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Entry version 71 (07 Oct 2020)
Sequence version 2 (20 Jun 2018)
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Protein

DNA ligase

Gene

lig3

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Unreviewed-Annotation score:

Annotation score:4 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

<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

  • ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.UniRule annotationARBA annotation EC:6.5.1.1

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+ARBA annotation

<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 functionLigaseUniRule annotationARBA annotation
Biological processDNA damage, DNA recombinationUniRule annotationARBA annotation, DNA repairUniRule annotation, DNA replicationUniRule annotationARBA annotation
LigandATP-bindingUniRule annotationARBA annotation, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-DRE-110381, Resolution of AP sites via the single-nucleotide replacement pathway
R-DRE-5649702, APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway
R-DRE-5685939, HDR through MMEJ (alt-NHEJ)
R-DRE-6782210, Gap-filling DNA repair synthesis and ligation in TC-NER

<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:
DNA ligaseUniRule annotation (EC:6.5.1.1UniRule annotation)
<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:lig3Imported
<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>OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)Imported
<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 identifieri7955 [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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesDanionidaeDanioninaeDanio
<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
  • UP000000437 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 5

Organism-specific databases

Zebrafish Information Network genome database

More...
ZFINi
ZDB-GENE-030131-8453, lig3

<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

NucleusARBA annotation

<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

Proteomic databases

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

More...
PaxDbi
F1QJL4

PRoteomics IDEntifications database

More...
PRIDEi
F1QJL4

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

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSDARG00000052553, Expressed in gastrula and 34 other tissues

<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

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
7955.ENSDARP00000068915

<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

3D structure databases

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

More...
SMRi
F1QJL4

Database of comparative protein structure models

More...
ModBasei
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>Domaini92 – 184PARP-typeInterPro annotationAdd BLAST93
Domaini582 – 716DNA_LIGASE_A3InterPro annotationAdd BLAST135
Domaini935 – 1011BRCTInterPro annotationAdd BLAST77

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>Regioni189 – 247DisorderedSequence analysisAdd BLAST59
Regioni839 – 928DisorderedSequence analysisAdd BLAST90

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 amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi193 – 211PolarSequence analysisAdd BLAST19
Compositional biasi224 – 240PolarSequence analysisAdd BLAST17
Compositional biasi841 – 877PolarSequence analysisAdd BLAST37
Compositional biasi896 – 914PolyampholyteSequence analysisAdd BLAST19

<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 ATP-dependent DNA ligase family.UniRule annotationARBA annotation

Keywords - Domaini

Zinc-fingerARBA annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG4437, Eukaryota

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000156492

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_011787_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
F1QJL4

KEGG Orthology (KO)

More...
KOi
K10776

TreeFam database of animal gene trees

More...
TreeFami
TF316220

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.3260.10, 1 hit
3.30.1740.10, 1 hit
3.40.50.10190, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001357, BRCT_dom
IPR036420, BRCT_dom_sf
IPR000977, DNA_ligase_ATP-dep
IPR012309, DNA_ligase_ATP-dep_C
IPR012310, DNA_ligase_ATP-dep_cent
IPR016059, DNA_ligase_ATP-dep_CS
IPR012308, DNA_ligase_ATP-dep_N
IPR036599, DNA_ligase_N_sf
IPR031916, LIG3_BRCT
IPR012340, NA-bd_OB-fold
IPR001510, Znf_PARP
IPR036957, Znf_PARP_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF04679, DNA_ligase_A_C, 1 hit
PF01068, DNA_ligase_A_M, 1 hit
PF04675, DNA_ligase_A_N, 1 hit
PF16759, LIG3_BRCT, 1 hit
PF00645, zf-PARP, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01336, zf-PARP, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF117018, SSF117018, 1 hit
SSF50249, SSF50249, 1 hit
SSF52113, SSF52113, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00574, dnl1, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50172, BRCT, 1 hit
PS00697, DNA_LIGASE_A1, 1 hit
PS00333, DNA_LIGASE_A2, 1 hit
PS50160, DNA_LIGASE_A3, 1 hit
PS00347, PARP_ZN_FINGER_1, 1 hit
PS50064, PARP_ZN_FINGER_2, 1 hit

<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>Sequencei

<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.

