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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; protein homodimerization activity; and protein-lysine N-methyltransferase activity. Predicted to be involved in several processes, including meiosis I; positive regulation of fertilization; and positive regulation of reciprocal meiotic recombination. Predicted to act upstream of or within several processes, including meiotic gene conversion; positive regulation of meiosis I; and positive regulation of transcription by RNA polymerase II. 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

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PRDM9 (PR/SET domain 9)	HGNC	EggNOG, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, PhylomeDB, Treefam
Mus musculus (house mouse):	Prdm9 (PR domain containing 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PRDM9 (PR/SET domain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PRDM9 (PR/SET domain 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	PRDM7 (PR/SET domain 7)	HGNC	Ensembl, OrthoDB, Panther, PhylomeDB
Alliance orthologs ³
Homo sapiens (human):	PRDM7 (PR/SET domain 7)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PhylomeDB)
Homo sapiens (human):	PRDM9 (PR/SET domain 9)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Prdm9 (PR domain containing 9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	prdm9 (PR domain containing 9)	Alliance	DIOPT (InParanoid\|OMA\|OrthoFinder)
Danio rerio (zebrafish):	prdm9 (PR domain containing 9)	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	ZAP1	Alliance	DIOPT (Hieranoid\|SonicParanoid)
Caenorhabditis elegans (roundworm):	set-17	Alliance	DIOPT (Ensembl Compara\|PhylomeDB)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	65,178,666 - 65,198,851 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	65,178,666 - 65,198,737 (-)	Ensembl				GRCr8
mRatBN7.2	1	56,505,579 - 56,525,726 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	56,505,579 - 56,525,652 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	61,354,897 - 61,375,171 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	70,018,454 - 70,038,727 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	63,264,880 - 63,285,154 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	57,533,602 - 57,555,155 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	57,533,577 - 57,555,048 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	58,463,710 - 58,484,066 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	54,444,598 - 54,452,679 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	52,710,859 - 52,730,930 (-)	NCBI		Celera
RGSC_v3.1	1	54,435,819 - 54,455,624 (-)	NCBI
Cytogenetic Map	1	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

hereditary breast ovarian cancer syndrome (ISO)

primary ovarian insufficiency 16 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (EXP)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4,4'-trichlorobiphenyl (ISO)

2,4-dinitrotoluene (EXP)

3-methylcholanthrene (ISO)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

alpha-Zearalanol (EXP)

amphetamine (EXP)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chlorpyrifos (ISO)

epoxiconazole (ISO)

folic acid (ISO)

paracetamol (EXP)

paraquat (EXP)

PCB138 (ISO)

perfluorooctanoic acid (EXP)

sodium arsenite (ISO)

tetrachloromethane (EXP)

thioacetamide (EXP)

titanium dioxide (ISO)

trichloroethene (EXP)

Triptolide (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

chromatin organization (IEA)

chromatin remodeling (IEA)

DNA-templated transcription (IEA)

double-strand break repair involved in meiotic recombination (ISO,ISS)

female gamete generation (ISO,ISS)

homologous chromosome pairing at meiosis (ISO,ISS)

homologous recombination (IEA)

male gamete generation (ISO,ISS)

meiosis I cell cycle process (IEA)

meiotic cell cycle (IEA)

meiotic gene conversion (ISO)

methylation (IEA)

negative regulation of apoptotic process (ISO,ISS)

positive regulation of fertilization (ISO,ISS)

positive regulation of meiosis I (ISO)

positive regulation of reciprocal meiotic recombination (IBA,IEA,ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of DNA-templated transcription (IEA)

regulation of gene expression (IBA)

spermatogenesis (ISO)

Cellular Component

chromatin (ISO)

chromosome (IEA)

nucleoplasm (IEA)

nucleus (IBA,IEA,ISO,ISS)

Molecular Function

DNA binding (IEA)

histone H3K36 methyltransferase activity (IBA,IEA,ISO,ISS)

histone H3K36 trimethyltransferase activity (IEA)

histone H3K4 methyltransferase activity (IBA,IEA,ISO,ISS)

histone H3K4 trimethyltransferase activity (IEA)

histone H3K9 trimethyltransferase activity (IEA)

histone H4K20 monomethyltransferase activity (IEA)

histone H4K20me methyltransferase activity (IEA)

histone methyltransferase activity (IEA)

metal ion binding (IEA)

methyltransferase activity (IEA)

protein binding (ISO)

protein homodimerization activity (ISO,ISS)

protein-lysine N-methyltransferase activity (IEA)

recombination hotspot binding (IBA,IEA,ISO,ISS)

sequence-specific DNA binding (IEA,ISO)

transcription cis-regulatory region binding (ISO,ISS)

transferase activity (IEA)

zinc ion binding (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

histone modification pathway (ISO)

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	PMID:35596034

Genomics

Comparative Map Data

Prdm9
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	65,178,666 - 65,198,851 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	65,178,666 - 65,198,737 (-)	Ensembl				GRCr8
mRatBN7.2	1	56,505,579 - 56,525,726 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	56,505,579 - 56,525,652 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	61,354,897 - 61,375,171 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	70,018,454 - 70,038,727 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	63,264,880 - 63,285,154 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	57,533,602 - 57,555,155 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	57,533,577 - 57,555,048 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	58,463,710 - 58,484,066 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	54,444,598 - 54,452,679 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	52,710,859 - 52,730,930 (-)	NCBI		Celera
RGSC_v3.1	1	54,435,819 - 54,455,624 (-)	NCBI
Cytogenetic Map	1	q12	NCBI

PRDM9
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	23,507,155 - 23,528,093 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	5	23,443,586 - 23,528,093 (+)	Ensembl			hg38	GRCh38
GRCh37	5	23,507,264 - 23,528,202 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	23,543,481 - 23,564,463 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	5	23,558,478 - 23,564,463	NCBI
Celera	5	23,396,917 - 23,417,900 (+)	NCBI		Celera
Cytogenetic Map	5	p14.2	NCBI
HuRef	5	23,474,996 - 23,495,995 (+)	NCBI		HuRef
CHM1_1	5	23,507,746 - 23,528,725 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	5	23,615,322 - 23,635,807 (+)	NCBI		T2T-CHM13v2.0

Prdm9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	15,763,334 - 15,784,636 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	15,763,341 - 15,784,616 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	17	15,543,072 - 15,564,374 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	15,543,079 - 15,564,354 (-)	Ensembl			mm10	GRCm38
MGSCv37	17	15,680,043 - 15,700,287 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	17	15,257,958 - 15,269,069 (-)	NCBI		MGSCv36	mm8
Celera	17	16,328,380 - 16,348,750 (-)	NCBI		Celera
Cytogenetic Map	17	A2	NCBI
cM Map	17	8.95	NCBI

PRDM9
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	4	86,822,013 - 86,909,494 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	5	84,975,693 - 85,063,141 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	5	86,847,131 - 86,856,802 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	5	92,377,523 - 92,395,930 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	92,377,523 - 92,395,486 (-)	Ensembl			panPan2	panpan1.1

PRDM9
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	4	22,902,119 - 22,922,193 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666064	5,471,165 - 5,488,370 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in Prdm9
198 total Variants

miRNA Target Status (No longer updated)

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.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1331732	Srn4	Serum renin concentration QTL 4	4.467		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	1	43457837	87558729	Rat
1357397	Bw41	Body weight QTL 41	4.19	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	29409279	74409279	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	51940904	101229020	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	39728272	132889942	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	46302615	91302615	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	51941022	208479811	Rat
1331792	Rf29	Renal function QTL 29	4.589		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	1	43457837	87558729	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	46302615	91302615	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	43509952	88509952	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	51940904	168768703	Rat
1354643	Foco2	Food consumption QTL 2	7.17	0.0001	eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	1	42122968	87122968	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34184556	172281316	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	46302615	91302615	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34565911	208798288	Rat
1331778	Rf28	Renal function QTL 28	4.66		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	1	43457837	87558729	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	46302615	91302615	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	51511344	153680016	Rat
1578756	Iddm22	Insulin dependent diabetes mellitus QTL 22	2.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	20508326	65508326	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	30708375	87558729	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	34565726	79565726	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	51909206	91302615	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	58769992	103769992	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	46302615	91302615	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	43509952	88509952	Rat
152025249	Scl82	Serum cholesterol level QTL 82	4.77		blood cholesterol amount (VT:0000180)		1	52891222	109116986	Rat
1354599	Bw29	Body weight QTL 29	3.46	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	42122968	87122968	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	46302615	91302615	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	43509952	88509952	Rat
634353	Rends2	Renal damage susceptibility QTL 2		0.05	kidney blood vessel morphology trait (VT:0000530)	organ lesion measurement (CMO:0000677)	1	20656420	65656420	Rat

