Prdm9 PR/SET domain 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Prdm9provided by RGD
Official Full Name: PR/SET domain 9provided by RGD
Primary source: RGD:1305247
See related: EnsemblRapid:ENSRNOG00000021493 AllianceGenome:RGD:1305247
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Prdm7
Summary: 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). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 21.9), Adrenal (RPKM 13.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q12

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (65178666..65198851, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (56505579..56525726, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (57533602..57555155, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Prdm9 deficiency of rat oocytes causes synapsis among non-homologous chromosomes and aneuploidy.
Title: Prdm9 deficiency of rat oocytes causes synapsis among non-homologous chromosomes and aneuploidy.
SET7/9 Recruitment to p21 Gene Promoter Was Increased under Diabetic Conditions
Title: Involvement of Histone Lysine Methylation in p21 Gene Expression in Rat Kidney In Vivo and Rat Mesangial Cells In Vitro under Diabetic Conditions.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables histone H3K36 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
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	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K4 methyltransferase activity	ISS Inferred from Sequence or Structural Similarity 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 homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables recombination hotspot binding	IBA Inferred from Biological aspect of Ancestor more info
enables recombination hotspot binding	ISO Inferred from Sequence Orthology more info
enables recombination hotspot binding	ISS Inferred from Sequence or Structural Similarity more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
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 biological_process	ND No biological Data available more info
involved_in double-strand break repair involved in meiotic recombination	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair involved in meiotic recombination	ISS Inferred from Sequence or Structural Similarity more info
involved_in female gamete generation	ISO Inferred from Sequence Orthology more info
involved_in female gamete generation	ISS Inferred from Sequence or Structural Similarity more info
involved_in homologous chromosome pairing at meiosis	ISO Inferred from Sequence Orthology more info
involved_in homologous chromosome pairing at meiosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in male gamete generation	ISO Inferred from Sequence Orthology more info
involved_in male gamete generation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of meiosis I	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of fertilization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of fertilization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of meiosis I	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase PRDM9

Names: PR domain 9; PR domain containing 7; PR domain containing 9; PR domain zinc finger protein 9; PR domain-containing protein 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; protein-lysine N-methyltransferase PRDM9

NP_001102373.2

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_038940774.1

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_001108903.2 → NP_001102373.2 histone-lysine N-methyltransferase PRDM9

See identical proteins and their annotated locations for NP_001102373.2

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

P0C6Y7

Related

ENSRNOP00000060531.2, ENSRNOT00000066370.5

Conserved Domains (5) summary

smart00349
Location:32 → 89

KRAB; krueppel associated box

COG5048
Location:402 → 748

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

sd00017
Location:576 → 596

ZF_C2H2; C2H2 Zn finger [structural 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

pfam09514
Location:175 → 205

SSXRD; SSXRD motif

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

65178666..65198851 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039084846.2 → XP_038940774.1 histone-lysine N-methyltransferase PRDM9 isoform X1

Conserved Domains (3) summary

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

pfam09514
Location:176 → 205

SSXRD; SSXRD motif

cl02581
Location:32 → 89

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