Histone-lysine N-methyltransferase PRDM9

Names and origin

Protein names

Recommended name:
    Histone-lysine N-methyltransferase PRDM9
    EC=2.1.1.43
Alternative name(s):
    PR domain zinc finger protein 9
    PR domain-containing protein 9
    Meiosis-induced factor containing a PR/SET domain and zinc-finger motif
    Hybrid sterility protein 1

Gene names

Name:	Prdm9
Synonyms:	Hst1, Meisetz

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus

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Protein attributes

Sequence length	843 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 during meiotic prophase and is 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 in the transcriptional activation of genes during early meiotic prophase. Ref.4
Catalytic activity	S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
Subcellular location	Nucleus Probable.
Tissue specificity	Specifically expressed in germ cells entering meiotic prophase in female fetal gonads and in postnatal testis. Ref.4
Developmental stage	Specifically expressed during meiotic prophase. Transiently increases in female gonads from E13.5 to E16.5, the time during which meiosis proceeds from pre-meiotic replication to pachytene stages. Its expression is barely detectable in fetal male gonads. In adults, it is expressed in testis, but not in any other tissue tested. Abundance increases from 10 d post partum (dpp) to 18 dpp, during which time the first wave of spermatogenesis proceeds synchronously from pre-leptotene to pachytene stages. Ref.4
Disruption phenotype	Sterility in both sexes due to severe impairment of the double-stranded break repair pathway, deficient pairing of homologous chromosomes and impaired sex body formation. In testis, H3 'Lys-4' trimethylation is attenuated and meiotic gene transcription is altered. Ref.4
Miscellaneous	Represents a speciation gene in mus genus. Prdm9 is one of several genes responsible for hybrid sterility between M.musculus and house mouse. Hybrid sterility is defined as a situation where parental forms, each fertile inter se, produce infertile offspring. Intersubspecific hybrids of house mouse display spermatogenic failures that are due to variations in the Prdm9 gene.
Sequence similarities	Contains 13 C2H2-type zinc fingers. Contains 1 KRAB-related domain. Contains 1 SET domain.

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Ontologies

Keywords
Biological process	Meiosis Transcription Transcription regulation
Cellular component	Chromosomal protein Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat Zinc-finger
Ligand	Metal-binding S-adenosyl-L-methionine Zinc
Molecular function	Activator Chromatin regulator Methyltransferase Transferase
Gene Ontology (GO)
Biological process	histone methylation Ref.4 Inferred from direct assay. Source: MGI meiotic prophase I Ref.4 Inferred from mutant phenotype. Source: MGI positive regulation of transcription from RNA polymerase II promoter Ref.4 Inferred from direct assay. Source: MGI transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chromosome Inferred from electronic annotation. Source: UniProtKB-KW nucleoplasm Ref.4 Inferred by curator. Source: MGI
Molecular function	histone methyltransferase activity (H3-K4 specific) Ref.4 Inferred from direct assay. Source: MGI nucleic acid binding Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q96EQ9-1) Also known as: Meisetz; This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q96EQ9-2) Also known as: Meisetz-S1; The sequence of this isoform differs from the canonical sequence as follows: 382-404: ELRTEIHPCLLCSLAFSSQKFLT → GGHYYDSLKKKEKREFSLRIFIF 405-843: Missing.

Isoform 3 (identifier: Q96EQ9-3) Also known as: Meisetz-S2; The sequence of this isoform differs from the canonical sequence as follows: 382-418: ELRTEIHPCLLCSLAFSSQKFLTQHMEWNHRTEIFPG → DLFIIICKYTVAVFRHTRRGSQILLRMVVSHHVVAGI 419-843: Missing.

Isoform 4 (identifier: Q96EQ9-4) The sequence of this isoform differs from the canonical sequence as follows: 1-121: Missing. 382-404: ELRTEIHPCLLCSLAFSSQKFLT → GGHYYDSLKKKEKREFSLRIFIF 405-843: Missing.