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	163	91	90	59	91	59	6	354	191	11	142	80	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001108903	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017589463	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017589464	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017589465	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039084846	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC121701	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474033	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000066370 ⟹ ENSRNOP00000060531

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	65,178,666 - 65,198,737 (-)	Ensembl
mRatBN7.2 Ensembl	1	56,505,579 - 56,525,652 (-)	Ensembl
Rnor_6.0 Ensembl	1	57,533,577 - 57,555,048 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000167576 ⟹ ENSRNOP00000101350

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	65,178,666 - 65,198,737 (-)	Ensembl

RefSeq Acc Id:

NM_001108903 ⟹ NP_001102373

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	65,178,666 - 65,198,737 (-)	NCBI
mRatBN7.2	1	56,505,579 - 56,525,652 (-)	NCBI
Rnor_6.0	1	57,533,602 - 57,555,048 (-)	NCBI
Rnor_5.0	1	58,463,710 - 58,484,066 (-)	NCBI
RGSC_v3.4	1	54,444,598 - 54,452,679 (-)	RGD
Celera	1	52,710,859 - 52,730,930 (-)	NCBI

Sequence:

show sequence

CTCCTCAGAAGGACGAACGGCGGCGGTGGCTGCAGAGCCACAGGATTCTGGACCATGAGTACAG
GCGAAACCTTCAAGACCAGCGAGACTTTCTAGGCTCAGCCCGACCATAGGACCCTGATCTTCTC
CAGGGAAATGTCCCGCACCATGAACACCAACAAGCCGGAAGAGAATAGTACTGAAGGAGATGCA
GGGAAACTCGAGTGGAAACCCAAGGTCAAAGATGAGTTCAAAGACATTTCCATATACTTCTCCA
AAGAAGAATGGGCAGAGATGGGAGAGTGGGAGAAAATTCGCTATAGAAATGTGAAAAGGAACTA
TAAAATGCTGATTTCTATAGGTCTCAGAGCCCCTAGACCAGCTTTCATGTGTTACCAAAGGCAG
GCAATCAAGCCCCAGATAAATGACAATGAGGATTCTGATGAGGAATGGACACCAAAGCAGCAAG
TCAGTTCTCCTTGGGTGCCTTTCCGGGTGAAGCACAGTAAACAACAGAAGGAAACACCCAGAAT
GCCATTAAGTGATAAATCTAGTGTGAAGGAAGTATTTGGAATAGAAAATTTGCTGAACACAAGT
GGCTCAGAGCATGCCCAGAAACCAGTGTGCTCCCCTGAAGAAGGGAATACCTCCGGACAGCACT
TTGGAAAAAAACTGAAACTCAGGAGAAAGAATGTTGAAGTGAATAGGTACAGGCTGCGAGAGAG
