PRDM6 Gene (Protein Coding)

PR/SET Domain 6

GC05P123089
GIFtS:
40
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] See more...

Aliases for PRDM6 Gene

Aliases for PRDM6 Gene

  • PR/SET Domain 6 2 3 5
  • Putative Histone-Lysine N-Methyltransferase PRDM6 3 4
  • PR Domain-Containing Protein 6 3 4
  • PR Domain Containing 6 2 3
  • PR Domain 6 2 3
  • KMT8C 2 3
  • PRISM 2 3
  • PR-Domain Zinc Finger Protein 6 3
  • PR Domain Zinc Finger Protein 6 4
  • EC 2.1.1.361 4
  • PRDM6 5
  • PDA3 3
  • PFM3 4

External Ids for PRDM6 Gene

Previous GeneCards Identifiers for PRDM6 Gene

  • GC05P122055
  • GC05P122751
  • GC05P122455
  • GC05P122480
  • GC05P122452
  • GC05U900559
  • GC05P117612
  • GC05P122424
  • GC05P123035

Summaries for PRDM6 Gene

Entrez Gene Summary for PRDM6 Gene

  • 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]

GeneCards Summary for PRDM6 Gene

PRDM6 (PR/SET Domain 6) is a Protein Coding gene. Diseases associated with PRDM6 include Patent Ductus Arteriosus 3 and Familial Patent Arterial Duct. Among its related pathways are Lysine degradation and Metabolism. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and histone-lysine N-methyltransferase activity. An important paralog of this gene is PRDM10.

UniProtKB/Swiss-Prot Summary for PRDM6 Gene

  • 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.

Additional gene information for PRDM6 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM6 Gene

Genomics for PRDM6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PRDM6 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRDM6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRDM6

Top Transcription factor binding sites by QIAGEN in the PRDM6 gene promoter:
  • ARP-1
  • C/EBPalpha
  • CHOP-10
  • Pax-4a
  • Sp1
  • SRF
  • SRF (504 AA)
  • USF-1
  • USF-1:USF-2
  • USF2

Genomic Locations for PRDM6 Gene

Latest Assembly
chr5:123,089,148-123,194,266
(GRCh38/hg38)
Size:
105,119 bases
Orientation:
Plus strand

Previous Assembly
chr5:122,424,936-122,529,960
(GRCh37/hg19 by Entrez Gene)
Size:
105,025 bases
Orientation:
Plus strand

chr5:122,424,816-122,529,960
(GRCh37/hg19 by Ensembl)
Size:
105,145 bases
Orientation:
Plus strand

Genomic View for PRDM6 Gene

Genes around PRDM6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM6 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PRDM6 Gene

Proteins for PRDM6 Gene

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  • Protein details for PRDM6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQX0-PRDM6_HUMAN
    Recommended name:
    Putative histone-lysine N-methyltransferase PRDM6
    Protein Accession:
    Q9NQX0
    Secondary Accessions:
    • B5MCJ4
    • Q9NQW9

    Protein attributes for PRDM6 Gene

    Size:
    595 amino acids
    Molecular mass:
    64452 Da
    Quaternary structure:
    • Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300.
    SequenceCaution:
    • Sequence=AAF78078.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAF78079.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PRDM6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM6 Gene

Protein Expression for PRDM6 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PRDM6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PRDM6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PRDM6 Gene

Domains & Families for PRDM6 Gene

Gene Families for PRDM6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for PRDM6 Gene

InterPro:

Suggested Antigen Peptide Sequences for PRDM6 Gene

GenScript: Design optimal peptide antigens:
  • PR domain-containing protein 6 (PRDM6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NQX0

UniProtKB/Swiss-Prot:

PRDM6_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with PRDM6: view

Function for PRDM6 Gene

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  6. Cell Lines for research

Molecular function for PRDM6 Gene

UniProtKB/Swiss-Prot 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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60344, Rhea:RHEA-COMP:15554, Rhea:RHEA-COMP:15555, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.361; Evidence={ECO:0000250|UniProtKB:Q3UZD5};.

