PRDM6 Gene
protein-coding GIFtS: 38
GCID: GC05P122424
|
|
PR domain containing 6
| |
Aliases
for PRDM6 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| PR Domain Containing 61 2 | | Putative Histone-Lysine N-Methyltransferase PRDM62 | | PR Domain Zinc Finger Protein 62 3 | | EC 2.1.1.433 | | PR Domain-Containing Protein 62 3 | | PFM33 | | PR-Domain Zinc Finger Protein 62 | | |
Export aliases for PRDM6 gene to outside databasesPrevious GC identifers: GC05P122055 GC05P122751 GC05P122455 GC05P122480 GC05P122452 GC05U900559 GC05P117612 |
Summaries
for PRDM6 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
UniProtKB/Swiss-Prot: PRDM6_HUMAN, Q9NQX0Function: 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 andmaintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in endothelial cells byinhibiting endothelial cell proliferation, survival and differentiation. It is unclear whether it has histonemethyltransferase activity in vivo. According to some authors, it does not act as a histone methyltransferase byitself and represses transcription by recruiting EHMT2/G9a. According to others, it possesses histonemethyltransferase activity when associated with other proteins and specifically methylates 'Lys-20' of histone H4 invitro. 'Lys-20' methylation represents a specific tag for epigenetic transcriptional repression (By similarity)
|
Genomic Views
for PRDM6 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000005.9 NC_018916.1 NT_034772.6
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the PRDM6 gene promoter:
SRF Sp1 SRF (504 AA) USF2 USF-1:USF-2 C/EBPalpha CHOP-10 USF-1 ARP-1 Pax-4a
Other transcription factors
Search SABiosciences Chromatin IP Primers for PRDM6
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRDM6 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 5q23.2 Ensembl cytogenetic band: 5q23.2 HGNC cytogenetic band: 5q21-q23PRDM6 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 5 GeneLoc Exon Structure GeneLoc location for GC05P122424: view genomic region
(about GC identifiers)
Start:
|
122,424,816 bp from pter |
End:
|
122,523,745 bp from pter |
Size:
|
98,930 bases |
Orientation:
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plus strand |
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Proteins
for PRDM6 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: PRDM6_HUMAN, Q9NQX0 (See
protein sequence)Recommended Name: Putative histone-lysine N-methyltransferase PRDM6 Size: 595 amino acids; 64452 Da
Subunit: Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300 (By similarity)
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=AAF78078.1; Type=Erroneous initiation; Sequence=AAF78079.1; Type=Erroneous initiation;
Secondary accessions: B5MCJ4 Q9NQW9Alternative splicing: 3 isoforms: Q9NQX0-3 Q9NQX0-2 Q9NQX0-1 Explore the universe of human proteins at neXtProt for PRDM6: NX_Q9NQX0
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9NQX0
PRDM6 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_001129711.1
ENSEMBL proteins: ENSP00000384725 ENSP00000390919
Human Recombinant Protein Products:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005634 | nucleus |
IEA | -- |
PRDM6 for ontologies About GeneDecksing
PRDM6 Antibody Products:
Assay Products for PRDM6: |
Protein
Domains /
Families
for PRDM6 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PRDM6 for domains About GeneDecksing
4 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9NQX0ProtoNet protein and cluster: Q9NQX0 UniProtKB/Swiss-Prot: PRDM6_HUMAN, Q9NQX0Similarity: Contains 4 C2H2-type zinc fingersSimilarity: Contains 1 SET domain |
Function
for PRDM6 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: PRDM6_HUMAN, Q9NQX0Function: 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 andmaintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in endothelial cells byinhibiting endothelial cell proliferation, survival and differentiation. It is unclear whether it has histonemethyltransferase activity in vivo. According to some authors, it does not act as a histone methyltransferase byitself and represses transcription by recruiting EHMT2/G9a. According to others, it possesses histonemethyltransferase activity when associated with other proteins and specifically methylates 'Lys-20' of histone H4 invitro. '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]Enzyme Number (IUBMB): EC 2.1.1.431
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM6
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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| |  | GenScript: all cDNA clones in your preferred vector: PRDM6 (NM_001136239) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PRDM6 | |  | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat PRDM6 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM6 |
Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0003676 | nucleic acid binding |
IEA | -- | | GO:0008270 | zinc ion binding |
IEA | -- | | GO:0018024 | histone-lysine N-methyltransferase activity |
IEA | -- | | GO:0042803 | protein homodimerization activity |
IEA | -- |
PRDM6 for ontologies About GeneDecksing
|
Pathways & Interactions
for PRDM6 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PRDM6
Gene Ontology (GO): 4 biological process terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006351 | transcription, DNA-dependent |
IEA | -- | | GO:0022008 | neurogenesis |
IEA | -- | | GO:0045892 | negative regulation of transcription, DNA-dependent |
IEA | -- | | GO:0051151 | negative regulation of smooth muscle cell differentiation |