AAAGGACCTTGCATATGAAGAGGTCAGCGAGCCCCAGGATGATGACTACCTCTATTGTGAGAAG
TGCCAGAATTTCTTCATCGACAGTTGTCCCAACCATGGGCCTCCTGTATTTGTAAAAGACAGTG
TGGTGGACAGGGGGCATCCCAACCACTCAGTCCTCAGTCTGCCCCCTGGGCTGAGAATTGGTCC
ATCAGGCATCCCTGAAGCTGGACTTGGAGTATGGAATGAAGCATCTGATCTACCAGTGGGTCTG
CACTTTGGTCCCTATAAGGGCCAGATTACAGAGGATGAAGAGGCAGCCAACAGTGGATACTCCT
GGCTGATCACCAAGGGAAGAAACTGCTATGAGTATGTGGATGGGCAGGATGAGTCCCAAGCCAA
CTGGATGAGGTATGTGAACTGTGCCCGGGATGACGAAGAGCAGAACCTGGTGGCCTTTCAATAT
CACAGGAAAATCTTCTATCGGACCTGCCGGGTCATCAGGCCAGGTCGCGAGCTTCTGGTCTGGT
ATGGGGATGAGTATGGCCAAGAGCTGGGCATCAAGTGGGGAAGCAAGATGAAGAAAGGATTCAC
AGCAGGAAGAGAACTAAGGACAGAGATTCATCCTTGTTTTTTGTGCTCTTTGGCCTTCTCAAGT
CAGAAATTCCTCACTCAACATGTAGAATGGAATCATCGCACAGAAATCTTCCCAGGAGCATCTG
CAAGGATAAATCCTAAGCCAGGAGATCCCTGTCCAGATCAGCTTCAGGAACATTTTGATTCACA
GAACAAGAATGACAAAGCCAGCAATGAAGTCAAAAGAAAATCCAAACCCAGGCATAAATGGACA
AGACAGAGGATTTCAACAGCCTTTTCCAGTACTCTCAAAGAACAAATGAGATCTGAGGAAAGTA
AGAGAACTGTAGAAGAAGAGCTTAGAACAGGCCAGACAACAAATATAGAGGACACAGCCAAATC
ATTTATTGCATCAGAAACCTCAAGAATTGAAAGGCAATGTGGGCAATGTTTCAGTGATAAGTCA
AATGTCAGTGAGCACCAGAGGACACACACAGGGGAGAAGCCCTACATTTGCAGGGAGTGTGGGC
GGGGCTTTTCACAGAAGTCAGACCTCATCAAGCACCAGAGGACACACACAGAGGAGAAGCCCTA
CATTTGCAGGGAGTGTGGGCGGGGCTTTACACAGAAGTCAGACCTCATCAAGCACCAGAGGACA
CACACAGAGGAGAAGCCCTACATTTGCAGGGAGTGTGGGCGGGGCTTTACACAGAAGTCAGACC
TCATCAAGCACCAGAGGACACACACAGGGGAGAAGCCCTACATTTGCAGGGAGTGTGGGCGGGG
CTTTACACAGAAGTCAGACCTCATCAAGCACCAGAGGACACACACAGAGGAGAAGCCCTACATT
TGCAGGGAGTGTGGGCGGGGCTTTACACAGAAGTCAAGCCTCATCCGGCACCAGAGGACACACA
CAGGGGAGAAGCCCTACATTTGCAGGGAGTGTGGGCTGGGCTTTACACAGAAGTCAAACCTCAT
CCGGCACCTGAGGACACACACAGGGGAGAAGCCCTACATTTGCAGGGAGTGTGGGCTGGGCTTT
ACACGGAAGTCAAACCTCATCCAGCACCAGAGGACACACACAGGGGAGAAGCCCTACATTTGCA
GGGAGTGTGGGCAGGGCCTTACATGGAAGTCAAGCCTCATCCAGCACCAGAGGACACACACAGG
GGAGAAGCCCTACATTTGCAGGGAGTGTGGGCGGGGCTTTACATGGAAGTCAAGCCTCATCCAG
CACCAGAGGACACACACAGTGGAGAAGTAATATCTTTTCAAAAAGAATGAGAAAGCCAATAGCA
ATAAAACCGCATCTCAACAATTACAGAAAGACCACTAAACATCTTCCCACCTGTTCTACTAAAA
CTTCTGAGAAGTCTGATTTTCAAAACTAGAGTATAAAATGATTAAAAAGGAAAATTAAATCCCC

hide sequence

RefSeq Acc Id:

XM_039084846 ⟹ XP_038940774

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	65,189,942 - 65,198,851 (-)	NCBI
mRatBN7.2	1	56,517,359 - 56,525,726 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001102373	(Get FASTA)	NCBI Sequence Viewer
	XP_038940774	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL99813	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000060531
	ENSRNOP00000060531.1
GenBank Protein	P0C6Y7	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001102373 ⟸ NM_001108903

- UniProtKB:

P0C6Y7 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSRTMNTNKPEENSTEGDAGKLEWKPKVKDEFKDISIYFSKEEWAEMGEWEKIRYRNVKRNYKM
LISIGLRAPRPAFMCYQRQAIKPQINDNEDSDEEWTPKQQVSSPWVPFRVKHSKQQKETPRMPL
SDKSSVKEVFGIENLLNTSGSEHAQKPVCSPEEGNTSGQHFGKKLKLRRKNVEVNRYRLRERKD
LAYEEVSEPQDDDYLYCEKCQNFFIDSCPNHGPPVFVKDSVVDRGHPNHSVLSLPPGLRIGPSG
IPEAGLGVWNEASDLPVGLHFGPYKGQITEDEEAANSGYSWLITKGRNCYEYVDGQDESQANWM
RYVNCARDDEEQNLVAFQYHRKIFYRTCRVIRPGRELLVWYGDEYGQELGIKWGSKMKKGFTAG
RELRTEIHPCFLCSLAFSSQKFLTQHVEWNHRTEIFPGASARINPKPGDPCPDQLQEHFDSQNK
NDKASNEVKRKSKPRHKWTRQRISTAFSSTLKEQMRSEESKRTVEEELRTGQTTNIEDTAKSFI
ASETSRIERQCGQCFSDKSNVSEHQRTHTGEKPYICRECGRGFSQKSDLIKHQRTHTEEKPYIC
RECGRGFTQKSDLIKHQRTHTEEKPYICRECGRGFTQKSDLIKHQRTHTGEKPYICRECGRGFT
QKSDLIKHQRTHTEEKPYICRECGRGFTQKSSLIRHQRTHTGEKPYICRECGLGFTQKSNLIRH
LRTHTGEKPYICRECGLGFTRKSNLIQHQRTHTGEKPYICRECGQGLTWKSSLIQHQRTHTGEK
PYICRECGRGFTWKSSLIQHQRTHTVEK

hide sequence

Ensembl Acc Id:

ENSRNOP00000060531 ⟸ ENSRNOT00000066370

RefSeq Acc Id:	XP_038940774 ⟸ XM_039084846
- Peptide Label:	isoform X1

Ensembl Acc Id:

ENSRNOP00000101350 ⟸ ENSRNOT00000167576

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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	57,555,081 - 57,555,141	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305247	AgrOrtholog
BioCyc Gene	G2FUF-61306	BioCyc
Ensembl Genes	ENSRNOG00000021493	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000066370	ENTREZGENE
	ENSRNOT00000066370.4	UniProtKB/Swiss-Prot
Gene3D-CATH	2.170.270.10	UniProtKB/Swiss-Prot
	6.10.140.140	UniProtKB/Swiss-Prot
	Classic Zinc Finger	UniProtKB/Swiss-Prot
InterPro	KRAB	UniProtKB/Swiss-Prot
	KRAB_dom_sf	UniProtKB/Swiss-Prot
	Krueppel-associated_box-rel	UniProtKB/Swiss-Prot
	PDRM9-like_Znf-C2H2	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
PANTHER	TRANSCRIPTIONAL REPRESSOR PROTEIN YY	UniProtKB/Swiss-Prot
	ZINC FINGER PROTEIN 143	UniProtKB/Swiss-Prot
Pfam	KRAB	UniProtKB/Swiss-Prot
	PRDM2_PR	UniProtKB/Swiss-Prot
	SSXRD	UniProtKB/Swiss-Prot
	zf-C2H2	UniProtKB/Swiss-Prot
	zf-C2H2_5	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
RatGTEx	ENSRNOG00000021493	RatGTEx
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	A0ABK0LKE6_RAT	UniProtKB/TrEMBL
	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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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