Enzyme Numbers (IUBMB) for PRDM6 Gene

Phenotypes From GWAS Catalog for PRDM6 Gene

Gene Ontology (GO) - Molecular Function for PRDM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0042802 identical protein binding IEA,IPI 32296183
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PRDM6: view
genes like me logo Genes that share phenotypes with PRDM6: view

Human Phenotype Ontology for PRDM6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PRDM6 Gene

MGI Knock Outs for PRDM6:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM6

No data available for Transcription Factor Targets and HOMER Transcription for PRDM6 Gene

Localization for PRDM6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM6 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PRDM6 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRDM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with PRDM6: view

Pathways & Interactions for PRDM6 Gene

PathCards logo

SuperPathways for PRDM6 Gene

SuperPathway Contained pathways
1 Lysine degradation
Lysine degradation
-
2 Metabolism
Metabolic pathways
.40
genes like me logo Genes that share pathways with PRDM6: view

Pathways by source for PRDM6 Gene

2 KEGG pathways for PRDM6 Gene

Gene Ontology (GO) - Biological Process for PRDM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 16537907
GO:0006325 chromatin organization IEA --
GO:0010468 regulation of gene expression IBA 21873635
GO:0022008 neurogenesis IEA --
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with PRDM6: view

No data available for SIGNOR curated interactions for PRDM6 Gene

Drugs & Compounds for PRDM6 Gene

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(1) Drugs for PRDM6 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for PRDM6 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-Amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
 485-80-3
genes like me logo Genes that share compounds with PRDM6: view

Transcripts for PRDM6 Gene

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mRNA/cDNA for PRDM6 Gene

1 REFSEQ mRNAs :
3 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM6

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM6 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9
SP1:
SP2: - -
SP3: -
SP4:

Relevant External Links for PRDM6 Gene

GeneLoc Exon Structure for
PRDM6

Expression for PRDM6 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRDM6 Gene

mRNA expression in normal human tissues for PRDM6 Gene
mRNA expression by BioGPS for PRDM6 GenemRNA expression by GTEx for PRDM6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PRDM6 Gene

This gene is overexpressed in Artery - Aorta (x12.0), Bladder (x7.4), Artery - Tibial (x5.6), and Artery - Coronary (x4.7).

Protein differential expression in normal tissues from HIPED for PRDM6 Gene

This gene is overexpressed in Cerebrospinal fluid (43.5) and Heart (25.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PRDM6 Gene



Protein tissue co-expression partners for PRDM6 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRDM6

SOURCE GeneReport for Unigene cluster for PRDM6 Gene:

Hs.135118

Evidence on tissue expression from TISSUES for PRDM6 Gene

  • Heart(2.7)
genes like me logo Genes that share expression patterns with PRDM6: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM6 Gene

Orthologs for PRDM6 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM6 Gene

Organism Taxonomy Gene Similarity Type Details
Platypus
(Ornithorhynchus anatinus)
 Mammalia PRDM6 30
  • 99 (a)
 OneToOne
Chimpanzee
(Pan troglodytes)
 Mammalia PRDM6 29 30
  • 97.7 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PRDM6 29 30
  • 92.82 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PRDM6 29 30
  • 91.71 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Prdm6 29
  • 88.89 (n)
Mouse
(Mus musculus)
 Mammalia Prdm6 29 16 30
  • 87.16 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia PRDM6 30
  • 87 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PRDM6 29 30
  • 82.16 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PRDM6 30
  • 81 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia prdm6 29
  • 79.77 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.12311 29
Zebrafish
(Danio rerio)
 Actinopterygii prdm6 30
  • 91 (a)
 OneToMany
PRDM6 (2 of 2) 30
  • 87 (a)
 OneToMany
LOC101886516 29
  • 75.24 (n)
Worm
(Caenorhabditis elegans)
 Secernentea set-17 30
  • 17 (a)
 OneToMany
Species where no ortholog for PRDM6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)

