Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PRDM2 Gene

Aliases for PRDM2 Gene

  • PR Domain Containing 2, With ZNF Domain 2 3
  • Retinoblastoma Protein-Interacting Zinc Finger Protein 2 3 4
  • MTE-Binding Protein 2 3 4
  • RIZ 3 4 6
  • Retinoblastoma Protein-Binding Zinc Finger Protein 2 3
  • Zinc-Finger DNA-Binding Protein 2 3
  • PR Domain-Containing Protein 2 3 4
  • Lysine N-Methyltransferase 8 3 4
  • GATA-3 Binding Protein G3B 2 3
  • GATA-3-Binding Protein G3B 3 4
  • Zinc Finger Protein RIZ 3 4
  • MTB-ZF 3 4
  • KMT8 3 4
  • PR Domain Zinc Finger Protein 2 3
  • EC 2.1.1.43 4
  • HUMHOXY1 3
  • RIZ1 3
  • RIZ2 3

External Ids for PRDM2 Gene

Summaries for PRDM2 Gene

Entrez Gene Summary for PRDM2 Gene

  • This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene. Although the functions of this protein have not been fully characterized, it may (1) play a role in transcriptional regulation during neuronal differentiation and pathogenesis of retinoblastoma, (2) act as a transcriptional activator of the heme-oxygenase-1 gene, and (3) be a specific effector of estrogen action. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

GeneCards Summary for PRDM2 Gene

PRDM2 (PR Domain Containing 2, With ZNF Domain) is a Protein Coding gene. Diseases associated with PRDM2 include retinoblastoma. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and histone-lysine N-methyltransferase activity.

UniProtKB/Swiss-Prot for PRDM2 Gene

  • S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates Lys-9 of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene.

Gene Wiki entry for PRDM2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRDM2 Gene

Genomics for PRDM2 Gene

Genomic Location for PRDM2 Gene

Start:
13,700,198 bp from pter
End:
13,825,079 bp from pter
Size:
124,882 bases
Orientation:
Plus strand

Genomic View for PRDM2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PRDM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM2 Gene

Regulatory Elements for PRDM2 Gene

Proteins for PRDM2 Gene

  • Protein details for PRDM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13029-PRDM2_HUMAN
    Recommended name:
    PR domain zinc finger protein 2
    Protein Accession:
    Q13029
    Secondary Accessions:
    • B1AJZ4
    • B5MC68
    • Q13149
    • Q14550
    • Q5THJ1
    • Q5VUL9

    Protein attributes for PRDM2 Gene

    Size:
    1718 amino acids
    Molecular mass:
    188915 Da
    Quaternary structure:
    • Binds to the retinoblastoma protein (RB). Interacts with GATA3.
    SequenceCaution:
    • Sequence=BAA08110.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PRDM2 Gene

    Alternative splice isoforms for PRDM2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM2 Gene

Proteomics data for PRDM2 Gene at MOPED

Post-translational modifications for PRDM2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PRDM2 Gene

Domains for PRDM2 Gene

Gene Families for PRDM2 Gene

HGNC:
  • KMT :Chromatin-modifying enzymes / K-methyltransferases

UniProtKB/Swiss-Prot:

PRDM2_HUMAN
Domain:
  • Contains 1 SET domain.:
    • Q13029
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.:
    • Q13029
Similarity:
  • Contains 8 C2H2-type zinc fingers.:
    • Q13029
genes like me logo Genes that share domains with PRDM2: view

Function for PRDM2 Gene

Molecular function for PRDM2 Gene

GENATLAS Biochemistry: PR domain containing 2,retinoblastoma RB1 protein interacting zinc finger RIZ,with two alternative spliced forms,280kDa (RIZ1),250kDa (RIZ2),acting as a putative tumor suppressor,with RIZ1 commonly underexpressed in breast cancer and other carcinomas
UniProtKB/Swiss-Prot CatalyticActivity: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]
UniProtKB/Swiss-Prot Function: S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates Lys-9 of histone H3. May function as a DNA-binding transcription factor. Binds to the macrophage-specific TPA-responsive element (MTE) of the HMOX1 (heme oxygenase 1) gene and may act as a transcriptional activator of this gene.

