Human Gene PRDM6 (ENST00000407847.5) from GENCODE V41
  Description: Homo sapiens PR/SET domain 6 (PRDM6), mRNA. (from RefSeq NM_001136239)
RefSeq Summary (NM_001136239): The protein encoded by this gene is a transcriptional repressor and a member of the PRDM family. Family members contain a PR domain and multiple zinc-finger domains. The encoded protein is involved in regulation of vascular smooth muscle cells (VSMC) contractile proteins. Mutations in this gene result in patent ductus arteriosus 3 (PDA3). [provided by RefSeq, Apr 2017]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000407847.5
Gencode Gene: ENSG00000061455.11
Transcript (Including UTRs)
   Position: hg38 chr5:123,089,241-123,194,266 Size: 105,026 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr5:123,090,015-123,187,201 Size: 97,187 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: 2022-05-14 09:57:26

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:123,089,241-123,194,266)mRNA (may differ from genome)Protein (595 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Putative histone-lysine N-methyltransferase PRDM6; EC=; AltName: Full=PR domain zinc finger protein 6; AltName: Full=PR domain-containing protein 6;
FUNCTION: Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression. Promotes the transition from differentiated to proliferative smooth muscle by suppressing differentiation and maintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in endothelial cells by inhibiting endothelial cell proliferation, survival and differentiation. It is unclear whether it has histone methyltransferase activity in vivo. According to some authors, it does not act as a histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to others, it possesses histone methyltransferase activity when associated with other proteins and specifically methylates 'Lys-20' of histone H4 in vitro. 'Lys-20' methylation represents a specific tag for epigenetic transcriptional repression (By similarity).
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBUNIT: Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300 (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 4 C2H2-type zinc fingers.
SIMILARITY: Contains 1 SET domain.
SEQUENCE CAUTION: Sequence=AAF78078.1; Type=Erroneous initiation; Sequence=AAF78079.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: PRDM6
Diseases sorted by gene-association score: patent ductus arteriosus 3* (1242), familial patent arterial duct* (247), patent ductus arteriosus (58), chromosome 1p36 deletion syndrome (5), left ventricular noncompaction (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.89 RPKM in Artery - Aorta
Total median expression: 50.40 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 -116.00294-0.395 Picture PostScript Text
3' UTR -1825.507065-0.258 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:
PF00856 - SET domain
PF00096 - Zinc finger, C2H2 type

ModBase Predicted Comparative 3D Structure on Q9NQX0
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:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0022008 neurogenesis
GO:0032259 methylation
GO:0034968 histone lysine methylation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0051151 negative regulation of smooth muscle cell differentiation

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  AK297992 - Homo sapiens cDNA FLJ60025 complete cds, highly similar to Mus musculus PR domain containing 6 (Prdm6), mRNA.
AF272898 - Homo sapiens PR-domain zinc finger protein 6 isoform A (PRDM6) mRNA, partial cds; alternatively spliced.
AF272899 - Homo sapiens PR-domain zinc finger protein 6 isoform B (PRDM6) mRNA, partial cds; alternatively spliced.
JD526182 - Sequence 507206 from Patent EP1572962.
JD453354 - Sequence 434378 from Patent EP1572962.
JD526161 - Sequence 507185 from Patent EP1572962.
JD151866 - Sequence 132890 from Patent EP1572962.
JD480535 - Sequence 461559 from Patent EP1572962.
JD227516 - Sequence 208540 from Patent EP1572962.
JD458585 - Sequence 439609 from Patent EP1572962.
JD407361 - Sequence 388385 from Patent EP1572962.
JD487855 - Sequence 468879 from Patent EP1572962.
JD389922 - Sequence 370946 from Patent EP1572962.
JD471072 - Sequence 452096 from Patent EP1572962.
JD301718 - Sequence 282742 from Patent EP1572962.
JD082228 - Sequence 63252 from Patent EP1572962.
JD477249 - Sequence 458273 from Patent EP1572962.
JD251611 - Sequence 232635 from Patent EP1572962.
JD163198 - Sequence 144222 from Patent EP1572962.
JD396275 - Sequence 377299 from Patent EP1572962.
JD494527 - Sequence 475551 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B5MCJ4, ENST00000407847.1, ENST00000407847.2, ENST00000407847.3, ENST00000407847.4, NM_001136239, PFM3, PRDM6_HUMAN, Q9NQW9, Q9NQX0, uc003kti.1, uc003kti.2, uc003kti.3, uc003kti.4, uc003kti.5
UCSC ID: ENST00000407847.5
RefSeq Accession: NM_001136239
Protein: Q9NQX0 (aka PRDM6_HUMAN or PRD6_HUMAN)
CCDS: CCDS47259.1

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