Prdm9 (PR/SET domain 9) - Rat Genome Database

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Gene: Prdm9 (PR/SET domain 9) Rattus norvegicus
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Symbol: Prdm9
Name: PR/SET domain 9
RGD ID: 1305247
Description: Predicted to enable DNA binding activity; histone-lysine N-methyltransferase activity; and protein homodimerization activity. Predicted to be involved in several processes, including histone lysine methylation; meiosis I; and positive regulation of histone methylation. Predicted to act upstream of or within several processes, including histone methylation; meiotic gene conversion; and positive regulation of meiosis I. Predicted to be located in chromatin. Predicted to be active in nucleus. Orthologous to several human genes including PRDM9 (PR/SET domain 9); PARTICIPATES IN histone modification pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: [histone H3]-lysine36 N-trimethyltransferase PRDM9; [histone H3]-lysine4 N-trimethyltransferase PRDM9; [histone H3]-lysine9 N-trimethyltransferase PRDM9; [histone H4]-lysine20 N-methyltransferase PRDM9; [histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9; histone-lysine N-methyltransferase PRDM9; LOC365155; PR domain 9; PR domain containing 7; PR domain containing 9; PR domain zinc finger protein 9; PR domain-containing protein 9; Prdm7; protein-lysine N-methyltransferase PRDM9
RGD Orthologs
Human
Mouse
Bonobo
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2156,505,579 - 56,525,726 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl156,505,579 - 56,525,652 (-)Ensembl
Rnor_6.0157,533,602 - 57,555,155 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl157,533,577 - 57,555,048 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,463,710 - 58,484,066 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,444,598 - 54,452,679 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,435,819 - 54,455,624 (-)NCBI
Celera152,710,859 - 52,730,930 (-)NCBICelera
Cytogenetic Map1q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cellular_component  (ND)
chromatin  (ISO)
nucleus  (IBA,ISO,ISS)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:16292313   PMID:19074312   PMID:20044538   PMID:20044539   PMID:21750151   PMID:22028627   PMID:24095733   PMID:24151354   PMID:24634223   PMID:24785241   PMID:25894966   PMID:26833727  
PMID:27362481   PMID:27652271   PMID:27932493   PMID:29072575   PMID:29478809  


Genomics

Comparative Map Data
Prdm9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2156,505,579 - 56,525,726 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl156,505,579 - 56,525,652 (-)Ensembl
Rnor_6.0157,533,602 - 57,555,155 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl157,533,577 - 57,555,048 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,463,710 - 58,484,066 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,444,598 - 54,452,679 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,435,819 - 54,455,624 (-)NCBI
Celera152,710,859 - 52,730,930 (-)NCBICelera
Cytogenetic Map1q12NCBI
PRDM9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38523,507,155 - 23,528,093 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl523,443,586 - 23,528,093 (+)EnsemblGRCh38hg38GRCh38
GRCh37523,507,264 - 23,528,202 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36523,543,481 - 23,564,463 (+)NCBINCBI36hg18NCBI36
Build 34523,558,478 - 23,564,463NCBI
Celera523,396,917 - 23,417,900 (+)NCBI
Cytogenetic Map5p14.2NCBI
HuRef523,474,996 - 23,495,995 (+)NCBIHuRef
CHM1_1523,507,746 - 23,528,725 (+)NCBICHM1_1
T2T-CHM13v2.0523,614,868 - 23,635,807 (+)NCBI
Prdm9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391715,763,334 - 15,784,636 (-)NCBIGRCm39mm39
GRCm39 Ensembl1715,763,341 - 15,784,616 (-)Ensembl
GRCm381715,543,072 - 15,564,374 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1715,543,079 - 15,564,354 (-)EnsemblGRCm38mm10GRCm38
MGSCv371715,680,043 - 15,700,287 (-)NCBIGRCm37mm9NCBIm37
MGSCv361715,257,958 - 15,269,069 (-)NCBImm8
Celera1716,328,380 - 16,348,750 (-)NCBICelera
Cytogenetic Map17A2NCBI
PRDM9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1592,377,523 - 92,395,930 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl592,377,523 - 92,395,486 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0586,847,131 - 86,856,802 (-)NCBIMhudiblu_PPA_v0panPan3
PRDM9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1422,902,119 - 22,922,193 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660645,471,165 - 5,488,370 (-)NCBIVero_WHO_p1.0


