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Reviewed, UniProtKB/Swiss-Prot P0C6Y7 (PRDM9_RAT)

Last modified November 3, 2009. Version 9. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended 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
Gene names
Name: Prdm9
OrganismRattus norvegicus (Rat)
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

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Protein attributes

Sequence length796 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceInferred from homology.

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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 By similarity.

Catalytic activity

S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N(6)-methyl-L-lysine.

Subcellular location

Nucleus By similarity.

Sequence similarities

Contains 11 C2H2-type zinc fingers.

Contains 1 KRAB-related domain.

Contains 1 SET domain.

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Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P0C6Y7-1)

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: P0C6Y7-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-125: Missing.
     386-408: ELRTEIHPCFLCSLAFSSQKFLT → GGYHYDSLKEKEKMDFSLRIFIF
     409-796: Missing.

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 796796Histone-lysine N-methyltransferase PRDM9
PRO_0000363961

Regions

Domain27 – 9064KRAB-related
Domain250 – 366117SET
Zinc finger392 – 41524C2H2-type 1
Zinc finger522 – 54019C2H2-type 2; degenerate
Zinc finger546 – 56823C2H2-type 3
Zinc finger574 – 59623C2H2-type 4
Zinc finger602 – 62423C2H2-type 5
Zinc finger630 – 65223C2H2-type 6
Zinc finger658 – 68023C2H2-type 7
Zinc finger686 – 70823C2H2-type 8
Zinc finger714 – 73623C2H2-type 9
Zinc finger742 – 76423C2H2-type 10
Zinc finger770 – 79223C2H2-type 11

Natural variations

Alternative sequence1 – 125125Missing in isoform 2.
VSP_036379
Alternative sequence386 – 40823ELRTE…QKFLT → GGYHYDSLKEKEKMDFSLRI FIF in isoform 2.
VSP_036380
Alternative sequence409 – 796388Missing in isoform 2.
VSP_036381

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Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified February 10, 2009. Version 1.
Checksum: 7FB5104B805F87D9

FASTA79692,579
        10         20         30         40         50         60 
MSRTMNTNKP EENSTEGDAG KLEWKPKVKD EFKDISIYFS KEEWAEMGEW EKIRYRNVKR 

        70         80         90        100        110        120 
NYKMLISIGL RAPRPAFMCY QRQAIKPQIN DNEDSDEEWT PKQQVSSPWV PFRVKHSKQQ 

       130        140        150        160        170        180 
KETPRMPLSD KSSVKEVFGI ENLLNTSGSE HAQKPVCSPE EGNTSGQHFG KKLKLRRKNV 

       190        200        210        220        230        240 
EVNRYRLRER KDLAYEEVSE PQDDDYLYCE KCQNFFIDSC PNHGPPVFVK DSVVDRGHPN 

       250        260        270        280        290        300 
HSVLSLPPGL RIGPSGIPEA GLGVWNEASD LPVGLHFGPY KGQITEDEEA ANSGYSWLIT 

       310        320        330        340        350        360 
KGRNCYEYVD GQDESQANWM RYVNCARDDE EQNLVAFQYH RKIFYRTCRV IRPGRELLVW 

       370        380        390        400        410        420 
YGDEYGQELG IKWGSKMKKG FTAGRELRTE IHPCFLCSLA FSSQKFLTQH VEWNHRTEIF 

       430        440        450        460        470        480 
PGASARINPK PGDPCPDQLQ EHFDSQNKND KASNEVKRKS KPRHKWTRQR ISTAFSSTLK 

       490        500        510        520        530        540 
EQMRSEESKR TVEEELRTGQ TTNIEDTAKS FIASETSRIE RQCGQCFSDK SNVSEHQRTH 

       550        560        570        580        590        600 
TGEKPYICRE CGRGFSQKSD LIKHQRTHTE EKPYICRECG RGFTQKSDLI KHQRTHTEEK 

       610        620        630        640        650        660 
PYICRECGRG FTQKSDLIKH QRTHTGEKPY ICRECGRGFT QKSDLIKHQR THTEEKPYIC 

       670        680        690        700        710        720 
RECGRGFTQK SSLIRHQRTH TGEKPYICRE CGLGFTQKSN LIRHLRTHTG EKPYICRECG 

       730        740        750        760        770        780 
LGFTRKSNLI QHQRTHTGEK PYICRECGQG LTWKSSLIQH QRTHTGEKPY ICRECGRGFT 

       790 
WKSSLIQHQR THTVEK

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Isoform 2.

Checksum: AE2D191116075BA2
Show »

FASTA28332,406

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References

[1]Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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Cross-references

Sequence databases

CH474033 Genomic DNA. Translation: EDL99813.1.
IPIIPI00563276.
IPI00921669.
RefSeqNP_001102373.1.

3D structure databases

ModBaseSearch...

Genome annotation databases

GeneID365155.
KEGGrno:365155.

Organism-specific databases

RGD1305247. Prdm9.

Phylogenomic databases

OMADGQDESQ.

Gene expression databases

GenevestigatorP0C6Y7.

Family and domain databases

InterProIPR001909. Krueppel-associated_box.
IPR003655. Krueppel-associated_box-rel.
IPR001214. SET.
IPR019041. SSXRD_motif.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
Gene3DG3DSA:3.30.160.60. Znf_C2H2/integrase_DNA-bd. 9 hits.
PfamPF01352. KRAB. 1 hit.
PF09514. SSXRD. 1 hit.
PF00096. zf-C2H2. 9 hits.
[Graphical view]
SMARTSM00349. KRAB. 1 hit.
SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 11 hits.
[Graphical view]
PROSITEPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 10 hits.
PS50157. ZINC_FINGER_C2H2_2. 10 hits.
[Graphical view]
ProtoNetSearch...

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Entry information

Entry namePRDM9_RAT
AccessionPrimary (citable) accession number: P0C6Y7
Entry history
Integrated into UniProtKB/Swiss-Prot: February 10, 2009
Last sequence update: February 10, 2009
Last modified: November 3, 2009
This is version 9 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)

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Relevant documents

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Alternative products · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents