Prdm9 PR domain containing 9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Prdm9provided by MGI
Official Full Name: PR domain containing 9provided by MGI
Primary source: MGI:MGI:2384854
See related: Ensembl:ENSMUSG00000051977 AllianceGenome:MGI:2384854
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Rcr1; Dsbc1; repro7; Meisetz; PRDM9-B; G1-419-29
Summary: Enables DNA binding activity; protein homodimerization activity; and protein-lysine N-methyltransferase activity. Involved in several processes, including male gamete generation; meiosis I; and positive regulation of fertilization. Acts upstream of or within positive regulation of meiotic nuclear division; positive regulation of transcription by RNA polymerase II; and spermatogenesis. Located in chromatin and nucleus. Is expressed in embryo; head; ovary; and testis. Orthologous to several human genes including PRDM9 (PR/SET domain 9). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in stomach adult (RPKM 2.6), spleen adult (RPKM 1.6) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 A2; 17 8.95 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (15763334..15784636, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (15543072..15564374, complement)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Natural variation in the zinc-finger-encoding exon of Prdm9 affects hybrid sterility phenotypes in mice.
Title: Natural variation in the zinc-finger-encoding exon of Prdm9 affects hybrid sterility phenotypes in mice.
Genic and chromosomal components of Prdm9-driven hybrid male sterility in mice (Mus musculus).
Title: Genic and chromosomal components of Prdm9-driven hybrid male sterility in mice (Mus musculus).
Altering the Binding Properties of PRDM9 Partially Restores Fertility across the Species Boundary.
Title: Altering the Binding Properties of PRDM9 Partially Restores Fertility across the Species Boundary.
Differential effects of two catalytic mutations on full-length PRDM9 and its isolated PR/SET domain reveal a case of pseudomodularity.
Title: Differential effects of two catalytic mutations on full-length PRDM9 and its isolated PR/SET domain reveal a case of pseudomodularity.
PRDM9-directed recombination hotspots depleted near meiotically transcribed genes.
Title: PRDM9-directed recombination hotspots depleted near meiotically transcribed genes.
EWSR1 affects PRDM9-dependent histone 3 methylation and provides a link between recombination hotspots and the chromosome axis protein REC8.
Title: EWSR1 affects PRDM9-dependent histone 3 methylation and provides a link between recombination hotspots and the chromosome axis protein REC8.
Meiotic epigenetic factor PRDM9 impacts sperm quality of hybrid mice.
Title: Meiotic epigenetic factor PRDM9 impacts sperm quality of hybrid mice.
Refined spatial temporal epigenomic profiling reveals intrinsic connection between PRDM9-mediated H3K4me3 and the fate of double-stranded breaks.
Title: Refined spatial temporal epigenomic profiling reveals intrinsic connection between PRDM9-mediated H3K4me3 and the fate of double-stranded breaks.
PRDM9 activity depends on HELLS and promotes local 5-hydroxymethylcytosine enrichment.
Title: PRDM9 activity depends on HELLS and promotes local 5-hydroxymethylcytosine enrichment.
Prdm9 Intersubspecific Interactions in Hybrid Male Sterility of House Mouse.
Title: Prdm9 Intersubspecific Interactions in Hybrid Male Sterility of House Mouse.

Submit: New GeneRIF Correction See all GeneRIFs (43)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (2) 1 citation
Endonuclease-mediated (8) 1 citation
Not Applicable (11) 1 citation
QTL (2) 1 citation
Targeted (7) 1 citation

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables histone H3K36 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K36 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36 methyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K36 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 methyltransferase activity	EXP Inferred from Experiment more info	PubMed
enables histone H3K4 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K4 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K4 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K20 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H4K20me methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables recombination hotspot binding	IBA Inferred from Biological aspect of Ancestor more info
enables recombination hotspot binding	IDA Inferred from Direct Assay more info	PubMed
enables recombination hotspot binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables recombination hotspot binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair involved in meiotic recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in female gamete generation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in homologous chromosome pairing at meiosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in male gamete generation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of meiosis I	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within meiotic gene conversion	ISO Inferred from Sequence Orthology more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of fertilization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of meiosis I	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of reciprocal meiotic recombination	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of reciprocal meiotic recombination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of reciprocal meiotic recombination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IC Inferred by Curator more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase PRDM9

Names: PR domain zinc finger protein 9; PR domain-containing protein 9; VPR domain containing 9; [histone H3]-lysine36 N-trimethyltransferase PRDM9; [histone H3]-lysine4 N-trimethyltransferase PRDM9; [histone H3]-lysine9 N-trimethyltransferase PRDM9; [histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9; [histone H4]-lysine20 N-methyltransferase PRDM9; histone H3 lysine-4 methyltransferase; hybrid sterility protein 1; meiosis-induced factor containing a PR/SET domain and zinc-finger motif; protein-lysine N-methyltransferase PRDM9