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:14
Count of miRNA genes:13
Interacting mature miRNAs:14
Transcripts:ENSRNOT00000066370
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4
Low 3 24 51 35 17 35 4 6 64 29 24 11 4
Below cutoff 19 6 6 2 6 4 5 10 6 13 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066370   ⟹   ENSRNOP00000060531
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl156,505,579 - 56,525,652 (-)Ensembl
Rnor_6.0 Ensembl157,533,577 - 57,555,048 (-)Ensembl
RefSeq Acc Id: NM_001108903   ⟹   NP_001102373
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2156,505,579 - 56,525,652 (-)NCBI
Rnor_6.0157,533,602 - 57,555,048 (-)NCBI
Rnor_5.0158,463,710 - 58,484,066 (-)NCBI
RGSC_v3.4154,444,598 - 54,452,679 (-)RGD
Celera152,710,859 - 52,730,930 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039084843   ⟹   XP_038940771
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2156,513,171 - 56,525,726 (-)NCBI
RefSeq Acc Id: XM_039084846   ⟹   XP_038940774
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2156,517,359 - 56,525,726 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001102373 (Get FASTA)   NCBI Sequence Viewer  
  XP_038940771 (Get FASTA)   NCBI Sequence Viewer  
  XP_038940774 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99813 (Get FASTA)   NCBI Sequence Viewer  
  P0C6Y7 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102373   ⟸   NM_001108903
- UniProtKB: P0C6Y7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000060531   ⟸   ENSRNOT00000066370
RefSeq Acc Id: XP_038940771   ⟸   XM_039084843
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940774   ⟸   XM_039084846
- Peptide Label: isoform X2
Protein Domains
KRAB-related   SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0C6Y7-F1-model_v2 AlphaFold P0C6Y7 1-796 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13689647
Promoter ID:EPDNEW_R172
Type:single initiation site
Name:Prdm9_1
Description:PR/SET domain 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0157,555,081 - 57,555,141EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 57533909 57533910 T A snv SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW)
1 57534026 57534027 C T snv SBN/Ygl (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW)
1 57534161 57534162 C A snv ACI/EurMcwi (MCW), FXLE18/Stm (2020), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), LEW/Crl (2019), LEXF1A/Stm (2019), FHL/EurMcwi (MCW), ACI/N (2020), FHH/EurMcwi (2019)
1 57534497 57534498 C A snv LEXF3/Stm (2020)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 58463928 58463929 A G snv KFRS3B/Kyo (KyushuU)
1 58463933 58463934 C T snv COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW)
1 58464134 58464135 C T snv SBH/Ygl (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), IS/Kyo (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZF (KyushuU), ZFDM (KyushuU), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)
1 58464269 58464270 C A snv FHH/EurMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), SBH/Ygl (MCW), SS/JrHsdMcwi (MCW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW)
1 58464437 58464438 C A snv FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 56506138 56506139 C A snv FHH/EurMcwi (2019), ACI/N (2020), LEXF1A/Stm (2019), FXLE18/Stm (2020), LEW/Crl (2019)
1 56506474 56506475 C A snv LEXF3/Stm (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305247 AgrOrtholog
BioCyc Gene G2FUF-61306 BioCyc
Ensembl Genes ENSRNOG00000021493 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000060531 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000066370 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.170.270.10 UniProtKB/Swiss-Prot
InterPro KRAB UniProtKB/Swiss-Prot
  KRAB_dom_sf UniProtKB/Swiss-Prot
  Krueppel-associated_box-rel UniProtKB/Swiss-Prot
  PRDM7_9_PR-SET UniProtKB/Swiss-Prot
  SET_dom UniProtKB/Swiss-Prot
  SET_dom_sf UniProtKB/Swiss-Prot
  SSXRD_motif UniProtKB/Swiss-Prot
  Znf_C2H2_sf UniProtKB/Swiss-Prot
  Znf_C2H2_type UniProtKB/Swiss-Prot
KEGG Report rno:365155 UniProtKB/Swiss-Prot
NCBI Gene 365155 ENTREZGENE
Pfam KRAB UniProtKB/Swiss-Prot
  SET UniProtKB/Swiss-Prot
  SSXRD UniProtKB/Swiss-Prot
  zf-C2H2 UniProtKB/Swiss-Prot
PhenoGen Prdm9 PhenoGen
PROSITE KRAB_RELATED UniProtKB/Swiss-Prot
  SET UniProtKB/Swiss-Prot
  ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot
  ZINC_FINGER_C2H2_2 UniProtKB/Swiss-Prot
SMART KRAB UniProtKB/Swiss-Prot
  SET UniProtKB/Swiss-Prot
  ZnF_C2H2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF109640 UniProtKB/Swiss-Prot
  SSF57667 UniProtKB/Swiss-Prot
  SSF82199 UniProtKB/Swiss-Prot
UniProt P0C6Y7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Prdm9  PR/SET domain 9  Prdm9  PR domain 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-03 Prdm9  PR domain 9  Prdm9  PR domain containing 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Prdm9  PR domain containing 9  Prdm7_predicted  PR domain containing 7 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Prdm7_predicted  PR domain containing 7 (predicted)      Symbol and Name status set to approved 70820 APPROVED