTD10 RNU4-32P
GH12I108605 Enhancer 0.9 dbSUPER 30.1 -844.7 -844721 1.5 HDGF ARNT ZNF493 YBX1 BRCA1 ZNF2 TCF12 ZNF416 ZNF207 FOS GC12M108565 SART3 PWP1 ALKBH2 PRDM4 RNU4-32P LOC101929162 UBE3B USP30 TMEM119
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PRDM4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRDM4 gene promoter:

Genomic Locations for PRDM4 Gene

Genomic Locations for PRDM4 Gene
chr12:107,732,866-107,761,272
(GRCh38/hg38)
Size:
28,407 bases
Orientation:
Minus strand
chr12:108,126,643-108,155,049
(GRCh37/hg19)

Genomic View for PRDM4 Gene

Genes around PRDM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM4 Gene

Proteins for PRDM4 Gene

  • Protein details for PRDM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UKN5-PRDM4_HUMAN
    Recommended name:
    PR domain zinc finger protein 4
    Protein Accession:
    Q9UKN5
    Secondary Accessions:
    • Q9UFA6

    Protein attributes for PRDM4 Gene

    Size:
    801 amino acids
    Molecular mass:
    87920 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PRDM4 Gene

neXtProt entry for PRDM4 Gene

Post-translational modifications for PRDM4 Gene

Other Protein References for PRDM4 Gene

No data available for DME Specific Peptides for PRDM4 Gene

Domains & Families for PRDM4 Gene

Gene Families for PRDM4 Gene

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

Protein Domains for PRDM4 Gene

Suggested Antigen Peptide Sequences for PRDM4 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UKN5

UniProtKB/Swiss-Prot:

PRDM4_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with PRDM4: view

Function for PRDM4 Gene

Molecular function for PRDM4 Gene

GENATLAS Biochemistry:
PR domain containing 4,widely expressed,involved in cell differentiation control and in tumorigenesis
UniProtKB/Swiss-Prot Function:
May function as a transcription factor involved in cell differentiation.

Enzyme Numbers (IUBMB) for PRDM4 Gene

Phenotypes From GWAS Catalog for PRDM4 Gene

Gene Ontology (GO) - Molecular Function for PRDM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with PRDM4: view
genes like me logo Genes that share phenotypes with PRDM4: view

Animal Models for PRDM4 Gene

MGI Knock Outs for PRDM4:

Animal Model Products

Clone Products

  • Addgene plasmids for PRDM4

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PRDM4 Gene

Localization for PRDM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM4 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 PRDM4 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PRDM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0035097 histone methyltransferase complex IEA,NAS 23048031
genes like me logo Genes that share ontologies with PRDM4: view

Pathways & Interactions for PRDM4 Gene

genes like me logo Genes that share pathways with PRDM4: view

Pathways by source for PRDM4 Gene

Gene Ontology (GO) - Biological Process for PRDM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA,TAS --
GO:0007165 signal transduction TAS 10552934
GO:0008283 cell proliferation TAS 10552934
genes like me logo Genes that share ontologies with PRDM4: view

No data available for SIGNOR curated interactions for PRDM4 Gene

Drugs & Compounds for PRDM4 Gene

No Compound Related Data Available

Transcripts for PRDM4 Gene

Unigene Clusters for PRDM4 Gene

PR domain containing 4:
Representative Sequences:

Clone Products

  • Addgene plasmids for PRDM4

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM4 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11 ^ 12 ^ 13
SP1: - -
SP2: - - - - -
SP3:
SP4:

Relevant External Links for PRDM4 Gene

GeneLoc Exon Structure for
PRDM4
ECgene alternative splicing isoforms for
PRDM4

Expression for PRDM4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRDM4 Gene

NURSA nuclear receptor signaling pathways regulating expression of PRDM4 Gene:

PRDM4

SOURCE GeneReport for Unigene cluster for PRDM4 Gene:

Hs.506655

mRNA Expression by UniProt/SwissProt for PRDM4 Gene:

Q9UKN5-PRDM4_HUMAN
Tissue specificity: Expressed in many tissues. Highly expressed in ovary, testis, pancreas, brain, heart and prostate.

Evidence on tissue expression from TISSUES for PRDM4 Gene

  • Nervous system(2.3)
genes like me logo Genes that share expression patterns with PRDM4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM4 Gene

Orthologs for PRDM4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRDM4 33 34
  • 99.63 (n)
dog
(Canis familiaris)
Mammalia PRDM4 33 34
  • 94.84 (n)
cow
(Bos Taurus)
Mammalia PRDM4 33 34
  • 93.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM4 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Prdm4 33 16 34
  • 90.79 (n)
rat
(Rattus norvegicus)
Mammalia Prdm4 33
  • 89.46 (n)
oppossum
(Monodelphis domestica)
Mammalia PRDM4 34
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM4 33 34
  • 80.64 (n)
lizard
(Anolis carolinensis)
Reptilia PRDM4 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm4 33
  • 70.38 (n)
African clawed frog
(Xenopus laevis)
Amphibia prdm4-prov 33
zebrafish
(Danio rerio)
Actinopterygii prdm4 33 34
  • 64.35 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG43347 34
  • 6 (a)
OneToMany
Species where no ortholog for PRDM4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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)
  • worm (Caenorhabditis elegans)

Evolution for PRDM4 Gene

ENSEMBL:
Gene Tree for PRDM4 (if available)
TreeFam:
Gene Tree for PRDM4 (if available)

Paralogs for PRDM4 Gene

Paralogs for PRDM4 Gene

genes like me logo Genes that share paralogs with PRDM4: view

Variants for PRDM4 Gene

Sequence variations from dbSNP and Humsavar for PRDM4 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000117037 -- 107,735,727(-) C/T intron_variant
rs1000172933 -- 107,747,928(-) C/T intron_variant
rs1000187788 -- 107,740,382(-) G/A intron_variant
rs1000251953 -- 107,758,327(-) T/G intron_variant
rs1000349061 -- 107,753,748(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PRDM4 Gene

Variant ID Type Subtype PubMed ID
nsv1038935 CNV gain 25217958
nsv560091 CNV gain 21841781
nsv820093 CNV loss 19587683

Variation tolerance for PRDM4 Gene

Residual Variation Intolerance Score: 5.19% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.23; 24.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM4 Gene

Disorders for PRDM4 Gene

Additional Disease Information for PRDM4

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

No disorders were found for PRDM4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PRDM4 Gene

Publications for PRDM4 Gene

  1. PFM1 (PRDM4), a new member of the PR-domain family, maps to a tumor suppressor locus on human chromosome 12q23-q24.1. (PMID: 10552934) Yang XH … Huang S (Genomics 1999) 2 3 4 22 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. 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 58
  4. Identification of Prdm genes in human corneal endothelium. (PMID: 28228349) Rolev K … Chittka A (Experimental eye research 2017) 3 58
  5. Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. (PMID: 24927181) Navarini AA … Barker JN (Nature communications 2014) 3 58

Products for PRDM4 Gene

Sources for PRDM4 Gene

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