NP_001348365.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

NP_659058.3

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_006524051.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_017172869.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_036016343.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_036016344.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_036016345.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_036016346.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_036016347.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_036016348.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_036016349.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

XP_036016350.1

EC 2.1.1.354

EC 2.1.1.355

EC 2.1.1.359

EC 2.1.1.361

EC 2.1.1.362

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001361436.1 → NP_001348365.1 histone-lysine N-methyltransferase PRDM9 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) includes a 3' terminal exon that extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

BC012016, CT033750

Consensus CDS

CCDS88997.1

Related

ENSMUSP00000118454.2, ENSMUST00000147532.8

Conserved Domains (2) summary

smart00317
Location:125 → 243

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

pfam09514
Location:50 → 80

SSXRD; SSXRD motif
NM_144809.3 → NP_659058.3 histone-lysine N-methyltransferase PRDM9 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC154378, BX518160, CT033750, HQ704391

Consensus CDS

CCDS49963.2

UniProtKB/Swiss-Prot

B8JJZ8, Q0D2N4, Q96EQ9

Related

ENSMUSP00000156841.2, ENSMUST00000233295.2

Conserved Domains (5) summary

COG5048
Location:535 → 840

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:539 → 559

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam09514
Location:171 → 201

SSXRD; SSXRD motif

cd19193
Location:240 → 368

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

cl02581
Location:28 → 85

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000083.7 Reference GRCm39 C57BL/6J

Range

15763334..15784636 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006523988.4 → XP_006524051.1 histone-lysine N-methyltransferase PRDM9 isoform X4

See identical proteins and their annotated locations for XP_006524051.1

UniProtKB/TrEMBL

E9Q4V2

Conserved Domains (5) summary

COG5048
Location:539 → 844

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:543 → 563

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam09514
Location:175 → 205

SSXRD; SSXRD motif

cd19193
Location:244 → 372

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

cl02581
Location:32 → 89

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
XM_036160452.1 → XP_036016345.1 histone-lysine N-methyltransferase PRDM9 isoform X3

Conserved Domains (5) summary

COG5048
Location:541 → 846

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:545 → 565

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19193
Location:246 → 374

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

pfam09514
Location:181 → 207

SSXRD; SSXRD motif

cl02581
Location:32 → 89

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
XM_036160454.1 → XP_036016347.1 histone-lysine N-methyltransferase PRDM9 isoform X6

Conserved Domains (5) summary

cd07765
Location:32 → 68

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

COG5048
Location:505 → 810

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:509 → 529

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19193
Location:210 → 338

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

pfam09514
Location:145 → 171

SSXRD; SSXRD motif
XM_036160451.1 → XP_036016344.1 histone-lysine N-methyltransferase PRDM9 isoform X3

Conserved Domains (5) summary

COG5048
Location:541 → 846

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:545 → 565

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19193
Location:246 → 374

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

pfam09514
Location:181 → 207

SSXRD; SSXRD motif

cl02581
Location:32 → 89

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
XM_036160455.1 → XP_036016348.1 histone-lysine N-methyltransferase PRDM9 isoform X7

Conserved Domains (4) summary

COG5048
Location:416 → 721

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:420 → 440

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19193
Location:121 → 249

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

pfam09514
Location:56 → 82

SSXRD; SSXRD motif
XM_036160457.1 → XP_036016350.1 histone-lysine N-methyltransferase PRDM9 isoform X8

Conserved Domains (4) summary

COG5048
Location:414 → 719

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:418 → 438

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19193
Location:119 → 247

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

pfam09514
Location:51 → 80

SSXRD; SSXRD motif
XM_036160456.1 → XP_036016349.1 histone-lysine N-methyltransferase PRDM9 isoform X7

Conserved Domains (4) summary

COG5048
Location:416 → 721

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:420 → 440

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19193
Location:121 → 249

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

pfam09514
Location:56 → 82

SSXRD; SSXRD motif
XM_036160453.1 → XP_036016346.1 histone-lysine N-methyltransferase PRDM9 isoform X5

Conserved Domains (5) summary

COG5048
Location:396 → 779

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:550 → 570

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19193
Location:251 → 379

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

pfam00096
Location:772 → 794

zf-C2H2; Zinc finger, C2H2 type

pfam09514
Location:186 → 212

SSXRD; SSXRD motif
XM_017317380.3 → XP_017172869.1 histone-lysine N-methyltransferase PRDM9 isoform X2

Conserved Domains (4) summary

COG5048
Location:544 → 849

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:548 → 568

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam09514
Location:180 → 210

SSXRD; SSXRD motif

cd19193
Location:249 → 377

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
XM_036160450.1 → XP_036016343.1 histone-lysine N-methyltransferase PRDM9 isoform X1

Conserved Domains (4) summary

COG5048
Location:546 → 851

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:550 → 570

ZF_C2H2; C2H2 Zn finger [structural motif]

cd19193
Location:251 → 379

PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins

pfam09514
Location:186 → 212

SSXRD; SSXRD motif