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Aliases for PRDM2 Gene

Aliases for PRDM2 Gene

  • PR Domain 2 2 3
  • Retinoblastoma Protein-Interacting Zinc Finger Protein 2 3 4
  • PR Domain Containing 2, With ZNF Domain 2 3 5
  • MTE-Binding Protein 2 3 4
  • 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
  • RIZ 3 4
  • EC 2.1.1.43 4
  • HUMHOXY1 3
  • RIZ1 3
  • RIZ2 3

External Ids for PRDM2 Gene

Previous GeneCards Identifiers for PRDM2 Gene

  • GC01P013428
  • GC01P013210
  • GC01P013394
  • GC01P013899
  • GC01P014026
  • GC01P012544

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 2) is a Protein Coding gene. Diseases associated with PRDM2 include retinoblastoma and wilms tumor susceptibility-5. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding 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

Regulatory Elements for PRDM2 Gene

Promoters for PRDM2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PRDM2 on UCSC Golden Path with GeneCards custom track

Genomic Location for PRDM2 Gene

Chromosome:
1
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

Genes around PRDM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Antibody Products

No data available for DME Specific Peptides for PRDM2 Gene

Domains & Families for PRDM2 Gene

Gene Families for PRDM2 Gene

Suggested Antigen Peptide Sequences for PRDM2 Gene

Graphical View of Domain Structure for InterPro Entry

Q13029

UniProtKB/Swiss-Prot:

PRDM2_HUMAN :
  • Contains 1 SET domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Contains 8 C2H2-type zinc fingers.
Domain:
  • Contains 1 SET domain.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Similarity:
  • Contains 8 C2H2-type zinc fingers.
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:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with PRDM2: view
genes like me logo Genes that share phenotypes with PRDM2: view

Animal Models for PRDM2 Gene

MGI Knock Outs for PRDM2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets 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
cytosol 2
golgi apparatus 2

No data available for Gene Ontology (GO) - Cellular Components for PRDM2 Gene

Pathways & Interactions for PRDM2 Gene

SuperPathways for PRDM2 Gene

No Data Available

Pathways by source for PRDM2 Gene

1 GeneTex pathway for PRDM2 Gene

Gene Ontology (GO) - Biological Process for PRDM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032355 response to estradiol IEA --
GO:0034968 histone lysine methylation IEA --
genes like me logo Genes that share ontologies with PRDM2: view

No data available for SIGNOR curated interactions for PRDM2 Gene

Drugs & Compounds for PRDM2 Gene

(13) Drugs for PRDM2 Gene - From: Novoseek and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Zinc Approved Pharma 1477
L-Lysine Approved Nutra Full agonist, Agonist 0
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 0
heme Pharma Agonist 0

(5) Additional Compounds for PRDM2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRDM2 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (65.5).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with PRDM2: view

Protein tissue co-expression partners for PRDM2 Gene

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for PRDM2 Gene

Orthologs for PRDM2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PRDM2 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PRDM2 35
  • 82.94 (n)
  • 86.19 (a)
PRDM2 36
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PRDM2 35
  • 84.36 (n)
  • 87.76 (a)
-- 36
  • 88 (a)
OneToMany
-- 36
  • 97 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Prdm2 35
  • 83.26 (n)
  • 84.76 (a)
Prdm2 16
Prdm2 36
  • 84 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PRDM2 35
  • 99.32 (n)
  • 99.32 (a)
PRDM2 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Prdm2 35
  • 82.81 (n)
  • 84.5 (a)
oppossum
(Monodelphis domestica)
Mammalia PRDM2 36
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM2 36
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves PRDM2 35
  • 73.14 (n)
  • 73.42 (a)
PRDM2 36
  • 72 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM2 36
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm2 35
  • 64.61 (n)
  • 60.57 (a)
Str.11503 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.19643 35
zebrafish
(Danio rerio)
Actinopterygii prdm2b 35
  • 56.83 (n)
  • 51.52 (a)
prdm2b 36
  • 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

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
rs2076324 - 13,778,644(-) TCATC(A/T)TCTTC intron-variant, reference, missense
rs17350795 - 13,779,144(+) TCCCA(A/G)TCTTG intron-variant, reference, missense
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

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

Variation tolerance for PRDM2 Gene

Residual Variation Intolerance Score: 49.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.01; 68.46% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PRDM2 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM2 Gene

Disorders for PRDM2 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PRDM2 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
retinoblastoma
  • retinoblastoma, trilateral
wilms tumor susceptibility-5
  • wilms tumor
retinal cancer
  • malignant neoplasm of retina
sensory system cancer
ocular cancer
  • eye neoplasm
- elite association - COSMIC cancer census association via MalaCards
Search PRDM2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PRDM2

Genetic Association Database (GAD)
PRDM2
Human Genome Epidemiology (HuGE) Navigator
PRDM2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PRDM2
genes like me logo Genes that share disorders with PRDM2: view

No data available for UniProtKB/Swiss-Prot and Genatlas 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 67
  2. DNA methylation of the RIZ1 tumor suppressor gene plays an important role in the tumorigenesis of cervical cancer. (PMID: 20159667) Cheng H.Y. … Lou G. (Eur. J. Med. Res. 2010) 3 23
  3. Expression of RIZ1 protein (Retinoblastoma-interacting zinc-finger protein 1) in prostate cancer epithelial cells changes with cancer grade progression and is modulated in vitro by DHT and E2. (PMID: 19746436) Rossi V. … Sinisi A.A. (J. Cell. Physiol. 2009) 3 23
  4. RIZ1 is potential CML tumor suppressor that is down-regulated during disease progression. (PMID: 19602237) Lakshmikuttyamma A. … Geyer C.R. (J Hematol Oncol 2009) 3 23
  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

Products for PRDM2 Gene

Sources for PRDM2 Gene

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