F1QJL4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MPSLWLGRAL RTLSRSSLTK ISWEPLFRAT LKHQYLQCSR TLIFTRGSES
60 70 80 90 100
SPSGVFFCAP HTPAFTLISS SYFHISWPVR RSEQADMAEQ RYCVEYAKRG
110 120 130 140 150
TAGCKKCKDK IMKGLVRIGK IVPNPFSESA GEMKEWYHVK CIFEKLERAR
160 170 180 190 200
ATTKKIEDIT ELEGWEELQD EDKDLINKHV SELAAKVNST PKKKVQAKLN
210 220 230 240 250
TSGQLSSPPA DPTVNAPRKF SGFTATKAGS SSSSPGPSPA KPAQGSVLSA
260 270 280 290 300
QMCDPTHKDN LLREFRKLCA LVAEKSGYNA KTEIVRDFLT KGSGGDKFRG
310 320 330 340 350
DLYLTVKLLL PGVVKNVYNL NDKQIVKLFS RILNCNQDDM VQDLEQGDVS
360 370 380 390 400
ETVRMFFEES KSFPPSAKSL LTIQEVDASL SRLSQLTKED DQQAELQSIA
410 420 430 440 450
KKCTGNDLKC YIRLVKHDLK INSGAKHILD AVDPNAYDAF KASRNLGDVI
460 470 480 490 500
DRVLRNQQDA SNGTGPRKIL SIEASLMTPV QPMLAEACKS IEYAMKKCPN
510 520 530 540 550
GMYSEIKYDG ERVQVHKNGN HFSYFSRSLK PVLPHKVAHF KDFIPQAFAG
560 570 580 590 600
GHSMILDAEV LLIDTKTSKP LPFGTLGVHK KAAFQDAQVG LFVFDCIYFN
610 620 630 640 650
GVSLMDKPLC ERRKFLHDNM VEVPNRILFS EMKHVTRAPD LAEMITRVIR
660 670 680 690 700
EGLEGLVLKD IKGLYEPGKR HWLKVKKDYL NEGAMADTAD LVVLGAFYGK
710 720 730 740 750
GSNGGIMSSF LMGCYDPESR KWCTVTKCSG GFDDAMLDRL QKDLDVIKIG
760 770 780 790 800
KDPSKIPGWL KIVKNYYPDF IIRDPQKAPV WEITGAEFSK SEMHTADGIS
810 820 830 840 850
IRFPRCTRMR DDKDWKTATN LQQLKELYRI SKENCDFEVT AGPSKANQND
860 870 880 890 900
KSSSGGESGG SSPSASRGAS TANKPKNGHT PKAKAAKTES SAPAVKRKLP
910 920 930 940 950
AEKQDVKKIK TESVHSNGQS KLKSVPTTDP KQEKTLLDIF TGVKLYLPES
960 970 980 990 1000
VKDFEKLRRY FLAYDGDLVP EYDSALATHT LGQPEDGSSA QKVTSNWIWE
1010
CIRKRRVVPP C
Length:1,011
Mass (Da):112,745
Last modified:June 20, 2018 - 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:iAB5FC72CA3FFC58E
GO

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
CU929413 Genomic DNA No translation available.

NCBI Reference Sequences

More...
RefSeqi
NP_001025345.2, NM_001030174.2

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSDART00000074426; ENSDARP00000068915; ENSDARG00000052553

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
563276

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
dre:563276

<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
CU929413 Genomic DNA No translation available.
RefSeqiNP_001025345.2, NM_001030174.2

3D structure databases

SMRiF1QJL4
ModBaseiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000068915

Proteomic databases

PaxDbiF1QJL4
PRIDEiF1QJL4

Genome annotation databases

EnsembliENSDART00000074426; ENSDARP00000068915; ENSDARG00000052553
GeneIDi563276
KEGGidre:563276

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
3980
ZFINiZDB-GENE-030131-8453, lig3

Phylogenomic databases

eggNOGiKOG4437, Eukaryota
GeneTreeiENSGT00940000156492
HOGENOMiCLU_011787_0_0_1
InParanoidiF1QJL4
KOiK10776
TreeFamiTF316220

Enzyme and pathway databases

ReactomeiR-DRE-110381, Resolution of AP sites via the single-nucleotide replacement pathway
R-DRE-5649702, APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway
R-DRE-5685939, HDR through MMEJ (alt-NHEJ)
R-DRE-6782210, Gap-filling DNA repair synthesis and ligation in TC-NER

Gene expression databases

BgeeiENSDARG00000052553, Expressed in gastrula and 34 other tissues

Family and domain databases

Gene3Di1.10.3260.10, 1 hit
3.30.1740.10, 1 hit
3.40.50.10190, 1 hit
InterProiView protein in InterPro
IPR001357, BRCT_dom
IPR036420, BRCT_dom_sf
IPR000977, DNA_ligase_ATP-dep
IPR012309, DNA_ligase_ATP-dep_C
IPR012310, DNA_ligase_ATP-dep_cent
IPR016059, DNA_ligase_ATP-dep_CS
IPR012308, DNA_ligase_ATP-dep_N
IPR036599, DNA_ligase_N_sf
IPR031916, LIG3_BRCT
IPR012340, NA-bd_OB-fold
IPR001510, Znf_PARP
IPR036957, Znf_PARP_sf
PfamiView protein in Pfam
PF04679, DNA_ligase_A_C, 1 hit
PF01068, DNA_ligase_A_M, 1 hit
PF04675, DNA_ligase_A_N, 1 hit
PF16759, LIG3_BRCT, 1 hit
PF00645, zf-PARP, 1 hit
SMARTiView protein in SMART
SM01336, zf-PARP, 1 hit
SUPFAMiSSF117018, SSF117018, 1 hit
SSF50249, SSF50249, 1 hit
SSF52113, SSF52113, 1 hit
TIGRFAMsiTIGR00574, dnl1, 1 hit
PROSITEiView protein in PROSITE
PS50172, BRCT, 1 hit
PS00697, DNA_LIGASE_A1, 1 hit
PS00333, DNA_LIGASE_A2, 1 hit
PS50160, DNA_LIGASE_A3, 1 hit
PS00347, PARP_ZN_FINGER_1, 1 hit
PS50064, PARP_ZN_FINGER_2, 1 hit

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 nameiF1QJL4_DANRE
<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: F1QJL4
<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/TrEMBL: May 3, 2011
Last sequence update: June 20, 2018
Last modified: October 7, 2020
This is version 71 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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

Proteomics identificationCombined sources, Reference proteomeImported
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