Human Gene PRDM2 (ENST00000376048.9) from GENCODE V38
  Description: Homo sapiens PR/SET domain 2 (PRDM2), transcript variant 4, mRNA. (from RefSeq NM_001135610)
RefSeq Summary (NM_001135610): 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].
Gencode Transcript: ENST00000376048.9
Gencode Gene: ENSG00000116731.22
Transcript (Including UTRs)
   Position: hg38 chr1:13,700,240-13,825,065 Size: 124,826 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr1:13,715,606-13,823,184 Size: 107,579 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2021-09-27 09:51:20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:13,700,240-13,825,065)mRNA (may differ from genome)Protein (226 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=PR domain zinc finger protein 2; EC=; AltName: Full=GATA-3-binding protein G3B; AltName: Full=Lysine N-methyltransferase 8; AltName: Full=MTB-ZF; AltName: Full=MTE-binding protein; AltName: Full=PR domain-containing protein 2; AltName: Full=Retinoblastoma protein-interacting zinc finger protein; AltName: Full=Zinc finger protein RIZ;
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.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBUNIT: Binds to the retinoblastoma protein (RB). Interacts with GATA3.
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.
SIMILARITY: Contains 8 C2H2-type zinc fingers.
SIMILARITY: Contains 1 SET domain.
SEQUENCE CAUTION: Sequence=BAA08110.1; Type=Erroneous initiation;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="";

-  MalaCards Disease Associations
  MalaCards Gene Search: PRDM2
Diseases sorted by gene-association score: retinoblastoma (49), wilms tumor susceptibility-5 (6), retinal cancer (4), sensory system cancer (4), ocular cancer (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.19 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 408.15 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -51.50126-0.409 Picture PostScript Text
3' UTR -639.501881-0.340 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009170 - RIZ_retinblastoma-bd_prot
IPR001214 - SET_dom
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00856 - SET domain
PF00096 - Zinc finger, C2H2 type

Protein Data Bank (PDB) 3-D Structure
MuPIT help


- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q13029
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0008340 determination of adult lifespan
GO:0032259 methylation
GO:0034968 histone lysine methylation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005794 Golgi apparatus

-  Descriptions from all associated GenBank mRNAs
  BC014468 - Homo sapiens PR domain containing 2, with ZNF domain, mRNA (cDNA clone IMAGE:4876775), with apparent retained intron.
U17838 - Homo sapiens zinc finger protein RIZ mRNA, complete cds.
BC172414 - Synthetic construct Homo sapiens clone IMAGE:100069108, MGC:199119 PR domain containing 2, with ZNF domain (PRDM2) mRNA, encodes complete protein.
BC032768 - Homo sapiens cDNA clone IMAGE:3872694, containing frame-shift errors.
D45132 - Homo sapiens mRNA for zinc-finger DNA-binding protein, complete cds.
AB208877 - Homo sapiens mRNA for PR-domain zinc finger protein 2 variant protein.
BX647310 - Homo sapiens mRNA; cDNA DKFZp686D2193 (from clone DKFZp686D2193).
AK307377 - Homo sapiens cDNA, FLJ97325.
AK308135 - Homo sapiens cDNA, FLJ98083.
AK300441 - Homo sapiens cDNA FLJ54548 partial cds, highly similar to PR domain zinc finger protein 2.
BC140012 - Homo sapiens cDNA clone IMAGE:8860424.
AK293725 - Homo sapiens cDNA FLJ53305 partial cds, highly similar to PR domain zinc finger protein 2.
AK311678 - Homo sapiens cDNA, FLJ18720.
BC051275 - Homo sapiens PR domain containing 2, with ZNF domain, mRNA (cDNA clone IMAGE:6215820), **** WARNING: chimeric clone ****.
U23736 - Human GATA-3 binding protein G3B mRNA, partial cds.
AK123605 - Homo sapiens cDNA FLJ41611 fis, clone CTONG3002020.
AK124197 - Homo sapiens cDNA FLJ42203 fis, clone THYMU2035388.
JD493926 - Sequence 474950 from Patent EP1572962.
JD127596 - Sequence 108620 from Patent EP1572962.
JD172829 - Sequence 153853 from Patent EP1572962.
JD281528 - Sequence 262552 from Patent EP1572962.
JD281529 - Sequence 262553 from Patent EP1572962.
JD553908 - Sequence 534932 from Patent EP1572962.
JD391522 - Sequence 372546 from Patent EP1572962.
JD142079 - Sequence 123103 from Patent EP1572962.
JD187833 - Sequence 168857 from Patent EP1572962.
JD327122 - Sequence 308146 from Patent EP1572962.
JD054873 - Sequence 35897 from Patent EP1572962.
JD519020 - Sequence 500044 from Patent EP1572962.
JD047074 - Sequence 28098 from Patent EP1572962.
JD154792 - Sequence 135816 from Patent EP1572962.
JD052693 - Sequence 33717 from Patent EP1572962.
JD208488 - Sequence 189512 from Patent EP1572962.
JD262900 - Sequence 243924 from Patent EP1572962.
JD131661 - Sequence 112685 from Patent EP1572962.
JD483864 - Sequence 464888 from Patent EP1572962.
JD501840 - Sequence 482864 from Patent EP1572962.
JD468385 - Sequence 449409 from Patent EP1572962.
JD539809 - Sequence 520833 from Patent EP1572962.
JD439079 - Sequence 420103 from Patent EP1572962.
JD350640 - Sequence 331664 from Patent EP1572962.
JD519602 - Sequence 500626 from Patent EP1572962.
JD474225 - Sequence 455249 from Patent EP1572962.
JD273254 - Sequence 254278 from Patent EP1572962.
JD538080 - Sequence 519104 from Patent EP1572962.
JD226634 - Sequence 207658 from Patent EP1572962.
JD454373 - Sequence 435397 from Patent EP1572962.
JD134715 - Sequence 115739 from Patent EP1572962.
JD564990 - Sequence 546014 from Patent EP1572962.
JD286855 - Sequence 267879 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000376048.1, ENST00000376048.2, ENST00000376048.3, ENST00000376048.4, ENST00000376048.5, ENST00000376048.6, ENST00000376048.7, ENST00000376048.8, KMT8, NM_001135610, PRDM2_HUMAN, Q13029, Q13149, Q14550, Q5VUL9, RIZ, uc001avg.1, uc001avg.2, uc001avg.3, uc001avg.4
UCSC ID: ENST00000376048.9
RefSeq Accession: NM_001135610
Protein: Q13029 (aka PRDM2_HUMAN or PRD2_HUMAN)
CCDS: CCDS44061.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.