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 843

843

Histone-lysine N-methyltransferase PRDM9

PRO_0000363960

Regions

Domain

23 – 86

64

KRAB-related

Domain

246 – 362

117

SET

Zinc finger

388 – 411

24

C2H2-type 1

Zinc finger

513 – 531

19

C2H2-type 2; degenerate

Zinc finger

537 – 559

23

C2H2-type 3

Zinc finger

565 – 587

23

C2H2-type 4

Zinc finger

593 – 615

23

C2H2-type 5

Zinc finger

621 – 643

23

C2H2-type 6

Zinc finger

649 – 671

23

C2H2-type 7

Zinc finger

677 – 699

23

C2H2-type 8

Zinc finger

705 – 727

23

C2H2-type 9

Zinc finger

733 – 755

23

C2H2-type 10

Zinc finger

761 – 783

23

C2H2-type 11

Zinc finger

789 – 811

23

C2H2-type 12

Zinc finger

817 – 839

23

C2H2-type 13

Natural variations

Alternative sequence

1 – 121

121

Missing in isoform 4.

VSP_036374

Alternative sequence

382 – 418

37

ELRTE…EIFPG → DLFIIICKYTVAVFRHTRRG SQILLRMVVSHHVVAGI in isoform 3.

VSP_036375

Alternative sequence

382 – 404

23

ELRTE…QKFLT → GGHYYDSLKKKEKREFSLRI FIF in isoform 2 and isoform 4.

VSP_036376

Alternative sequence

405 – 843

439

Missing in isoform 2 and isoform 4.

VSP_036377

Alternative sequence

419 – 843

425

Missing in isoform 3.

