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Entry version 176 (25 May 2022)
Sequence version 2 (04 Nov 2008)
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Protein

Histone-lysine N-methyltransferase PRDM9

Gene

PRDM9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Histone methyltransferase that sequentially mono-, di-, and tri-methylates both 'Lys-4' (H3K4) and 'Lys-36' (H3K36) of histone H3 to produce respectively trimethylated 'Lys-4' (H3K4me3) and trimethylated 'Lys-36' (H3K36me3) histone H3 and plays a key role in meiotic prophase by determining hotspot localization thereby promoting meiotic recombination (PubMed:24634223, PubMed:24095733, PubMed:26833727, PubMed:27129774).

Also can methylate all four core histones with H3 being the best substrate and the most highly modified (PubMed:24095733, PubMed:24634223, PubMed:26833727).

Is also able, on one hand, to mono and di-methylate H4K20 and on other hand to trimethylate H3K9 with the di-methylated H3K9 as the best substrate (By similarity).

During meiotic prophase, binds specific DNA sequences through its zinc finger domains thereby determining hotspot localization where it promotes local H3K4me3 and H3K36me3 enrichment on the same nucleosomes through its histone methyltransferase activity (PubMed:26833727).

Thereby promotes double-stranded breaks (DSB) formation, at this subset of PRDM9-binding sites, that initiates meiotic recombination for the proper meiotic progression (By similarity).

During meiotic progression hotspot-bound PRDM9 interacts with several complexes; in early leptonema binds CDYL and EHMT2 followed by EWSR1 and CXXC1 by the end of leptonema. EWSR1 joins PRDM9 with the chromosomal axis through REC8 (By similarity).

In this way, controls the DSB repair pathway, pairing of homologous chromosomes and sex body formation (By similarity).

Moreover plays a central role in the transcriptional activation of genes during early meiotic prophase thanks to H3K4me3 and H3K36me3 enrichment that represents a specific tag for epigenetic transcriptional activation (By similarity).

In addition performs automethylation (By similarity).

Acetylation and phosphorylation of histone H3 attenuate or prevent histone H3 methylation (By similarity).

By similarity3 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Inhibited by suramin with an IC50 of 4.1 µM.1 Publication

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

All kinetic experiments are done with 10 mm Tris-HCl, 0.01% Triton X-100, and 10 mm DTT and at pH 8.5.1 Publication
  1. KM=1 µM for H3K4me01 Publication
  2. KM=1 µM for H3K4me11 Publication
  3. KM=3 µM for H3K4me21 Publication
  4. KM=1.5 µM for H3K36me01 Publication
  5. KM=2.4 µM for H3K36me11 Publication
  6. KM=2.5 µM for H3K36me21 Publication
  7. KM=0.7 µM for native H3-H4 tetramer1 Publication
  8. KM=120 µM for S-adenosyl-L-methionine (with H3K4me0 as substrate)1 Publication
  9. KM=170 µM for S-adenosyl-L-methionine (with H3K4me1 as substrate)1 Publication
  10. KM=140 µM for S-adenosyl-L-methionine (with H3K4me2 as substrate)1 Publication
  11. KM=87 µM for S-adenosyl-L-methionine (with H3K36me0 as substrate)1 Publication
  12. KM=130 µM for S-adenosyl-L-methionine (with H3K36me1 as substrate)1 Publication
  13. KM=62 µM for S-adenosyl-L-methionine (with H3K36me2 as substrate)1 Publication
  14. KM=240 µM for S-adenosyl-L-methionine (with native H3-H4 tetramer as substrate)1 Publication

pH dependencei

Optimum pH is 8.5.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi205Zinc 1Combined sources2 Publications1
Metal bindingi208Zinc 1Combined sources2 Publications1
Metal bindingi216Zinc 1Combined sources2 Publications1
Metal bindingi219Zinc 1; via pros nitrogenCombined sources2 Publications1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei291S-adenosyl-L-methionine1 Publication1
Binding sitei357SubstrateBy similarity1
Metal bindingi390Zinc 2Combined sources1 Publication1
Metal bindingi393Zinc 2Combined sources1 Publication1
Metal bindingi406Zinc 2; via tele nitrogenCombined sources1 Publication1
Metal bindingi411Zinc 2; via tele nitrogenCombined sources1 Publication1
Metal bindingi722Zinc 3Combined sources1 Publication1
Metal bindingi725Zinc 3Combined sources1 Publication1
Metal bindingi738Zinc 3; via tele nitrogenCombined sources1 Publication1
Metal bindingi742Zinc 3; via tele nitrogenCombined sources1 Publication1
Metal bindingi750Zinc 4Combined sources1 Publication1
Metal bindingi753Zinc 4Combined sources1 Publication1
Metal bindingi766Zinc 4; via tele nitrogenCombined sources1 Publication1
Metal bindingi770Zinc 4; via tele nitrogenCombined sources1 Publication1
Metal bindingi778Zinc 5Combined sources1 Publication1
Metal bindingi781Zinc 5Combined sources1 Publication1
Metal bindingi794Zinc 5; via tele nitrogenCombined sources1 Publication1
Metal bindingi798Zinc 5; via tele nitrogenCombined sources1 Publication1
Metal bindingi806Zinc 6Combined sources1 Publication1
Metal bindingi809Zinc 6Combined sources1 Publication1
Metal bindingi822Zinc 6; via tele nitrogenCombined sources1 Publication1
Metal bindingi826Zinc 6; via tele nitrogenCombined sources1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri388 – 411C2H2-type 1PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri524 – 546C2H2-type 2; degeneratePROSITE-ProRule annotationAdd BLAST23
Zinc fingeri552 – 574C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri580 – 602C2H2-type 4PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri608 – 630C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri636 – 658C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri664 – 686C2H2-type 7PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri692 – 714C2H2-type 8PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri720 – 742C2H2-type 9PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri748 – 770C2H2-type 10PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri776 – 798C2H2-type 11PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri804 – 826C2H2-type 12PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri832 – 854C2H2-type 13PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri860 – 882C2H2-type 14PROSITE-ProRule annotationAdd BLAST23

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionActivator, Chromatin regulator, DNA-binding, Methyltransferase, Transferase
Biological processMeiosis, Transcription, Transcription regulation
LigandMetal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
2.1.1.359, 2681

Pathway Commons web resource for biological pathway data

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PathwayCommonsi
Q9NQV7

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-HSA-3214841, PKMTs methylate histone lysines
R-HSA-912446, Meiotic recombination

SignaLink: a signaling pathway resource with multi-layered regulatory networks

More...
SignaLinki
Q9NQV7

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Histone-lysine N-methyltransferase PRDM9Curated
Alternative name(s):
PR domain zinc finger protein 9
PR domain-containing protein 9
Protein-lysine N-methyltransferase PRDM9By similarity (EC:2.1.1.-By similarity)
[histone H3]-lysine36 N-trimethyltransferase PRDM9Curated (EC:2.1.1.3591 Publication)
[histone H3]-lysine4 N-trimethyltransferase PRDM9Curated (EC:2.1.1.3543 Publications)
[histone H3]-lysine9 N-trimethyltransferase PRDM9By similarity (EC:2.1.1.355By similarity)
[histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9By similarity (EC:2.1.1.362By similarity)
[histone H4]-lysine20 N-methyltransferase PRDM9By similarity (EC:2.1.1.361By similarity)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:PRDM9Imported
Synonyms:PFM6
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiHomo sapiens (Human)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri9606 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000005640 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 5

Organism-specific databases

Human Gene Nomenclature Database

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HGNCi
HGNC:13994, PRDM9

Online Mendelian Inheritance in Man (OMIM)

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MIMi
609760, gene

neXtProt; the human protein knowledge platform

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neXtProti
NX_Q9NQV7

Eukaryotic Pathogen, Vector and Host Database Resources

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VEuPathDBi
HostDB:ENSG00000164256

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Chromosome, Nucleus

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi199D → Y: Increases histone-lysine N-methyltransferase activity; when associated with D-374. 1 Publication1
Mutagenesisi357Y → S: Loss of histone-lysine N-methyltransferase activity. 1 Publication1
Mutagenesisi374K → D: Increases histone-lysine N-methyltransferase activity; when associated with Y-199. 1 Publication1

Organism-specific databases

DisGeNET

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DisGeNETi
56979

Open Targets

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OpenTargetsi
ENSG00000164256

The Pharmacogenetics and Pharmacogenomics Knowledge Base

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PharmGKBi
PA33721

Miscellaneous databases

Pharos NIH Druggable Genome Knowledgebase

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Pharosi
Q9NQV7, Tbio

Chemistry databases

ChEMBL database of bioactive drug-like small molecules

More...
ChEMBLi
CHEMBL3588737

Genetic variation databases

BioMuta curated single-nucleotide variation and disease association database

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BioMutai
PRDM9

Domain mapping of disease mutations (DMDM)

More...
DMDMi
212276459

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000477661 – 894Histone-lysine N-methyltransferase PRDM9Add BLAST894

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei368N6,N6,N6-trimethyllysine; alternateBy similarity1
Modified residuei368N6-methyllysine; alternateBy similarity1
Modified residuei372N6-methyllysineBy similarity1
Modified residuei374N6-methyllysineBy similarity1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Mono-methylated; automethylated. Tri-methylated; automethylated. Mono-methylation is predominant; automethylation is lower and slower than H3 peptide methylation and is in a highest S-adenosyl-L-methionine concentration-dependent. There are two major sites for automethylation at Lys-368 and Lys-374. Lysines can be simultaneously methylated, such as Lys-368(me3)/Lys-372(me1), Lys-368(me1)/Lys-374(me1) and Lys-368(me1)/Lys-372(me1)/Lys-374(me1). Automethylation is an intramolecular (cis) process.By similarity

Keywords - PTMi

Methylation

Proteomic databases

MassIVE - Mass Spectrometry Interactive Virtual Environment

More...
MassIVEi
Q9NQV7

PaxDb, a database of protein abundance averages across all three domains of life

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PaxDbi
Q9NQV7

PeptideAtlas

More...
PeptideAtlasi
Q9NQV7

PRoteomics IDEntifications database

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PRIDEi
Q9NQV7

ProteomicsDB: a multi-organism proteome resource

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ProteomicsDBi
82198

PTM databases

GlyGen: Computational and Informatics Resources for Glycoscience

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GlyGeni
Q9NQV7, 1 site, 1 O-linked glycan (1 site)

iPTMnet integrated resource for PTMs in systems biology context

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iPTMneti
Q9NQV7

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...
PhosphoSitePlusi
Q9NQV7

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

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Bgeei
ENSG00000164256, Expressed in testis and 63 other tissues

ExpressionAtlas, Differential and Baseline Expression

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ExpressionAtlasi
Q9NQV7, baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

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Genevisiblei
Q9NQV7, HS

Organism-specific databases

Human Protein Atlas

More...
HPAi
ENSG00000164256, Tissue enhanced (brain, epididymis, testis)

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer (PubMed:26833727, PubMed:24095733, Ref. 10).

Interacts with EHMT2 and CDYL; interaction only takes place when PRDM9 is bound to hotspot DNA.

Interacts with CXXC1; this interaction does not link PRDM9-activated recombination hotspot sites with DSB machinery and is not required for the hotspot recognition pathway.

Forms a complex with EWSR1, REC8, SYCP3 and SYCP1; complex formation is dependent of phosphorylated form of REC8 and requires PRDM9 bound to hotspot DNA; EWSR1 joins PRDM9 with the chromosomal axis through REC8 (By similarity).

By similarity3 Publications

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

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BioGRIDi
121297, 7 interactors

Protein interaction database and analysis system

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IntActi
Q9NQV7, 6 interactors

Molecular INTeraction database

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MINTi
Q9NQV7

STRING: functional protein association networks

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STRINGi
9606.ENSP00000296682

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

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RNActi
Q9NQV7, protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1894
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

AlphaFold Protein Structure Database

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AlphaFoldDBi
Q9NQV7

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
Q9NQV7

Database of comparative protein structure models

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ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

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PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini23 – 86KRAB-relatedPROSITE-ProRule annotationAdd BLAST64
Domaini244 – 358SETPROSITE-ProRule annotationAdd BLAST115

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 23DisorderedSequence analysisAdd BLAST23
Regioni143 – 174DisorderedSequence analysisAdd BLAST32
Regioni256 – 258S-adenosyl-L-methionine binding1 Publication3
Regioni288 – 294Substrate bindingBy similarity7
Regioni320 – 321S-adenosyl-L-methionine binding1 Publication2
Regioni408 – 469DisorderedSequence analysisAdd BLAST62
Regioni730 – 820DNA-binding1 PublicationAdd BLAST91

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular type of amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi143 – 165Polar residuesSequence analysisAdd BLAST23
Compositional biasi443 – 468Basic and acidic residuesSequence analysisAdd BLAST26

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The C2H2-type zinc fingers determine the hotspot localization through its binding to specific DNA sequences. Variations in their sequence affect affinity towards DNA-binding motif.By similarity

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri388 – 411C2H2-type 1PROSITE-ProRule annotationAdd BLAST24
Zinc fingeri524 – 546C2H2-type 2; degeneratePROSITE-ProRule annotationAdd BLAST23
Zinc fingeri552 – 574C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri580 – 602C2H2-type 4PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri608 – 630C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri636 – 658C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri664 – 686C2H2-type 7PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri692 – 714C2H2-type 8PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri720 – 742C2H2-type 9PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri748 – 770C2H2-type 10PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri776 – 798C2H2-type 11PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri804 – 826C2H2-type 12PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri832 – 854C2H2-type 13PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri860 – 882C2H2-type 14PROSITE-ProRule annotationAdd BLAST23

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
KOG1721, Eukaryota
KOG2461, Eukaryota

Ensembl GeneTree

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GeneTreei
ENSGT00940000163405

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
CLU_002678_32_0_1

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
Q9NQV7

Identification of Orthologs from Complete Genome Data

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OMAi
RSCNDKT

Database of Orthologous Groups

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OrthoDBi
1318335at2759

Database for complete collections of gene phylogenies

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PhylomeDBi
Q9NQV7

TreeFam database of animal gene trees

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TreeFami
TF338096

Family and domain databases

Conserved Domains Database

More...
CDDi
cd07765, KRAB_A-box, 1 hit
cd19193, PR-SET_PRDM7_9, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.170.270.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001909, KRAB
IPR036051, KRAB_dom_sf
IPR003655, Krueppel-associated_box-rel
IPR044417, PRDM7_9_PR-SET
IPR001214, SET_dom
IPR046341, SET_dom_sf
IPR019041, SSXRD_motif
IPR036236, Znf_C2H2_sf
IPR013087, Znf_C2H2_type

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01352, KRAB, 1 hit
PF00856, SET, 1 hit
PF09514, SSXRD, 1 hit
PF00096, zf-C2H2, 9 hits

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00349, KRAB, 1 hit
SM00355, ZnF_C2H2, 14 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF109640, SSF109640, 1 hit
SSF57667, SSF57667, 7 hits
SSF82199, SSF82199, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50806, KRAB_RELATED, 1 hit
PS50280, SET, 1 hit
PS00028, ZINC_FINGER_C2H2_1, 13 hits
PS50157, ZINC_FINGER_C2H2_2, 14 hits

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequence (1+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

Q9NQV7-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSPEKSQEES PEEDTERTER KPMVKDAFKD ISIYFTKEEW AEMGDWEKTR
60 70 80 90 100
YRNVKRNYNA LITIGLRATR PAFMCHRRQA IKLQVDDTED SDEEWTPRQQ
110 120 130 140 150
VKPPWMALRV EQRKHQKGMP KASFSNESSL KELSRTANLL NASGSEQAQK
160 170 180 190 200
PVSPSGEAST SGQHSRLKLE LRKKETERKM YSLRERKGHA YKEVSEPQDD
210 220 230 240 250
DYLYCEMCQN FFIDSCAAHG PPTFVKDSAV DKGHPNRSAL SLPPGLRIGP
260 270 280 290 300
SGIPQAGLGV WNEASDLPLG LHFGPYEGRI TEDEEAANNG YSWLITKGRN
310 320 330 340 350
CYEYVDGKDK SWANWMRYVN CARDDEEQNL VAFQYHRQIF YRTCRVIRPG
360 370 380 390 400
CELLVWYGDE YGQELGIKWG SKWKKELMAG REPKPEIHPC PSCCLAFSSQ
410 420 430 440 450
KFLSQHVERN HSSQNFPGPS ARKLLQPENP CPGDQNQEQQ YPDPHSRNDK
460 470 480 490 500
TKGQEIKERS KLLNKRTWQR EISRAFSSPP KGQMGSCRVG KRIMEEESRT
510 520 530 540 550
GQKVNPGNTG KLFVGVGISR IAKVKYGECG QGFSVKSDVI THQRTHTGEK
560 570 580 590 600
LYVCRECGRG FSWKSHLLIH QRIHTGEKPY VCRECGRGFS WQSVLLTHQR
610 620 630 640 650
THTGEKPYVC RECGRGFSRQ SVLLTHQRRH TGEKPYVCRE CGRGFSRQSV
660 670 680 690 700
LLTHQRRHTG EKPYVCRECG RGFSWQSVLL THQRTHTGEK PYVCRECGRG
710 720 730 740 750
FSWQSVLLTH QRTHTGEKPY VCRECGRGFS NKSHLLRHQR THTGEKPYVC
760 770 780 790 800
RECGRGFRDK SHLLRHQRTH TGEKPYVCRE CGRGFRDKSN LLSHQRTHTG
810 820 830 840 850
EKPYVCRECG RGFSNKSHLL RHQRTHTGEK PYVCRECGRG FRNKSHLLRH
860 870 880 890
QRTHTGEKPY VCRECGRGFS DRSSLCYHQR THTGEKPYVC REDE
Length:894
Mass (Da):103,376
Last modified:November 4, 2008 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iDE53094C32EFF83B
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A0U1RQY2A0A0U1RQY2_HUMAN
Histone-lysine N-methyltransferase ...
PRDM9
411Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
D6RD68D6RD68_HUMAN
Histone-lysine N-methyltransferase ...
PRDM9
100Annotation score:

Annotation score:1 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAF87242 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti295I → VRRACHF in AAF87242 (PubMed:10668202).Curated1
Sequence conflicti377 – 381Missing in AAF87242 (PubMed:10668202).Curated5

<p>This subsection of the 'Sequence' section provides information on polymorphic variants. If the variant is associated with a disease state, the description of the latter can be found in the <a href="http://www.uniprot.org/manual/involvement%5Fin%5Fdisease">'Involvement in disease'</a> subsection.<p><a href='/help/polymorphism' target='_top'>More...</a></p>Polymorphismi

Several alleles exist depending on both the number of zinc finger C2H2 type domains and their identity (PubMed:26833727). Each allele binds to a specific hotspot set (PubMed:26833727). Variations in the zinc finger C2H2 type domains are associated with significant differences in affinity towards DNA-binding motif (PubMed:26833727). The sequence shown is that of allele B.1 Publication

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural variantiVAR_054417335Y → H Variant of uncertain significance; may be a genetic risk for patients with azoospermia caused by meiotic arrest. 1 Publication1
Natural variantiVAR_082281681T → S in allele A. 1 PublicationCorresponds to variant dbSNP:rs6875787EnsemblClinVar.1
Natural variantiVAR_082282788K → E in allele L9/24; significantly reduces affinity for the DNA-binding motif 5'-GCCTCCCTAGCCACG-3'. 1 PublicationCorresponds to variant dbSNP:rs146505774Ensembl.1
Natural variantiVAR_082283790N → H in allele L20; reduces affinity for the DNA-binding motif 5?-GCCTCCCTAGCCACG-3'. 1 PublicationCorresponds to variant dbSNP:rs77287813EnsemblClinVar.1
Natural variantiVAR_082284814S → R in allele L13; Increases affinity for the DNA-binding motif 5'-GCCTCCCTAGCCACG-3'. 1 PublicationCorresponds to variants dbSNP:rs1445421439 and dbSNP:rs61051796EnsemblEnsembl.1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
DQ388610 mRNA Translation: ABD47939.1
AK301776 mRNA Translation: BAG63234.1
AC025451 Genomic DNA No translation available.
AF275816 mRNA Translation: AAF87242.1 Different initiation.

The Consensus CDS (CCDS) project

More...
CCDSi
CCDS43307.1

NCBI Reference Sequences

More...
RefSeqi
NP_001297143.1, NM_001310214.1
NP_064612.2, NM_020227.3

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENST00000296682.4; ENSP00000296682.4; ENSG00000164256.11

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
56979

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
hsa:56979

Matched Annotation from NCBI and EMBL-EBI (MANE) - Phase one

More...
MANE-Selecti
ENST00000296682.4; ENSP00000296682.4; NM_020227.4; NP_064612.2

UCSC genome browser

More...
UCSCi
uc003jgo.3, human

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ388610 mRNA Translation: ABD47939.1
AK301776 mRNA Translation: BAG63234.1
AC025451 Genomic DNA No translation available.
AF275816 mRNA Translation: AAF87242.1 Different initiation.
CCDSiCCDS43307.1
RefSeqiNP_001297143.1, NM_001310214.1
NP_064612.2, NM_020227.3

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4IJDX-ray2.15A/B195-415[»]
5EGBX-ray1.98A717-858[»]
5EH2X-ray2.05E/F717-858[»]
5EI9X-ray1.92E/F717-858[»]
6NM4X-ray2.58A/B195-385[»]
AlphaFoldDBiQ9NQV7
SMRiQ9NQV7
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi121297, 7 interactors
IntActiQ9NQV7, 6 interactors
MINTiQ9NQV7
STRINGi9606.ENSP00000296682

Chemistry databases

ChEMBLiCHEMBL3588737

PTM databases

GlyGeniQ9NQV7, 1 site, 1 O-linked glycan (1 site)
iPTMnetiQ9NQV7
PhosphoSitePlusiQ9NQV7

Genetic variation databases

BioMutaiPRDM9
DMDMi212276459

Proteomic databases

MassIVEiQ9NQV7
PaxDbiQ9NQV7
PeptideAtlasiQ9NQV7
PRIDEiQ9NQV7
ProteomicsDBi82198

Protocols and materials databases

Antibodypedia a portal for validated antibodies

More...
Antibodypediai
22638, 86 antibodies from 24 providers

The DNASU plasmid repository

More...
DNASUi
56979

Genome annotation databases

EnsembliENST00000296682.4; ENSP00000296682.4; ENSG00000164256.11
GeneIDi56979
KEGGihsa:56979
MANE-SelectiENST00000296682.4; ENSP00000296682.4; NM_020227.4; NP_064612.2
UCSCiuc003jgo.3, human

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
56979
DisGeNETi56979

GeneCards: human genes, protein and diseases

More...
GeneCardsi
PRDM9
HGNCiHGNC:13994, PRDM9
HPAiENSG00000164256, Tissue enhanced (brain, epididymis, testis)
MIMi609760, gene
neXtProtiNX_Q9NQV7
OpenTargetsiENSG00000164256
PharmGKBiPA33721
VEuPathDBiHostDB:ENSG00000164256

GenAtlas: human gene database

More...
GenAtlasi
Search...

Phylogenomic databases

eggNOGiKOG1721, Eukaryota
KOG2461, Eukaryota
GeneTreeiENSGT00940000163405
HOGENOMiCLU_002678_32_0_1
InParanoidiQ9NQV7
OMAiRSCNDKT
OrthoDBi1318335at2759
PhylomeDBiQ9NQV7
TreeFamiTF338096

Enzyme and pathway databases

BRENDAi2.1.1.359, 2681
PathwayCommonsiQ9NQV7
ReactomeiR-HSA-3214841, PKMTs methylate histone lysines
R-HSA-912446, Meiotic recombination
SignaLinkiQ9NQV7

Miscellaneous databases

BioGRID ORCS database of CRISPR phenotype screens

More...
BioGRID-ORCSi
56979, 17 hits in 1068 CRISPR screens

The Gene Wiki collection of pages on human genes and proteins

More...
GeneWikii
PRDM9

Database of phenotypes from RNA interference screens in Drosophila and Homo sapiens

More...
GenomeRNAii
56979
PharosiQ9NQV7, Tbio

Protein Ontology

More...
PROi
PR:Q9NQV7
RNActiQ9NQV7, protein

The Stanford Online Universal Resource for Clones and ESTs

More...
SOURCEi
Search...

Gene expression databases

BgeeiENSG00000164256, Expressed in testis and 63 other tissues
ExpressionAtlasiQ9NQV7, baseline and differential
GenevisibleiQ9NQV7, HS

Family and domain databases

CDDicd07765, KRAB_A-box, 1 hit
cd19193, PR-SET_PRDM7_9, 1 hit
Gene3Di2.170.270.10, 1 hit
InterProiView protein in InterPro
IPR001909, KRAB
IPR036051, KRAB_dom_sf
IPR003655, Krueppel-associated_box-rel
IPR044417, PRDM7_9_PR-SET
IPR001214, SET_dom
IPR046341, SET_dom_sf
IPR019041, SSXRD_motif
IPR036236, Znf_C2H2_sf
IPR013087, Znf_C2H2_type
PfamiView protein in Pfam
PF01352, KRAB, 1 hit
PF00856, SET, 1 hit
PF09514, SSXRD, 1 hit
PF00096, zf-C2H2, 9 hits
SMARTiView protein in SMART
SM00349, KRAB, 1 hit
SM00355, ZnF_C2H2, 14 hits
SUPFAMiSSF109640, SSF109640, 1 hit
SSF57667, SSF57667, 7 hits
SSF82199, SSF82199, 1 hit
PROSITEiView protein in PROSITE
PS50806, KRAB_RELATED, 1 hit
PS50280, SET, 1 hit
PS00028, ZINC_FINGER_C2H2_1, 13 hits
PS50157, ZINC_FINGER_C2H2_2, 14 hits

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPRDM9_HUMAN
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9NQV7
Secondary accession number(s): B4DX22, Q27Q50
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: November 4, 2008
Last modified: May 25, 2022
This is version 176 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with genetic variants
    List of human entries with genetic variants
  3. Human variants curated from literature reports
    Index of human variants curated from literature reports
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families
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