Evolution for PRDM6 Gene

ENSEMBL:
Gene Tree for PRDM6 (if available)
TreeFam:
Gene Tree for PRDM6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM6: view image
Alliance of Genome Resources:
Additional Orthologs for PRDM6

Paralogs for PRDM6 Gene

Paralogs for PRDM6 Gene

(45) SIMAP similar genes for PRDM6 Gene using alignment to 2 proteins:

  • PRDM6_HUMAN
  • H7BZR2_HUMAN
genes like me logo Genes that share paralogs with PRDM6: view

Variants for PRDM6 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRDM6 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
1031874 Uncertain Significance: Patent ductus arteriosus 3 123,187,194(+) T/G
NM_001136239.4(PRDM6):c.1781T>G (p.Val594Gly) 		MISSENSE
992789 Uncertain Significance: Heart, malformation of 123,159,516(+) C/T
NM_001136239.4(PRDM6):c.1031C>T (p.Ser344Leu) 		MISSENSE
rs70988558 Benign: not provided 123,090,276(+) A/ACCTCCGCCT
NM_001136239.4(PRDM6):c.268_276GCCTCCTCC[3] (p.90_92ASS[3]) 		NON_CODING_TRANSCRIPT_VARIANT,INFRAME_INSERTION
rs768810414 Benign: not provided 123,090,181(+) C/CG
NM_001136239.4(PRDM6):c.167_168insG (p.Pro58fs) 		FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT
rs879253872 Pathogenic: Patent ductus arteriosus 3. Patent ductus arteriosus 3 (PDA3) [MIM:617039] 123,170,997(+) A/Gp.Gln462Arg
NM_001136239.4(PRDM6):c.1385A>G (p.Gln462Arg) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PRDM6 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PRDM6 Gene

Variant ID Type Subtype PubMed ID
esv2730710 CNV deletion 23290073
esv2730712 CNV deletion 23290073
esv2730713 CNV deletion 23290073
esv3575879 CNV gain 25503493
esv3575880 CNV gain 25503493
nsv1016658 CNV loss 25217958
nsv1017500 CNV loss 25217958
nsv4979 CNV insertion 18451855
nsv520349 CNV loss 19592680
nsv950128 CNV deletion 24416366

Variation tolerance for PRDM6 Gene

Gene Damage Index Score: 12.09; 93.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM6 Gene

Human Gene Mutation Database (HGMD)
PRDM6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM6
Leiden Open Variation Database (LOVD)
PRDM6

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM6 Gene

Disorders for PRDM6 Gene

MalaCards: The human disease database

(6) MalaCards diseases for PRDM6 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search PRDM6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PRDM6_HUMAN
  • Patent ductus arteriosus 3 (PDA3) [MIM:617039]: A congenital heart defect characterized by the persistent opening of fetal ductus arteriosus that fails to close after birth. Fetal ductus arteriosus connects the pulmonary artery to the descending aorta, allowing unoxygenated blood to bypass the lung and flow to the placenta. Normally, the ductus occludes shortly after birth. {ECO:0000269 PubMed:27181681}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for PRDM6

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PRDM6: view

No data available for Genatlas for PRDM6 Gene

Publications for PRDM6 Gene

  1. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. (PMID: 27181681) Li N … Mani A (American journal of human genetics 2016) 3 4 72
  2. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. (PMID: 27716515) Li N … Mani A (American journal of human genetics 2016) 2 3
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  4. PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. (PMID: 16537907) Davis CA … Olson EN (Molecular and cellular biology 2006) 2 3
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

ExternalLinks

View latest publications for PRDM6 gene in Mastermind

Products for PRDM6 Gene

  • Addgene plasmids for PRDM6

Sources for PRDM6 Gene