Enzyme Numbers (IUBMB) for PRDM2 Gene

Gene Ontology (GO) - Molecular Function for PRDM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 sequence-specific DNA binding transcription factor activity NAS 7590293
GO:0005515 protein binding --
GO:0008270 zinc ion binding NAS 7538672
GO:0018024 histone-lysine N-methyltransferase activity IEA --
genes like me logo Genes that share ontologies with PRDM2: view

Phenotypes for PRDM2 Gene

MGI mutant phenotypes for PRDM2:
inferred from 1 alleles
genes like me logo Genes that share phenotypes with PRDM2: view

Animal Models for PRDM2 Gene

MGI Knock Outs for PRDM2:

miRNA for PRDM2 Gene

miRTarBase miRNAs that target PRDM2

No data available for Transcription Factor Targeting and HOMER Transcription for PRDM2 Gene

Localization for PRDM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM2 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PRDM2 Gene COMPARTMENTS Subcellular localization image for PRDM2 gene
Compartment Confidence
nucleus 5
golgi apparatus 4
cytosol 2

Gene Ontology (GO) - Cellular Components for PRDM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS 7538672
GO:0005794 Golgi apparatus IDA --
genes like me logo Genes that share ontologies with PRDM2: view

Pathways for PRDM2 Gene

SuperPathways for PRDM2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PRDM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated NAS 7590293
GO:0034968 histone lysine methylation IEA --
genes like me logo Genes that share ontologies with PRDM2: view

No data available for Pathways by source for PRDM2 Gene

Compounds for PRDM2 Gene

(3) HMDB Compounds for PRDM2 Gene

Compound Synonyms Cas Number PubMed IDs
Heme
  • (protoporphyrinato)iron
14875-96-8
L-Lysine
  • (+)-S-Lysine
56-87-1
Zinc
  • Zinc
7440-66-6

(14) Novoseek inferred chemical compound relationships for PRDM2 Gene

Compound -log(P) Hits PubMed IDs
zinc 78.8 77
5-aza-2deoxycytidine 55.1 4
vidarabine 43.1 2
estrogen 26.5 10
12-o-tetradecanoylphorbol 13-acetate 23.7 2
genes like me logo Genes that share compounds with PRDM2: view

Transcripts for PRDM2 Gene

Unigene Clusters for PRDM2 Gene

PR domain containing 2, with ZNF domain:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM2 Gene

No ASD Table

Relevant External Links for PRDM2 Gene

GeneLoc Exon Structure for
PRDM2
ECgene alternative splicing isoforms for
PRDM2

Expression for PRDM2 Gene

mRNA expression in normal human tissues for PRDM2 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PRDM2 Gene

SOURCE GeneReport for Unigene cluster for PRDM2 Gene Hs.371823

mRNA Expression by UniProt/SwissProt for PRDM2 Gene

Q13029-PRDM2_HUMAN
Tissue specificity: Highly expressed in retinoblastoma cell lines and in brain tumors. Also expressed in a number of other cell lines and in brain, heart, skeletal muscle, liver and spleen. Isoform 1 is expressed in testis at much higher level than isoform 3.
genes like me logo Genes that share expressions with PRDM2: view

Orthologs for PRDM2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PRDM2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRDM2 36
  • 99.32 (n)
  • 99.32 (a)
PRDM2 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PRDM2 36
  • 82.94 (n)
  • 86.19 (a)
PRDM2 37
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 37
  • 88 (a)
OneToMany
-- 37
  • 97 (a)
OneToMany
PRDM2 36
  • 84.36 (n)
  • 87.76 (a)
mouse
(Mus musculus)
Mammalia Prdm2 36
  • 83.26 (n)
  • 84.76 (a)
Prdm2 16
Prdm2 37
  • 84 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PRDM2 37
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM2 37
  • 75 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Prdm2 36
  • 82.81 (n)
  • 84.5 (a)
chicken
(Gallus gallus)
Aves PRDM2 36
  • 73.14 (n)
  • 73.42 (a)
PRDM2 37
  • 72 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM2 37
  • 63 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.19643 36
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm2 36
  • 64.61 (n)
  • 60.57 (a)
Str.11503 36
zebrafish
(Danio rerio)
Actinopterygii prdm2b 36
  • 56.83 (n)
  • 51.52 (a)
prdm2b 37
  • 45 (a)
OneToOne
Species with no ortholog for PRDM2:
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 PRDM2 Gene

