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UniProtKB - Q96EQ9 (PRDM9_MOUSE)

Entry version 149 (12 Aug 2020)
Sequence version 2 (10 Feb 2009)
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Protein

Histone-lysine N-methyltransferase PRDM9

Gene

Prdm9

Organism
Mus musculus (Mouse)
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:16292313, PubMed:24095733, PubMed:27362481, PubMed:24785241, PubMed:29478809). Also can methylate all four core histones with H3 being the best substrate and the most highly modified (PubMed:24785241, PubMed:27362481). 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 (PubMed:24785241, PubMed:27362481). 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:22028627, PubMed:27362481, PubMed:29478809). Thereby promotes double-stranded breaks (DSB) formation, at this subset of PRDM9-binding sites, that initiates meiotic recombination for the proper meiotic progression (PubMed:16292313, PubMed:29478809). 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 (PubMed:27932493). EWSR1 joins PRDM9 with the chromosomal axis through REC8 (PubMed:27932493). In this way, controls the DSB repair pathway, pairing of homologous chromosomes and sex body formation (PubMed:25894966, PubMed:16292313). 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 (PubMed:16292313). In addition performs automethylation (PubMed:28126738). Acetylation and phosphorylation of histone H3 attenuate or prevent histone H3 methylation (PubMed:27362481).9 Publications

Miscellaneous

Represents a speciation gene in mus genus. Prdm9 is one of several genes responsible for hybrid sterility between M.musculus and house mouse (PubMed:19074312). Hybrid sterility is defined as a situation where parental forms, each fertile inter se, produce infertile offspring (PubMed:19074312). Intersubspecific hybrids of house mouse display spermatogenic failures that are due to variations in the Prdm9 gene (PubMed:19074312).1 Publication

Caution

Firstly described as not catalyzing the monomethylation of unmethylated H3 peptide (PubMed:16292313). However other in vitro experiments described that can also methylate unmodified 'Lys-4' of histone H3 (PubMed:24095733, PubMed:24785241, PubMed:27362481).4 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 '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

  1. KM=0.17 µM for histone octamer1 Publication
  2. KM=0.19 µM for H3 protein1 Publication
  3. KM=3.21 µM for H3 peptide 1-211 Publication
  4. KM=5.47 µM for H4 peptide 1-361 Publication
  5. KM=22.29 µM for S-adenosyl-L-methionine (with histone octamer as substrate)1 Publication
  6. KM=19.01 µM for S-adenosyl-L-methionine (with H3 protein as substrate)1 Publication
  7. KM=8.23 µM for S-adenosyl-L-methionine (with H3 peptide 1-21 as substrate)1 Publication
  8. KM=81.66 µM for S-adenosyl-L-methionine (with H4 peptide 1-36 as substrate)1 Publication
  9. KM=34.7 µM for automethylation1 Publication
  10. KM=8.23 µM for H3 peptide1 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 sources1 Publication1
    Metal bindingi208Zinc 1Combined sources1 Publication1
    Metal bindingi216Zinc 1Combined sources1 Publication1
    Metal bindingi219Zinc 1; via pros nitrogenCombined sources1 Publication1
    <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-methionineCombined sources1 Publication1
    Binding sitei357SubstrateCombined sources1 Publication1
    Metal bindingi390Zinc 2By similarity1
    Metal bindingi393Zinc 2By similarity1
    Metal bindingi406Zinc 2; via tele nitrogenBy similarity1
    Metal bindingi411Zinc 2; via tele nitrogenBy similarity1
    Metal bindingi707Zinc 3By similarity1
    Metal bindingi710Zinc 3By similarity1
    Metal bindingi723Zinc 3; via tele nitrogenBy similarity1
    Metal bindingi727Zinc 3; via tele nitrogenBy similarity1
    Metal bindingi735Zinc 4By similarity1
    Metal bindingi738Zinc 4By similarity1
    Metal bindingi751Zinc 4; via tele nitrogenBy similarity1
    Metal bindingi755Zinc 4; via tele nitrogenBy similarity1
    Metal bindingi763Zinc 5By similarity1
    Metal bindingi766Zinc 5By similarity1
    Metal bindingi779Zinc 5; via tele nitrogenBy similarity1
    Metal bindingi783Zinc 5; via tele nitrogenBy similarity1
    Metal bindingi791Zinc 6By similarity1
    Metal bindingi794Zinc 6By similarity1
    Metal bindingi807Zinc 6; via tele nitrogenBy similarity1
    Metal bindingi811Zinc 6; via tele nitrogenBy similarity1

    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 fingeri513 – 531C2H2-type 2; degeneratePROSITE-ProRule annotationAdd BLAST19
    Zinc fingeri537 – 559C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri565 – 587C2H2-type 4PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri593 – 615C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri621 – 643C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri649 – 671C2H2-type 7PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri677 – 699C2H2-type 8PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri705 – 727C2H2-type 9PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri733 – 755C2H2-type 10PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri761 – 783C2H2-type 11PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri789 – 811C2H2-type 12PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri817 – 839C2H2-type 13PROSITE-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

    Complete GO annotation on QuickGO ...

    GO - Biological processi

    Complete GO annotation on QuickGO ...

    <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

    Reactome - a knowledgebase of biological pathways and processes

    More...    Reactomei    		R-MMU-212436, Generic Transcription Pathway
    R-MMU-3214841, PKMTs methylate histone lysines

    <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):
    Hybrid sterility protein 1
    Meiosis-induced factor containing a PR/SET domain and zinc-finger motif
    PR domain zinc finger protein 9
    PR domain-containing protein 9
    Protein-lysine N-methyltransferase PRDM9Curated (EC:2.1.1.-1 Publication)
    [histone H3]-lysine36 N-trimethyltransferase PRDM9Curated (EC:2.1.1.3592 Publications)
    [histone H3]-lysine4 N-trimethyltransferase PRDM9Curated (EC:2.1.1.3544 Publications)
    [histone H3]-lysine9 N-trimethyltransferase PRDM9Curated (EC:2.1.1.3551 Publication)
    [histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9Curated (EC:2.1.1.3621 Publication)
    [histone H4]-lysine20 N-methyltransferase PRDM9Curated (EC:2.1.1.3611 Publication)
    <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:Hst1, Meisetz
    <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>OrganismiMus musculus (Mouse)
    <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 identifieri10090 [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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus
    <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
    • UP000000589 <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 17

    Organism-specific databases

    Mouse genome database (MGD) from Mouse Genome Informatics (MGI)

    More...    MGIi    		MGI:2384854, Prdm9

    <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

    Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

    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

    <p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

    Knockout homozygous mice are sterile in both sexes.2 Publications

    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>Mutagenesisi207K → A: Does not affect histone-lysine N-methyltransferase activity. Does not affect protein-lysine N-methyltransferas activity. 1 Publication1
    Mutagenesisi226K → A: Does not affect histone-lysine N-methyltransferase activity. Does not affect protein-lysine N-methyltransferas activity. 1 Publication1
    Mutagenesisi276Y → F: Abolishes histone-lysine N-methyltransferase activity. 2 Publications1
    Mutagenesisi278G → A: Abolishes histone-lysine N-methyltransferase activity. 1 Publication1
    Mutagenesisi297K → A: Does not affect histone-lysine N-methyltransferase activity. Does not affect protein-lysine N-methyltransferas activity. 1 Publication1
    Mutagenesisi321C → P: Abolishes histone-lysine N-methyltransferase activity over enzyme concentration of 0-80 nM. Weakened histone-lysine N-methyltransferase activity over enzyme concentration > 5 uM. Abolishes binding with S-adenosyl-L-methionine. Abolishes protein-lysine N-methyltransferas. 2 Publications1
    Mutagenesisi338K → A: Does not affect histone-lysine N-methyltransferase activity. Does not affect protein-lysine N-methyltransferas activity. 1 Publication1
    Mutagenesisi341Y → F: Abolishes histone-lysine N-methyltransferase activity. 1 Publication1
    Mutagenesisi357Y → F: Abolishes histone-lysine N-methyltransferase activity. 1 Publication1
    Mutagenesisi368K → A: Does not affect histone-lysine N-methyltransferase activity. Does not affect protein-lysine N-methyltransferas activity. 1 Publication1
    Mutagenesisi372K → A: Does not affect histone-lysine N-methyltransferase activity. Does not affect protein-lysine N-methyltransferas activity. 1 Publication1
    Mutagenesisi374K → A: Does not affect histone-lysine N-methyltransferase activity. Does not affect protein-lysine N-methyltransferas activity. 1 Publication1
    Mutagenesisi375K → A: Does not affect histone-lysine N-methyltransferase activity. Does not affect protein-lysine N-methyltransferase activity. 1 Publication1

    <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_00003639601 – 843Histone-lysine N-methyltransferase PRDM9Add BLAST843

    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; alternate1 Publication1
    Modified residuei368N6-methyllysine; alternate1 Publication1
    Modified residuei372N6-methyllysine1 Publication1
    Modified residuei374N6-methyllysine1 Publication1

    <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 (PubMed:28126738). Tri-methylated; automethylated (PubMed:28126738). Mono-methylation is predominant; automethylation is lower and slower than H3 peptide methylation and is in a highest S-adenosyl-L-methionine concentration-dependent (PubMed:28126738). There are two major sites for automethylation at Lys-368 and Lys-374 (PubMed:28126738). 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) (PubMed:28126738). Automethylation is an intramolecular (cis) process (PubMed:28126738).1 Publication

    Keywords - PTMi

    Methylation

    Proteomic databases

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

    More...    PaxDbi    		Q96EQ9

    PRoteomics IDEntifications database

    More...    PRIDEi    		Q96EQ9

    PTM databases

    iPTMnet integrated resource for PTMs in systems biology context

    More...    iPTMneti    		Q96EQ9

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

    More...    PhosphoSitePlusi    		Q96EQ9

    <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

    <p>This subsection of the 'Expression' section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified 'at protein level'.<br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

    Specifically expressed in germ cells entering meiotic prophase in female fetal gonads and in postnatal testis (PubMed:16292313). Expressed in early meiotic prophase (PubMed:27932493).2 Publications

    <p>This subsection of the 'Expression' section provides information on the expression of the gene product at various stages of a cell, tissue or organism development. By default, the information is derived from experiments at the mRNA level, unless specified 'at the protein level'.<p><a href='/help/developmental_stage' target='_top'>More...</a></p>Developmental stagei

    Specifically expressed during meiotic prophase. Transiently increases in female gonads from 13.5 dpc to 16.5 dpc, 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.1 Publication

    Gene expression databases

    Bgee dataBase for Gene Expression Evolution

    More...    Bgeei    		ENSMUSG00000051977, Expressed in retinal neural layer and 84 other tissues

    ExpressionAtlas, Differential and Baseline Expression

    More...    ExpressionAtlasi    		Q96EQ9, baseline and differential

    Genevisible search portal to normalized and curated expression data from Genevestigator

    More...    Genevisiblei    		Q96EQ9, MM

    <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:24095733).

    Interacts with EHMT2 and CDYL; interaction only takes place when PRDM9 is bound to hotspot DNA (PubMed:27932493).

    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 (PubMed:27932493, PubMed:30365547).

    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 (PubMed:27932493).

    3 Publications

    GO - Molecular functioni

    Complete GO annotation on QuickGO ...

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...    STRINGi    		10090.ENSMUSP00000131871

    Miscellaneous databases

    RNAct, Protein-RNA interaction predictions for model organisms.

    More...    RNActi    		Q96EQ9, 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

    1843
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

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

    More...    SMRi    		Q96EQ9

    Database of comparative protein structure models

    More...    ModBasei    		Search...

    Protein Data Bank in Europe - Knowledge Base

    More...    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>Regioni256 – 258S-adenosyl-L-methionine bindingCombined sources1 Publication3
    Regioni288 – 294Substrate bindingCombined sources1 Publication7
    Regioni320 – 321S-adenosyl-L-methionine bindingCombined sources1 Publication2
    Regioni715 – 805DNA-bindingBy similarityAdd BLAST91

    <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 (PubMed:22028627, PubMed:29478809). Variations in their sequence affect affinity towards DNA-binding motif (PubMed:22028627, PubMed:29478809).2 Publications

    <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 fingeri513 – 531C2H2-type 2; degeneratePROSITE-ProRule annotationAdd BLAST19
    Zinc fingeri537 – 559C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri565 – 587C2H2-type 4PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri593 – 615C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri621 – 643C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri649 – 671C2H2-type 7PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri677 – 699C2H2-type 8PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri705 – 727C2H2-type 9PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri733 – 755C2H2-type 10PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri761 – 783C2H2-type 11PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri789 – 811C2H2-type 12PROSITE-ProRule annotationAdd BLAST23
    Zinc fingeri817 – 839C2H2-type 13PROSITE-ProRule annotationAdd BLAST23

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...    eggNOGi    		KOG1721, Eukaryota
    KOG2461, Eukaryota

    Ensembl GeneTree

    More...    GeneTreei    		ENSGT00940000158211

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...    HOGENOMi    		CLU_983403_0_0_1

    InParanoid: Eukaryotic Ortholog Groups

    More...    InParanoidi    		Q96EQ9

    Database for complete collections of gene phylogenies

    More...    PhylomeDBi    		Q96EQ9

    Family and domain databases

    Conserved Domains Database

    More...    CDDi    		cd07765, KRAB_A-box, 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
    IPR001214, SET_dom
    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, 11 hits

    Simple Modular Architecture Research Tool; a protein domain database

    More...    SMARTi    		View protein in SMART
    SM00349, KRAB, 1 hit
    SM00355, ZnF_C2H2, 13 hits

    Superfamily database of structural and functional annotation

    More...    SUPFAMi    		SSF109640, SSF109640, 1 hit
    SSF57667, SSF57667, 6 hits

    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, 12 hits
    PS50157, ZINC_FINGER_C2H2_2, 12 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>Sequences (4+)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 describes 4 <p>This subsection of the 'Sequence' section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform. This section is only present in reviewed entries, i.e. in UniProtKB/Swiss-Prot.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket

    This entry has 4 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

    Isoform 1 (identifier: Q96EQ9-1) [UniParc]FASTAAdd to basket
    Also known as: Meisetz

    This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide
            10         20         30         40         50
    MNTNKLEENS PEEDTGKFEW KPKVKDEFKD ISIYFSKEEW AEMGEWEKIR 
            60         70         80         90        100
    YRNVKRNYKM LISIGLRAPR PAFMCYQRQA MKPQINDSED SDEEWTPKQQ 
           110        120        130        140        150
    VSPPWVPFRV KHSKQQKESS RMPFSGESNV KEGSGIENLL NTSGSEHVQK 
           160        170        180        190        200
    PVSSLEEGNT SGQHSGKKLK LRKKNVEVKM YRLRERKGLA YEEVSEPQDD 
           210        220        230        240        250
    DYLYCEKCQN FFIDSCPNHG PPLFVKDSMV DRGHPNHSVL SLPPGLRISP 
           260        270        280        290        300
    SGIPEAGLGV WNEASDLPVG LHFGPYEGQI TEDEEAANSG YSWLITKGRN 
           310        320        330        340        350
    CYEYVDGQDE SQANWMRYVN CARDDEEQNL VAFQYHRKIF YRTCRVIRPG 
           360        370        380        390        400
    CELLVWYGDE YGQELGIKWG SKMKKGFTAG RELRTEIHPC LLCSLAFSSQ 
           410        420        430        440        450
    KFLTQHMEWN HRTEIFPGTS ARINPKPGDP CSDQLQEQHV DSQNKNDKAS 
           460        470        480        490        500
    NEVKRKSKPR QRISTTFPST LKEQMRSEES KRTVEELRTG QTTNTEDTVK 
           510        520        530        540        550
    SFIASEISSI ERQCGQYFSD KSNVNEHQKT HTGEKPYVCR ECGRGFTQNS 
           560        570        580        590        600
    HLIQHQRTHT GEKPYVCREC GRGFTQKSDL IKHQRTHTGE KPYVCRECGR 
           610        620        630        640        650
    GFTQKSDLIK HQRTHTGEKP YVCRECGRGF TQKSVLIKHQ RTHTGEKPYV 
           660        670        680        690        700
    CRECGRGFTQ KSVLIKHQRT HTGEKPYVCR ECGRGFTAKS VLIQHQRTHT 
           710        720        730        740        750
    GEKPYVCREC GRGFTAKSNL IQHQRTHTGE KPYVCRECGR GFTAKSVLIQ 
           760        770        780        790        800
    HQRTHTGEKP YVCRECGRGF TAKSVLIQHQ RTHTGEKPYV CRECGRGFTQ 
           810        820        830        840 
    KSNLIKHQRT HTGEKPYVCR ECGWGFTQKS DLIQHQRTHT REK
    Length:843
    Mass (Da):97,365
    Last modified:February 10, 2009 - 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:i323DD4F00447D598
    GO
    Isoform 2 (identifier: Q96EQ9-2) [UniParc]FASTAAdd to basket
    Also known as: Meisetz-S1

    The sequence of this isoform differs from the canonical sequence as follows:
         382-404: ELRTEIHPCLLCSLAFSSQKFLT → GGHYYDSLKKKEKREFSLRIFIF
         405-843: Missing.

    Show »
    Length:404
    Mass (Da):46,856
    Checksum:iE8D64C40EFB5EC84
    GO
    Isoform 3 (identifier: Q96EQ9-3) [UniParc]FASTAAdd to basket
    Also known as: Meisetz-S2

    The sequence of this isoform differs from the canonical sequence as follows:
         382-418: ELRTEIHPCLLCSLAFSSQKFLTQHMEWNHRTEIFPG → DLFIIICKYTVAVFRHTRRGSQILLRMVVSHHVVAGI
         419-843: Missing.

    Show »
    Length:418
    Mass (Da):48,244
    Checksum:i0EBDF88F535CEE94
    GO
    Isoform 4 (identifier: Q96EQ9-4) [UniParc]FASTAAdd to basket

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

    Show »
    Length:283
    Mass (Da):32,241
    Checksum:iF4FE5CE36B04C03E
    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 is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
    EntryEntry nameProtein names
    		Gene namesLengthAnnotation
    E9Q4V2E9Q4V2_MOUSE
    Histone-lysine N-methyltransferase
    Prdm9
    		847Annotation score:

    Annotation score:2 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 AAH49903 differs from that shown. Reason: Erroneous initiation.Curated

    <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:22028627). Each allele binds to a specific hotspot set (PubMed:29478809). Both polymorphisms in the zinc finger C2H2 type domains and in DNA target sequence control recombination at hotspot (PubMed:22028627). The affinity of each allele for its DNA-binding site can vary histone methyltransferase activity (PubMed:29478809).2 Publications

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Sequence' section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_0363741 – 121Missing in isoform 4. 1 PublicationAdd BLAST121
    Alternative sequenceiVSP_036375382 – 418ELRTE…EIFPG → DLFIIICKYTVAVFRHTRRG SQILLRMVVSHHVVAGI in isoform 3. CuratedAdd BLAST37
    Alternative sequenceiVSP_036376382 – 404ELRTE…QKFLT → GGHYYDSLKKKEKREFSLRI FIF in isoform 2 and isoform 4. 1 PublicationAdd BLAST23
    Alternative sequenceiVSP_036377405 – 843Missing in isoform 2 and isoform 4. 1 PublicationAdd BLAST439
    Alternative sequenceiVSP_036378419 – 843Missing in isoform 3. CuratedAdd BLAST425

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...    EMBLi

    GenBank nucleotide sequence database

    More...    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...    DDBJi
    Links Updated
    		AY294423 Genomic DNA Translation: AAQ01511.1
    AC154378 Genomic DNA No translation available.
    CT033750 Genomic DNA No translation available.
    BC012016 mRNA Translation: AAH12016.1
    BC049903 mRNA Translation: AAH49903.1 Different initiation.

    The Consensus CDS (CCDS) project

    More...    CCDSi    		CCDS49963.2 [Q96EQ9-1]
    CCDS88997.1 [Q96EQ9-4]

    Genome annotation databases

    Ensembl eukaryotic genome annotation project

    More...    Ensembli    		ENSMUST00000147532; ENSMUSP00000118454; ENSMUSG00000051977 [Q96EQ9-4]
    ENSMUST00000167994; ENSMUSP00000131871; ENSMUSG00000051977 [Q96EQ9-1]

    UCSC genome browser

    More...    UCSCi    		uc008aos.1, mouse [Q96EQ9-4]
    uc029tan.1, mouse [Q96EQ9-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    <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
    		AY294423 Genomic DNA Translation: AAQ01511.1
    AC154378 Genomic DNA No translation available.
    CT033750 Genomic DNA No translation available.
    BC012016 mRNA Translation: AAH12016.1
    BC049903 mRNA Translation: AAH49903.1 Different initiation.
    CCDSiCCDS49963.2 [Q96EQ9-1]
    CCDS88997.1 [Q96EQ9-4]

    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
    4C1QX-ray2.30A/B198-368[»]
    SMRiQ96EQ9
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi10090.ENSMUSP00000131871

    PTM databases

    iPTMnetiQ96EQ9
    PhosphoSitePlusiQ96EQ9

    Proteomic databases

    PaxDbiQ96EQ9
    PRIDEiQ96EQ9

    Protocols and materials databases

    Antibodypedia a portal for validated antibodies

    More...    Antibodypediai    		67566, 60 antibodies

    Genome annotation databases

    EnsembliENSMUST00000147532; ENSMUSP00000118454; ENSMUSG00000051977 [Q96EQ9-4]
    ENSMUST00000167994; ENSMUSP00000131871; ENSMUSG00000051977 [Q96EQ9-1]
    UCSCiuc008aos.1, mouse [Q96EQ9-4]
    uc029tan.1, mouse [Q96EQ9-1]

    Organism-specific databases

    MGIiMGI:2384854, Prdm9

    Phylogenomic databases

    eggNOGiKOG1721, Eukaryota
    KOG2461, Eukaryota
    GeneTreeiENSGT00940000158211
    HOGENOMiCLU_983403_0_0_1
    InParanoidiQ96EQ9
    PhylomeDBiQ96EQ9

    Enzyme and pathway databases

    ReactomeiR-MMU-212436, Generic Transcription Pathway
    R-MMU-3214841, PKMTs methylate histone lysines

    Miscellaneous databases

    ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

    More...    ChiTaRSi    		Prdm9, mouse

    Protein Ontology

    More...    PROi    		PR:Q96EQ9
    RNActiQ96EQ9, protein

    The Stanford Online Universal Resource for Clones and ESTs

    More...    SOURCEi    		Search...

    Gene expression databases

    BgeeiENSMUSG00000051977, Expressed in retinal neural layer and 84 other tissues
    ExpressionAtlasiQ96EQ9, baseline and differential
    GenevisibleiQ96EQ9, MM

    Family and domain databases

    CDDicd07765, KRAB_A-box, 1 hit
    InterProiView protein in InterPro
    IPR001909, KRAB
    IPR036051, KRAB_dom_sf
    IPR003655, Krueppel-associated_box-rel
    IPR001214, SET_dom
    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, 11 hits
    SMARTiView protein in SMART
    SM00349, KRAB, 1 hit
    SM00355, ZnF_C2H2, 13 hits
    SUPFAMiSSF109640, SSF109640, 1 hit
    SSF57667, SSF57667, 6 hits
    PROSITEiView protein in PROSITE
    PS50806, KRAB_RELATED, 1 hit
    PS50280, SET, 1 hit
    PS00028, ZINC_FINGER_C2H2_1, 12 hits
    PS50157, ZINC_FINGER_C2H2_2, 12 hits

    ProtoNet; Automatic hierarchical classification of proteins

    More...    ProtoNeti    		Search...

    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_MOUSE
    <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: Q96EQ9
    Secondary accession number(s): B8JJZ8, Q0D2N4
    <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: February 10, 2009
    Last sequence update: February 10, 2009
    Last modified: August 12, 2020
    This is version 149 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

    <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. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
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