Human Gene PRDM16 (ENST00000378391.6)
  Description: Homo sapiens PR/SET domain 16 (PRDM16), transcript variant 2, mRNA. (from RefSeq NM_199454)
RefSeq Summary (NM_199454): The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal PR domain. The translocation results in the overexpression of a truncated version of this protein that lacks the PR domain, which may play an important role in the pathogenesis of MDS and AML. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000378391.6
Gencode Gene: ENSG00000142611.17
Transcript (Including UTRs)
   Position: hg38 chr1:3,069,197-3,435,421 Size: 366,225 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg38 chr1:3,069,260-3,433,811 Size: 364,552 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2021-01-14 15:32:12

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:3,069,197-3,435,421)mRNA (may differ from genome)Protein (1257 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=PR domain zinc finger protein 16; AltName: Full=PR domain-containing protein 16; AltName: Full=Transcription factor MEL1; Short=MDS1/EVI1-like gene 1;
FUNCTION: Binds DNA and functions as a transcriptional regulator. Functions in the differentiation of brown adipose tissue (BAT) which is specialized in dissipating chemical energy in the form of heat in response to cold or excess feeding while white adipose tissue (WAT) is specialized in the storage of excess energy and the control of systemic metabolism. Together with CEBPB, regulates the differentiation of myoblastic precursors into brown adipose cells. Functions also as a repressor of TGF-beta signaling. Isoform 4 may regulate granulocytes differentiation.
SUBUNIT: Interacts with CEBPA, CEBPB and CEBPD; the interaction is direct. Interacts with PPARG and PPARA; controls brown adipocytes differentiation. Interacts with CTBP1 and CTBP2; represses the expression of WAT-specific genes. Interacts with PPARGC1A and PPARGC1B; interaction with PPARGC1A or PPARGC1B activates the transcription of BAT-specific gene. Interacts with SMAD3 (By similarity). Interacts with HDAC1, SKI, SMAD2 and SMAD3; the interaction with SKI promotes the recruitment of SMAD3-HDAC1 complex on the promoter of TGF-beta target genes.
INTERACTION: P56546:Ctbp2 (xeno); NbExp=2; IntAct=EBI-4566658, EBI-1384883;
TISSUE SPECIFICITY: Expressed in uterus and kidney.
DISEASE: Note=A chromosomal aberration involving PRDM16 is found in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Reciprocal translocation t(1;3)(p36;q21). Isoform 4 is specifically expressed in adult T-cell leukemia.
SIMILARITY: Contains 10 C2H2-type zinc fingers.
SIMILARITY: Contains 1 SET domain.
SEQUENCE CAUTION: Sequence=BAB21766.2; Type=Erroneous initiation;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="";

-  MalaCards Disease Associations
  MalaCards Gene Search: PRDM16
Diseases sorted by gene-association score: left ventricular noncompaction 8* (1200), prdm16-related dilated cardiomyopathy* (500), left ventricular noncompaction* (252), familial isolated dilated cardiomyopathy* (124), chromosome 1p36 deletion syndrome* (19), myelodysplastic syndrome (16), adult t-cell leukemia (13), myeloid leukemia (5), image syndrome (4), cardiomyopathy (3)
* = Manually curated disease association

-  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: 12.06 RPKM in Artery - Aorta
Total median expression: 96.22 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 -17.3063-0.275 Picture PostScript Text
3' UTR -596.201610-0.370 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
IPR001214 - SET_dom
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

Pfam Domains:
PF00096 - Zinc finger, C2H2 type

ModBase Predicted Comparative 3D Structure on Q9HAZ2
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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0018024 histone-lysine N-methyltransferase activity
GO:0033613 activating transcription factor binding
GO:0043565 sequence-specific DNA binding
GO:0046332 SMAD binding
GO:0046872 metal ion binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0019827 stem cell population maintenance
GO:0022008 neurogenesis
GO:0030154 cell differentiation
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0030853 negative regulation of granulocyte differentiation
GO:0034968 histone lysine methylation
GO:0035019 somatic stem cell population maintenance
GO:0043457 regulation of cellular respiration
GO:0043586 tongue development
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0050872 white fat cell differentiation
GO:0050873 brown fat cell differentiation
GO:0060021 palate development
GO:0090336 positive regulation of brown fat cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0016235 aggresome
GO:0017053 transcriptional repressor complex

-  Descriptions from all associated GenBank mRNAs
  AF294278 - Homo sapiens PR-domain-containing protein 16 (PRDM16) mRNA, complete cds.
AB078876 - Homo sapiens mRNA for transcription factor MEL1, complete cds.
AB051462 - Homo sapiens KIAA1675 mRNA for KIAA1675 protein.
BC161614 - Homo sapiens PR domain containing 16, mRNA (cDNA clone MGC:166915 IMAGE:8860117), complete cds.
BC110593 - Homo sapiens cDNA clone IMAGE:40027532, containing frame-shift errors.
BC168363 - Synthetic construct Homo sapiens clone IMAGE:100068259, MGC:195876 PR domain containing 16 (PRDM16) mRNA, encodes complete protein.
AB385494 - Synthetic construct DNA, clone: pF1KA1675, Homo sapiens PRDM16 gene for PR domain zinc finger protein 16, complete cds, without stop codon, in Flexi system.
AK309078 - Homo sapiens cDNA, FLJ99119.
JD479993 - Sequence 461017 from Patent EP1572962.
JD201161 - Sequence 182185 from Patent EP1572962.
JD203886 - Sequence 184910 from Patent EP1572962.
JD333649 - Sequence 314673 from Patent EP1572962.
JD069410 - Sequence 50434 from Patent EP1572962.
JD370826 - Sequence 351850 from Patent EP1572962.
JD186066 - Sequence 167090 from Patent EP1572962.
JD455777 - Sequence 436801 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9HAZ2 (Reactome details) participates in the following event(s):

R-HSA-5634802 MECOM (KMT8E), PRDM16 (KMT8F) methylate lysine-10 of replicative histone H3 (H3K9)
R-HSA-3214841 PKMTs methylate histone lysines
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: A6NHQ8, B1AJP7, B1AJP8, B1AJP9, B1WB48, ENST00000378391.1, ENST00000378391.2, ENST00000378391.3, ENST00000378391.4, ENST00000378391.5, KIAA1675, MEL1, NM_199454, PFM13, PRD16_HUMAN, Q8WYJ9, Q9C0I8, Q9HAZ2, uc001ake.1, uc001ake.2, uc001ake.3, uc001ake.4
UCSC ID: ENST00000378391.6
RefSeq Accession: NM_199454
Protein: Q9HAZ2 (aka PRD16_HUMAN or PRDG_HUMAN)
CCDS: CCDS41236.2, CCDS44048.2

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