ENSEMBL:
Gene Tree for PRDM2 (if available)
TreeFam:
Gene Tree for PRDM2 (if available)

Paralogs for PRDM2 Gene

Selected SIMAP similar genes for PRDM2 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with PRDM2: view

No data available for Paralogs for PRDM2 Gene

Variants for PRDM2 Gene

Sequence variations from dbSNP and Humsavar for PRDM2 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs2277 -- 13,730,763(-) TGTTC(C/T)AGCCA intron-variant
rs2903 -- 13,825,011(-) CTGTC(A/G)TCTTG utr-variant-3-prime
rs727985 -- 13,803,656(+) CCCTG(A/C)ACTTC intron-variant
rs738437 -- 13,814,093(-) AAACA(A/G)AGCTG intron-variant
rs742355 -- 13,799,866(+) ATTGC(A/T)GTCCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PRDM2 Gene

Variant ID Type Subtype PubMed ID
nsv871035 CNV Gain 21882294
nsv3187 CNV Loss 18451855
esv2744086 CNV Deletion 23290073
nsv871863 CNV Gain 21882294

Relevant External Links for PRDM2 Gene

HapMap Linkage Disequilibrium report
PRDM2
Human Gene Mutation Database (HGMD)
PRDM2

Disorders for PRDM2 Gene

(1) MalaCards Diseases for PRDM2 Gene

Search for PRDM2 Gene in MalaCards »

(1) University of Copenhagen DISEASES for PRDM2 Gene

(23) Novoseek inferred disease relationships for PRDM2 Gene

Disease -log(P) Hits PubMed IDs
retinoblastoma 70.9 23
microsatellite instability 63.6 9
wilms tumor 58.6 8
tumors 39.9 65
allelic loss 33.5 3

Relevant External Links for PRDM2

Genetic Association Database (GAD)
PRDM2
Human Genome Epidemiology (HuGE) Navigator
PRDM2
genes like me logo Genes that share disorders with PRDM2: view

No data available for UniProtKB/Swiss-Prot for PRDM2 Gene

Publications for PRDM2 Gene

  1. The retinoblastoma protein binds to RIZ, a zinc-finger protein that shares an epitope with the adenovirus E1A protein. (PMID: 7538672) Buyse I.M. … Huang S. (Proc. Natl. Acad. Sci. U.S.A. 1995) 2 3 4 23
  2. cDNA cloning of a novel protein containing two zinc-finger domains that may function as a transcription factor for the human heme- oxygenase-1 gene. (PMID: 8654390) Muraosa Y. … Shibahara S. (Eur. J. Biochem. 1996) 3 4 23
  3. Inactivation of a histone methyltransferase by mutations in human cancers. (PMID: 14633678) Kim K.-C. … Huang S. (Cancer Res. 2003) 3 4 23
  4. Genetic polymorphisms in the Rb-binding zinc finger gene RIZ and the risk of lung cancer. (PMID: 17693662) Yoon K.A. … Lee J.S. (Carcinogenesis 2007) 3 23 49
  5. The RIZ Pro704 insertion-deletion polymorphism, bone mineral density and fracture risk: the Rotterdam study. (PMID: 18037365) Stolk L. … Uitterlinden A.G. (Bone 2008) 3 23 49

Products for PRDM2 Gene

  • Addgene plasmids for PRDM2

Sources for PRDM2 Gene

Back to Top

Content