IEA | -- |
PRDM6 for ontologies About GeneDecksing
|
Drugs & Compounds
for PRDM6 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for PRDM6
Search CenterWatch for drugs/clinical trials and news about PRDM6
|
Transcripts
for PRDM6 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for PRDM6 gene: NM_001136239.1 Unigene Cluster for PRDM6: PR domain containing 6 Hs.135118 [show with all ESTs]Unigene Representative Sequence: NM_0011362394 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000407847(uc003kti.3 uc003ktj.3) ENST00000434521 ENST00000464424
ENST00000427739
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM6 (see all 2)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM6
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: PRDM6 (NM_001136239) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PRDM6 | | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat PRDM6 |
Additional cDNA sequence: AF272898.1 AK297992.1 4 DOTS entries: DT.100743089 DT.106068 DT.70104022 DT.91738989
GeneLoc Exon Structure
4 Alternative Splicing Database (ASD) splice patterns (SP) for PRDM6 About this scheme
| ExUns: | 1 | ^ | 2 | ^ | 3 | ^ | 4a | · | 4b | ^ | 5 | ^ | 6 | ^ | 7a | · | 7b | ^ | 8 | ^ | 9 |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | - | | - | | | | | | | | | | |
| SP3: | | | | | | | | | | | | | - | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for PRDM6
|
Expression
for PRDM6 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| PRDM6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TAAAATGTAC
About this image
See PRDM6 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PRDM6
SOURCE GeneReport for Unigene cluster: Hs.135118
SABiosciences Custom PCR Arrays for PRDM6
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PRDM6
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat PRDM6 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PRDM6 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM6 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM6 |
Orthologs
for PRDM6 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of chordates.
Orthologs for PRDM6 gene from 5/12 species (see all 12) About this table
ENSEMBL Gene Tree for PRDM6 (if available)
TreeFam Gene Tree for PRDM6 (if available) |
Paralogs
for PRDM6 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for PRDM6 gene
- PRDM92 PRDM122 PRDM142 PRDM72 PRDM112 PRDM42
18/48 SIMAP similar genes for PRDM6 using alignment to 2 protein entries: PRDM6_HUMAN (see all proteins)
(see all similar genes):smap-7 kr-znf3 ZNF78L1 ZNF826P HZF16 ZFS-5
ZNF664 ZNF DKFZp434J0650 ZNF697 ZFP41 ZNF808
DKFZp686M04222 DKFZp686N0199 ZFS-2 ZNF22 ZNF702P zf30
PRDM6 for paralogs About GeneDecksing
|
Genomic Variants
for PRDM6 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 5 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for PRDM6 (122424816 - 122523745 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for PRDM6: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PRDM6 |
|
Disorders
/ Diseases
for PRDM6 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
PRDM6 for disorders About GeneDecksing
2  diseases for PRDM6: About MalaCardsintracranial aneurysm homocysteine
Human Genome Epidemiology (HuGE) Navigator: PRDM6 (1 document)
Export disorders for PRDM6 gene to outside databases
|
Publications
for PRDM6 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for PRDM6 gene integrated from 9 sources:
(articles sorted by number of sources associating them with PRDM6) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
- The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (2004)
- The yin-yang of PR-domain family genes in tumorigenesis. (PubMed id 10668202)2 Jiang G.L. and Huang S. (2000)
|
External Searches for PRDM6 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing PRDM6 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PRDM6 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing PRDM6 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for PRDM6 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for PRDM6 gene:
Search GeneIP for patents involving PRDM6
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for PRDM6 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
| | |  | Browse OriGene Antibodies | | OriGene shRNA RFP for PRDM6 | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PRDM6 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PRDM6 | | | Browse OriGene Protein Over-expression Lysates | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for PRDM6 | | OriGene 3'-UTR Clone for PRDM6 | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM6 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM6 | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | Browse OriGene full length recombinant human proteins expressed in human HEK293 cells | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat PRDM6 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PRDM6 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRDM6 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PRDM6 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM6 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PRDM6 |
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| |  |  |  |  | | | | |
 |
 |
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 | | | PRDM6 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM6 |
|  |  |  | | | | Search ThermoFisher Antibodies for PRDM6 |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat PRDM6 |
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