PRDM9 Gene
protein-coding GIFtS: 52
GCID: GC05P023558
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PR domain containing 9(Previous names: minisatellite binding protein 3, 115kDa, minisatellite...) (Previous symbol: MSBP3)
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Aliases for PRDM9 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 91 2 | | PR Domain Zinc Finger Protein 92 3 | | PFM61 2 3 | | EC 2.1.1.433 8 | | MSBP31 2 | | MEISETZ2 | | ZNF8991 2 | | PRMD92 | | Minisatellite Binding Protein 3 (115kD)1 2 | | Histone-Lysine N-Methyltransferase PRDM92 | | Minisatellite Binding Protein 3, 115kDa1 2 | | PR Domain-Containing Protein 93 |
Export aliases for PRDM9 gene to outside databasesPrevious GC identifers: GC05P023203 GC05P023959 GC05P023522 GC05P023568 |
Summaries for PRDM9 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| Entrez Gene summary for PRDM9: The PR domain is a protein-protein interaction module of about 100 amino acids. PR domain-containing proteins, such asPRDM9, are often involved in transcriptional regulation (Jiang and Huang, 2000 (PubMed 10668202)).(supplied by OMIM,Mar 2008) UniProtKB/Swiss-Prot: PRDM9_HUMAN, Q9NQV7Function: Histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 during meiotic prophase andis essential for proper meiotic progression. Does not have the ability to mono- and dimethylate 'Lys-4' of histone H3.H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role inthe transcriptional activation of genes during early meiotic prophase (By similarity) Gene Wiki entry for PRDM9
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Genomic Views for PRDM9 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_006576.16
Regulatory elements: SABiosciences Regulatory transcription factor binding sites in the PRDM9 gene promoter: HSF1 (long) LCR-F1 PPAR-gamma1 POU2F1 POU2F1b POU2F1a HSF1short POU2F1c PPAR-gamma2 Pax-4a Other transcription factors
Search SABiosciences Chromatin IP Primers for PRDM9
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRDM9 |
Genomic Location: Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 5p14 Ensembl cytogenetic band: 5p14.2 HGNC cytogenetic band: 5p14.2PRDM9 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 GC05P023558: view genomic region
(about GC identifiers)
Start:
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23,507,264 bp from pter |
End:
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23,528,706 bp from pter |
Size:
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21,443 bases |
Orientation:
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plus strand |
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Proteins for PRDM9 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: PRDM9_HUMAN, Q9NQV7 (See
protein sequence)Recommended Name: Histone-lysine N-methyltransferase PRDM9 Size: 894 amino acids; 103376 Da
Subcellular location: Nucleus (By similarity). Chromosome (By similarity)
Sequence caution: Sequence=AAF87242.1; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for PRDM9:4IJD (3D)
 
Secondary accessions: B4DX22 Q27Q50Explore the universe of human proteins at neXtProt for PRDM9: NX_Q9NQV7
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9NQV7 4/5 DME Specific Peptides for PRDM9 (Q9NQV7) (see all 5)
PRDM9 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_064612.2 ENSEMBL proteins: ENSP00000425471 ENSP00000296682 Reactome Protein details: Q9NQV7 Human Recombinant Protein Products:
Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table
PRDM9 for ontologies About GeneDecksing
PRDM9 Antibody Products: Assay Products for PRDM9: |
Protein
Domains / Families for PRDM9 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PRDM9 for domains About GeneDecksing
5/7 InterPro domains/families (see all 7):Graphical View of Domain Structure for InterPro Entry Q9NQV7ProtoNet protein and cluster: Q9NQV7 UniProtKB/Swiss-Prot: PRDM9_HUMAN, Q9NQV7Similarity: Contains 14 C2H2-type zinc fingersSimilarity: Contains 1 KRAB-related domainSimilarity: Contains 1 SET domain |
Function for PRDM9 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: PRDM9_HUMAN, Q9NQV7Function: Histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 during meiotic prophase andis essential for proper meiotic progression. Does not have the ability to mono- and dimethylate 'Lys-4' of histone H3.H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role inthe transcriptional activation of genes during early meiotic prophase (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 2
Clone Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM9 (see all 5) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM9 OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: PRDM9 (NM_020227) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PRDM9 | |  | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat PRDM9  |
In Situ Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM9 |
Gene Ontology (GO): 5/6 molecular function terms (GO ID links to tree view) (see all 6): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0003676 | nucleic acid binding |
-- | -- | | GO:0008270 | zinc ion binding |
IEA | -- | | GO:0010844 | recombination hotspot binding |
IEA | -- | | GO:0018024 | histone-lysine N-methyltransferase activity |
-- | -- | | GO:0042800 | histone methyltransferase activity (H3-K4 specific) |
IEA | -- |
PRDM9 for ontologies About GeneDecksing
3 GenomeRNAi human phenotypes for PRDM9: Animal Models: Mouse knock-out Prdm9tm1Ymat for PRDM9 4 MGI mutant phenotypes (inferred from 3 alleles ) (MGI details for Prdm9):
PRDM9 for phenotypes About GeneDecksing
|
Pathways & Interactions for PRDM9 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
| Unified GeneCards pathways  About this table  See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | Meiotic Synapsis | |
Pathway sources See GeneCards unified pathways Show all pathways
2
Reactome Pathways for PRDM9
PRDM9 for pathways About GeneDecksing
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PRDM9
Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7): About this table
PRDM9 for ontologies About GeneDecksing
|
Drugs & Compounds for PRDM9 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 PRDM9 Search CenterWatch for drugs/clinical trials and news about PRDM9 
|
Transcripts for PRDM9 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 PRDM9 gene: NM_020227.2 Unigene Cluster for PRDM9: PR domain containing 9 Hs.283096 [show with all ESTs]Unigene Representative Sequence: NM_0202272 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000502755 ENST00000296682(uc003jgo.3)
Clone Products: |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM9 (see all 5) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM9 OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: PRDM9 (NM_020227) | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PRDM9 | |  | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat PRDM9  |
Additional cDNA sequence: AF275816.1 AK301776.1 DQ388610.1 1 DOTS entry: DT.91734208 4 AceView cDNA sequences: AF275816 NM_020227 AL704903 AL704902 GeneLoc Exon Structure
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Expression for PRDM9 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
| PRDM9 expression in normal human tissues (normalized intensities) See probesets specificity/sensitivity at GeneAnnot About this imageBioGPS CGAP TAG: GCAGAGGGAG
About this image See PRDM9 Protein Expression from SPIRE MOPED and PaxDB Genevestigator expression for PRDM9
SOURCE GeneReport for Unigene cluster: Hs.283096 SABiosciences Custom PCR Arrays for PRDM9
Primer Products: |  | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PRDM9 Browse OriGene validated miRNA SYBR primer pairs
| |  | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat PRDM9 | |  | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PRDM9 | |  | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM9 | In Situ Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM9 |
Orthologs for PRDM9 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 human and mouse.
Orthologs for PRDM9 gene from 1/7 species (see all 7) About this table
ENSEMBL Gene Tree for PRDM9 (if available) TreeFam Gene Tree for PRDM9 (if available)  |
Paralogs for PRDM9 gene(Paralogs according to
1HomoloGene, 2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68) About This Section
| Paralogs for PRDM9 gene
- PRDM62 PRDM122 PRDM142 PRDM72 PRDM112 PRDM42
18/548 SIMAP similar genes for PRDM9 using alignment to 30 protein entries: PRDM9_HUMAN (see all proteins)
(see all similar genes):PRDM7_V2 PRMD9 ZFS-5 ZFS-4 PRDM7 HKR1 ZNF133 ZNF497 ZNF337 ZNF500 ZNF436 ZNF78L1 ZNF84 HZF36 ZNF418 kr-znf3 ZNF432 DKFZp547L155
PRDM9 for paralogs About GeneDecksing
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Genomic Variants for PRDM9 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 |
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HapMap Linkage Disequilibrium report for PRDM9 (23507264 - 23528706 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions) Database of Genomic Variants (DGV): 2 variations for PRDM9 2 CNVs: 80867 92949 Human Gene Mutation Database (HGMD): PRDM9
 | SABiosciences Cancer Mutation PCR Assays |
|  | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PRDM9 |
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Disorders
/ Diseases for PRDM9 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
|
PRDM9 for disorders About GeneDecksing
OMIM gene information: 609760
OMIM disorders: --
2 diseases for PRDM9: About MalaCardsazoospermia homocysteine 1 disease from the University of Copenhagen DISEASES database for PRDM9:Male infertility Human Genome Epidemiology (HuGE) Navigator: PRDM9 (2 documents) Export disorders for PRDM9 gene to outside databases
|
Publications for PRDM9 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 PRDM9 gene, integrated from 9 sources (see all 17): (articles sorted by number of sources associating them with PRDM9) | |  | Utopia: connect your pdf to the dynamic world of online information |
- The yin-yang of PR-domain family genes in tumorigenesis. (PubMed id 10668202)1, 2, 3 Jiang G.L. and Huang S. (2000)
- Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest. (PubMed id 18941885)1, 2 Miyamoto T....Sengoku K. (2008)
- Two hypervariable minisatellite DNA binding proteins. (PubMed id 2062643)1, 3 Wahls W.P....Moore P.D. (1991)
- Evaluation of PRDM9 variation as a risk factor for rec urrent genomic disorders and chromosomal non-disjunction. (PubMed id 22643917)1 Borel C....Sharp A.J. (2012)
- The case of the fickle fingers: how the PRDM9 zinc fin ger protein specifies meiotic recombination hotspots in humans. (PubMed id 22162947)1 Segurel L....Przeworski M. (2011)
- Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populat ions. (PubMed id 21750151)1 Berg I.L....Jeffreys A.J. (2011)
- PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans. (PubMed id 20818382)1 Berg I.L.... Jeffreys A.J. (2010)
- PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. (PubMed id 20044539)1 Baudat F....de Massy B. (2010)
- Prdm9 controls activation of mammalian recombination hotspots. (PubMed id 20044538)1 Parvanov E.D....Paigen K. (2010)
- Drive against hotspot motifs in primates implicates t he PRDM9 gene in meiotic recombination. (PubMed id 20044541)1 Myers S....Donnelly P. (2010)
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External Searches for PRDM9 gene
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
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Genome Databases showing PRDM9 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PRDM9 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing PRDM9 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 PRDM9 | Pharmacogenomics, SNPs, Pathways |
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| | |
About This Section
| Patent Information for PRDM9 gene: Search GeneIP for patents involving PRDM9
GeneCards and IP: Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Products for PRDM9 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
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| | | | Browse OriGene Antibodies | | OriGene shRNA RFP for PRDM9 | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PRDM9 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PRDM9 | | Browse OriGene Protein Over-expression Lysates | | Browse OriGene Fluorogenic Cell Assay Kits | | OriGene siRNA for PRDM9 | | Browse 3'-UTR reporter clones for miRNA target validation | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM9 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM9 | | 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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 | | PRDM9 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM9 |
|  |  |  | | | Search ThermoFisher Antibodies for PRDM9 |
| | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat PRDM9 |
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