VSP_036378

Experimental info

Mutagenesis

276

1

Y → F: Abolishes enzyme methyltransferase. Ref.4

Mutagenesis

278

1

G → A: Abolishes enzyme methyltransferase. Ref.4

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Sequences

Sequence		Length	Mass (Da)
Isoform 1 (Meisetz) [UniParc]. Last modified February 10, 2009. Version 2. Checksum: 323DD4F00447D598 Show »	FASTA	843	97,365
10 20 30 40 50 60 MNTNKLEENS PEEDTGKFEW KPKVKDEFKD ISIYFSKEEW AEMGEWEKIR YRNVKRNYKM 70 80 90 100 110 120 LISIGLRAPR PAFMCYQRQA MKPQINDSED SDEEWTPKQQ VSPPWVPFRV KHSKQQKESS 130 140 150 160 170 180 RMPFSGESNV KEGSGIENLL NTSGSEHVQK PVSSLEEGNT SGQHSGKKLK LRKKNVEVKM 190 200 210 220 230 240 YRLRERKGLA YEEVSEPQDD DYLYCEKCQN FFIDSCPNHG PPLFVKDSMV DRGHPNHSVL 250 260 270 280 290 300 SLPPGLRISP SGIPEAGLGV WNEASDLPVG LHFGPYEGQI TEDEEAANSG YSWLITKGRN 310 320 330 340 350 360 CYEYVDGQDE SQANWMRYVN CARDDEEQNL VAFQYHRKIF YRTCRVIRPG CELLVWYGDE 370 380 390 400 410 420 YGQELGIKWG SKMKKGFTAG RELRTEIHPC LLCSLAFSSQ KFLTQHMEWN HRTEIFPGTS 430 440 450 460 470 480 ARINPKPGDP CSDQLQEQHV DSQNKNDKAS NEVKRKSKPR QRISTTFPST LKEQMRSEES 490 500 510 520 530 540 KRTVEELRTG QTTNTEDTVK SFIASEISSI ERQCGQYFSD KSNVNEHQKT HTGEKPYVCR 550 560 570 580 590 600 ECGRGFTQNS HLIQHQRTHT GEKPYVCREC GRGFTQKSDL IKHQRTHTGE KPYVCRECGR 610 620 630 640 650 660 GFTQKSDLIK HQRTHTGEKP YVCRECGRGF TQKSVLIKHQ RTHTGEKPYV CRECGRGFTQ 670 680 690 700 710 720 KSVLIKHQRT HTGEKPYVCR ECGRGFTAKS VLIQHQRTHT GEKPYVCREC GRGFTAKSNL 730 740 750 760 770 780 IQHQRTHTGE KPYVCRECGR GFTAKSVLIQ HQRTHTGEKP YVCRECGRGF TAKSVLIQHQ 790 800 810 820 830 840 RTHTGEKPYV CRECGRGFTQ KSNLIKHQRT HTGEKPYVCR ECGWGFTQKS DLIQHQRTHT REK « Hide
Isoform 2 (Meisetz-S1). Checksum: E8D64C40EFB5EC84 Show »	FASTA	404	46,856
10 20 30 40 50 60 MNTNKLEENS PEEDTGKFEW KPKVKDEFKD ISIYFSKEEW AEMGEWEKIR YRNVKRNYKM 70 80 90 100 110 120 LISIGLRAPR PAFMCYQRQA MKPQINDSED SDEEWTPKQQ VSPPWVPFRV KHSKQQKESS 130 140 150 160 170 180 RMPFSGESNV KEGSGIENLL NTSGSEHVQK PVSSLEEGNT SGQHSGKKLK LRKKNVEVKM 190 200 210 220 230 240 YRLRERKGLA YEEVSEPQDD DYLYCEKCQN FFIDSCPNHG PPLFVKDSMV DRGHPNHSVL 250 260 270 280 290 300 SLPPGLRISP SGIPEAGLGV WNEASDLPVG LHFGPYEGQI TEDEEAANSG YSWLITKGRN 310 320 330 340 350 360 CYEYVDGQDE SQANWMRYVN CARDDEEQNL VAFQYHRKIF YRTCRVIRPG CELLVWYGDE 370 380 390 400 YGQELGIKWG SKMKKGFTAG RGGHYYDSLK KKEKREFSLR IFIF « Hide
Isoform 3 (Meisetz-S2). Checksum: 0EBDF88F535CEE94 Show »	FASTA	418	48,244
10 20 30 40 50 60 MNTNKLEENS PEEDTGKFEW KPKVKDEFKD ISIYFSKEEW AEMGEWEKIR YRNVKRNYKM 70 80 90 100 110 120 LISIGLRAPR PAFMCYQRQA MKPQINDSED SDEEWTPKQQ VSPPWVPFRV KHSKQQKESS 130 140 150 160 170 180 RMPFSGESNV KEGSGIENLL NTSGSEHVQK PVSSLEEGNT SGQHSGKKLK LRKKNVEVKM 190 200 210 220 230 240 YRLRERKGLA YEEVSEPQDD DYLYCEKCQN FFIDSCPNHG PPLFVKDSMV DRGHPNHSVL 250 260 270 280 290 300 SLPPGLRISP SGIPEAGLGV WNEASDLPVG LHFGPYEGQI TEDEEAANSG YSWLITKGRN 310 320 330 340 350 360 CYEYVDGQDE SQANWMRYVN CARDDEEQNL VAFQYHRKIF YRTCRVIRPG CELLVWYGDE 370 380 390 400 410 YGQELGIKWG SKMKKGFTAG RDLFIIICKY TVAVFRHTRR GSQILLRMVV SHHVVAGI « Hide
Isoform 4. Checksum: F4FE5CE36B04C03E Show »	FASTA	283	32,241
10 20 30 40 50 60 MPFSGESNVK EGSGIENLLN TSGSEHVQKP VSSLEEGNTS GQHSGKKLKL RKKNVEVKMY 70 80 90 100 110 120 RLRERKGLAY EEVSEPQDDD YLYCEKCQNF FIDSCPNHGP PLFVKDSMVD RGHPNHSVLS 130 140 150 160 170 180 LPPGLRISPS GIPEAGLGVW NEASDLPVGL HFGPYEGQIT EDEEAANSGY SWLITKGRNC 190 200 210 220 230 240 YEYVDGQDES QANWMRYVNC ARDDEEQNLV AFQYHRKIFY RTCRVIRPGC ELLVWYGDEY 250 260 270 280 GQELGIKWGS KMKKGFTAGR GGHYYDSLKK KEKREFSLRI FIF « Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genomic sequence analysis in the mouse T-complex region." Brathwaite M., Waeltz P., Nagaraja R. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6J.
[2]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. Ponting C.P. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed: 19468303] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6J.
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4). Tissue: Eye.
[4]	"A histone H3 methyltransferase controls epigenetic events required for meiotic prophase." Hayashi K., Yoshida K., Matsui Y. Nature 438:374-378(2005) [PubMed: 16292313] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, ALTERNATIVE SPLICING (ISOFORMS 1; 2 AND 3), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE, MUTAGENESIS OF TYR-276 AND GLY-278.
[5]	"A mouse speciation gene encodes a meiotic histone H3 methyltransferase." Mihola O., Trachtulec Z., Vlcek C., Schimenti J.C., Forejt J. Science 323:373-375(2009) [PubMed: 19074312] [Abstract] Cited for: IDENTIFICATION AS A SPECIATION GENE.
+	Additional computationally mapped references.

