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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 Signaling by GPCR and Development HGF signaling pathway. GO annotations related to this gene include methyltransferase activity. An important paralog of this gene is PRDM6.

UniProtKB/Swiss-Prot for PRDM4 Gene

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

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

Genomics for PRDM4 Gene

Regulatory Elements for PRDM4 Gene

Enhancers for PRDM4 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
GH12F108587 0.8 Ensembl ENCODE 47 -827.7 -827745 2.4 HDGF YBX3 ATF1 ZNF493 INSM2 YBX1 PLRG1 ZNF155 GATA2 FOS SART3 PWP1 PRDM4 UBE3B ALKBH2 LOC101929162 RNU4-32P SELPLG TMEM119 ISCU
GH12F108578 0.2 ENCODE 21.7 -817.8 -817787 0.8 HDGF ATF1 ZNF211 TSC22D4 YBX1 ZKSCAN1 ZFHX2 ZNF791 ZNF169 ZNF239 SART3 PWP1 PRDM4 UBE3B LOC101929162 KCTD10 RNU4-32P TMEM119 ISCU
GH12F108605 0.6 Ensembl 21.5 -844.5 -844529 0.8 HDGF ZNF493 YBX1 ZNF2 RARA ZNF416 ZNF207 FOS BCLAF1 EGR2 SART3 PWP1 PRDM4 UBE3B LOC644746 ENSG00000257129 LINC01486 ALKBH2 TMEM119 GC12M108565
GH12F107784 0.5 ENCODE 21.2 -23.4 -23355 0.7 NFE2 ZNF548 PRDM4 PWP1 SART3 CRY1 GC12P107784 ASCL4
GH12F108626 0.8 FANTOM5 ENCODE 20.4 -872.2 -872174 13.4 MLX CREB3L1 ZFP64 DMAP1 FEZF1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 SART3 PWP1 UBE3B PRDM4 CORO1C FICD SELPLG TMEM119 RPL17P38 RNU7-169P
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PRDM4 on UCSC Golden Path with GeneCards custom track

Promoters for PRDM4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000436609 672 2800 CREB3L1 ARID4B SIN3A FEZF1 YY1 ZNF143 ZNF207 FOS KLF13 SP5

Genomic Location for PRDM4 Gene

Chromosome:
12
Start:
107,732,866 bp from pter
End:
107,761,272 bp from pter
Size:
28,407 bases
Orientation:
Minus strand

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

  • Ubiquitination at Lys 412
  • Modification sites at PhosphoSitePlus

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

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 :
  • Contains 1 SET domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Contains 6 C2H2-type zinc fingers.
Domain:
  • Contains 1 SET domain.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Similarity:
  • Contains 6 C2H2-type zinc fingers.
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

Gene Ontology (GO) - Molecular Function for PRDM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0008168 methyltransferase activity IEA --
GO:0008270 zinc ion binding TAS 10552934
GO:0016740 transferase activity IEA --
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

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PRDM4

Flow Cytometry Products

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
Jensen Localization Image for PRDM4 Gene COMPARTMENTS Subcellular localization image for PRDM4 gene
Compartment Confidence
nucleus 5
cytosol 2

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 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 from RNA polymerase II promoter 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

Transcripts for PRDM4 Gene

Unigene Clusters for PRDM4 Gene

PR domain containing 4:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PRDM4

Flow Cytometry Products

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 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.
genes like me logo Genes that share expression patterns with PRDM4: view

Primer Products

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 and Protein tissue co-expression partners 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 34 35
  • 99.63 (n)
dog
(Canis familiaris)
Mammalia PRDM4 34 35
  • 94.84 (n)
cow
(Bos Taurus)
Mammalia PRDM4 34 35
  • 93.8 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM4 35
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Prdm4 34 16 35
  • 90.79 (n)
rat
(Rattus norvegicus)
Mammalia Prdm4 34
  • 89.46 (n)
oppossum
(Monodelphis domestica)
Mammalia PRDM4 35
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM4 34 35
  • 80.64 (n)
lizard
(Anolis carolinensis)
Reptilia PRDM4 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm4 34
  • 70.38 (n)
African clawed frog
(Xenopus laevis)
Amphibia prdm4-prov 34
zebrafish
(Danio rerio)
Actinopterygii prdm4 34 35
  • 64.35 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG43347 35
  • 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 Sequence Context AA Info Type
rs10083011 -- 107,734,985(+) TTTTT(A/T)AAATT intron-variant, upstream-variant-2KB
rs10219501 -- 107,751,181(+) CTTCA(C/T)ATTTC intron-variant
rs1045739 -- 107,734,001(-) GTCCT(A/G)TTTTA nc-transcript-variant, utr-variant-3-prime
rs1045741 -- 107,733,496(-) ACCTG(C/G)TTATT nc-transcript-variant, utr-variant-3-prime
rs1045749 -- 107,733,077(-) CTCCC(A/G)TGCAC downstream-variant-500B, utr-variant-3-prime

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)

Relevant External Links 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

Relevant External Links for PRDM4

Genetic Association Database (GAD)
PRDM4
Human Genome Epidemiology (HuGE) Navigator
PRDM4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PRDM4

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 X.-H. … Huang S. (Genomics 1999) 2 3 4 22 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. 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 64
  4. Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. (PMID: 24927181) Navarini A.A. … Barker J.N. (Nat Commun 2014) 3 64
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3 64

Products for PRDM4 Gene

Sources for PRDM4 Gene

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