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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 RET signaling. 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

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
GH12H108626 2 FANTOM5 Ensembl ENCODE dbSUPER 20.4 -877.6 -877592 24 HDGF PKNOX1 ARNT FEZF1 ZNF766 CBX5 ZNF207 ZNF143 ZNF548 FOS PWP1 SART3 PRDM4 UBE3B RNU4-32P CORO1C FICD LOC101929162 SELPLG TMEM119
GH12H107758 1.3 ENCODE dbSUPER 28.5 +0.8 806 3 ARID4B SIN3A FEZF1 YY1 ZNF143 ZNF207 FOS SP3 SP5 REST PWP1 PRDM4 SART3 CORO1C GC12M107739
GH12H108578 0.7 ENCODE 39.1 -817.8 -817787 0 HDGF ZNF211 TSC22D4 YBX1 SALL2 ZKSCAN1 ZFHX2 ZNF791 ZNF239 ZNF169 SART3 PWP1 PRDM4 UBE3B WSCD2 ALKBH2 LOC101929162 USP30 KCTD10 RNU4-32P
GH12H108684 2 FANTOM5 Ensembl ENCODE dbSUPER 12.4 -930.4 -930364 13 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 CORO1C SART3 LOC101929162 ALKBH2 UBE3B PRDM4 RNU7-169P SELPLG RNU4-32P KCTD10
GH12H108605 0.9 dbSUPER 21.5 -844.7 -844721 1 HDGF ZNF473 ARNT ZNF493 YBX1 ZNF2 BRCA1 RARA TCF12 ZNF416 SART3 PWP1 ALKBH2 LOC101929162 PRDM4 UBE3B LINC01486 LOC644746 RNU4-32P USP30
- Elite enhancer and/or Elite enhancer-gene association 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
ENSR00000056998 672 2401 ARID4B SIN3A FEZF1 YY1 ZNF143 ZNF207 FOS SP5 REST ZNF592

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 isoforms=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

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 core promoter proximal region sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific 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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PRDM4
  • Applied Biological Materials Clones for PRDM4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 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

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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PRDM4
  • Applied Biological Materials Clones for PRDM4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

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 , 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 34 33
  • 80.64 (n)
OneToOne
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 Sequence Context AA Info Type
rs1000117037 -- 107,735,727(+) AAGAA(C/T)CTTAG intron-variant, upstream-variant-2KB
rs1000172933 -- 107,747,928(+) TAATA(C/T)TTTTG intron-variant
rs1000187788 -- 107,740,382(+) CTCAG(A/G)AGGCT intron-variant
rs1000251953 -- 107,758,327(+) CTGAC(G/T)GCTGC intron-variant, nc-transcript-variant
rs1000349061 -- 107,753,748(+) TGTTA(C/T)GTGCC 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)

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 XH … Huang S (Genomics 1999) 2 3 4 22 60
  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 45 60
  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 60
  4. Identification of Prdm genes in human corneal endothelium. (PMID: 28228349) Rolev K … Chittka A (Experimental eye research 2017) 3 60
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 60

Products for PRDM4 Gene

  • Addgene plasmids for PRDM4

Sources for PRDM4 Gene

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