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Cross-references

Sequence databases
EMBL GenBank DDBJ	AY294423 Genomic DNA. Translation: AAQ01511.1. AC154378 Genomic DNA. No translation available. CT033750 Genomic DNA. Translation: CAX15894.1. BC012016 mRNA. Translation: AAH12016.1. BC049903 mRNA. Translation: AAH49903.1. Different initiation.
IPI	IPI00808336. IPI00850969. IPI00921630. IPI00921635.
RefSeq	XP_619431.3.
UniGene	Mm.215162
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	Q96EQ9.
Proteomic databases
PRIDE	Q96EQ9.
Genome annotation databases
Ensembl	ENSMUST00000038416; ENSMUSP00000040727; ENSMUSG00000051977; Mus musculus. [Genome view]
GeneID	213389.
UCSC	uc008aos.1. mouse.
Organism-specific databases
CTD	213389.
MGI	MGI:2384854. Prdm9.
Phylogenomic databases
eggNOG	roNOG16471.
HOVERGEN	Q96EQ9.
Gene expression databases
ArrayExpress	Q96EQ9.
Bgee	Q96EQ9.
Genevestigator	Q96EQ9.
Family and domain databases
InterPro	IPR001909. Krueppel-associated_box. IPR003655. Krueppel-associated_box-rel. IPR001214. SET_dom. IPR019041. SSXRD_motif. IPR007087. Znf_C2H2. IPR015880. Znf_C2H2-like. IPR013087. Znf_C2H2/integrase_DNA-bd. [Graphical view]
Gene3D	G3DSA:3.30.160.60. Znf_C2H2/integrase_DNA-bd. 11 hits.
Pfam	PF01352. KRAB. 1 hit. PF09514. SSXRD. 1 hit. PF00096. zf-C2H2. 11 hits. [Graphical view]
SMART	SM00349. KRAB. 1 hit. SM00317. SET. 1 hit. SM00355. ZnF_C2H2. 13 hits. [Graphical view]
PROSITE	PS50806. KRAB_RELATED. 1 hit. PS50280. SET. 1 hit. PS00028. ZINC_FINGER_C2H2_1. 12 hits. PS50157. ZINC_FINGER_C2H2_2. 12 hits. [Graphical view]
ProtoNet	Search...
Other Resources
SOURCE	Search...

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Entry information

Entry name

PRDM9_MOUSE

Accession

Primary (citable) accession number: Q96EQ9
Secondary accession number(s): B8JJZ8, Q0D2N4

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 10, 2009
Last sequence update:	February 10, 2009
Last modified:	February 9, 2010
This is version 63 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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Relevant documents

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Molecule processing

Regions

Natural variations

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents