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Entry version 156 (25 May 2022)
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).

10 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

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

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
<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)

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MGIi
MGI:2384854, Prdm9

Eukaryotic Pathogen, Vector and Host Database Resources

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VEuPathDBi
HostDB:ENSMUSG00000051977

<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

<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

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PRIDEi
Q96EQ9

ProteomicsDB: a multi-organism proteome resource

More...
ProteomicsDBi
289889 [Q96EQ9-1]
289890 [Q96EQ9-2]
289891 [Q96EQ9-3]
289892 [Q96EQ9-4]

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 98 other tissues

ExpressionAtlas, Differential and Baseline Expression

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ExpressionAtlasi
Q96EQ9, baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

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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

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

AlphaFold Protein Structure Database

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AlphaFoldDBi
Q96EQ9

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

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SMRi
Q96EQ9

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>Regioni85 – 104DisorderedSequence analysisAdd BLAST20
Regioni110 – 170DisorderedSequence analysisAdd BLAST61
Regioni256 – 258S-adenosyl-L-methionine bindingCombined sources1 Publication3
Regioni288 – 294Substrate bindingCombined sources1 Publication7
Regioni320 – 321S-adenosyl-L-methionine bindingCombined sources1 Publication2
Regioni418 – 493DisorderedSequence analysisAdd BLAST76
Regioni715 – 805DNA-bindingBy similarityAdd 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 biasi119 – 165Polar residuesSequence analysisAdd BLAST47
Compositional biasi440 – 459Basic and acidic residuesSequence analysisAdd BLAST20

<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
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, 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
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, 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.<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 <p><strong>What is the canonical sequence?</strong><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[»]
AlphaFoldDBiQ96EQ9
SMRiQ96EQ9
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000131871

PTM databases

iPTMnetiQ96EQ9
PhosphoSitePlusiQ96EQ9

Proteomic databases

PaxDbiQ96EQ9
PRIDEiQ96EQ9
ProteomicsDBi289889 [Q96EQ9-1]
289890 [Q96EQ9-2]
289891 [Q96EQ9-3]
289892 [Q96EQ9-4]

Protocols and materials databases

Antibodypedia a portal for validated antibodies

More...
Antibodypediai
67566, 64 antibodies from 16 providers

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
VEuPathDBiHostDB:ENSMUSG00000051977

Phylogenomic databases

eggNOGiKOG1721, Eukaryota
KOG2461, Eukaryota
GeneTreeiENSGT00940000158211
HOGENOMiCLU_983403_0_0_1
InParanoidiQ96EQ9
PhylomeDBiQ96EQ9

Enzyme and pathway databases

ReactomeiR-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 98 other tissues
ExpressionAtlasiQ96EQ9, baseline and differential
GenevisibleiQ96EQ9, MM

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, 11 hits
SMARTiView protein in SMART
SM00349, KRAB, 1 hit
SM00355, ZnF_C2H2, 13 hits
SUPFAMiSSF109640, SSF109640, 1 hit
SSF57667, SSF57667, 6 hits
SSF82199, SSF82199, 1 hit
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

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: May 25, 2022
This is version 156 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
UniProt is an ELIXIR core data resource
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