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Entry version 111 (16 Oct 2019)
Sequence version 1 (30 May 2006)
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Protein
Submitted name:

Jumonji domain containing 2B

Gene

kdm4b

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Unreviewed-Annotation 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>
-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>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

LigandMetal-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-DRE-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-DRE-9018519 Estrogen-dependent gene expression

<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_and_taxonomy_section">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
Submitted name:
Jumonji domain containing 2BImported
Submitted name:
Lysine (K)-specific demethylase 4BImported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:kdm4bImported
Synonyms:jmjd2bImported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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_and_taxonomy_section">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_and_taxonomy_section">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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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_manual">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 22

Organism-specific databases

Zebrafish Information Network genome database

More...
ZFINi
ZDB-GENE-060503-664 kdm4b

<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

NucleusSAAS annotation

<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
ENSDARG00000099675 Expressed in 29 organ(s), highest expression level in head

<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.ENSDARP00000106448

<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_and_domains_section">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>Domaini95 – 137JmjNInterPro annotationAdd BLAST43
Domaini223 – 389JmjCInterPro annotationAdd BLAST167
Domaini780 – 893PHD-typeInterPro annotationAdd BLAST114

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 87DisorderedSequence analysisAdd BLAST87
Regioni517 – 555DisorderedSequence analysisAdd BLAST39
Regioni597 – 619DisorderedSequence analysisAdd BLAST23
Regioni1028 – 1061DisorderedSequence analysisAdd BLAST34

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 biasi532 – 546PolyampholyteSequence analysisAdd BLAST15
Compositional biasi597 – 611BasicSequence analysisAdd BLAST15
Compositional biasi1046 – 1060Pro-richSequence analysisAdd BLAST15

Keywords - Domaini

Zinc-fingerSAAS annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG0958 Eukaryota
COG5141 LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000159248

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000231125

KEGG Orthology (KO)

More...
KOi
K06709

Identification of Orthologs from Complete Genome Data

More...
OMAi
CDNLHPE

Database of Orthologous Groups

More...
OrthoDBi
1186832at2759

TreeFam database of animal gene trees

More...
TreeFami
TF106449

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.40.10, 2 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR034732 EPHD
IPR003347 JmjC_dom
IPR003349 JmjN
IPR040477 KDM4_Tudor_2
IPR002999 Tudor
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR013083 Znf_RING/FYVE/PHD

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02373 JmjC, 1 hit
PF02375 JmjN, 1 hit
PF18104 Tudor_2, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00558 JmjC, 1 hit
SM00545 JmjN, 1 hit
SM00249 PHD, 2 hits
SM00333 TUDOR, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF57903 SSF57903, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51805 EPHD, 1 hit
PS51184 JMJC, 1 hit
PS51183 JMJN, 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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

Q1LUQ0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDPSLPPDPN PAETEPSADV TPPADTDQDS PINPLVDPQP CDTPISDLVH
60 70 80 90 100
EPAAPAEPTP AQGLKPELPA PELTTQNLIP GPAPAPPPGA NFNKIMTFRP
110 120 130 140 150
TMEEFKDFGK YIAYMETQGA HVAGLAKVIP PKEWKPRRSY ETIEDMVIPA
160 170 180 190 200
PIMQVVTGQS GLFTQYNIQK KSMTVGEYRK LANSKKYNTP QHKDFDDLER
210 220 230 240 250
KYWKNLTFVS PIYGADISGS LYDPDISEWN IGHLNTLLDM VEQECGIVIE
260 270 280 290 300
GVNTPYLYFG MWKTTFAWHT EDMDLYSINY LHFGKPKSWY AIPPEHGKRL
310 320 330 340 350
ERLAQGFFPG SSQGCDAFLR HKMTLISPSI LKKYSIPFDR ITQEEGEFMI
360 370 380 390 400
TFPYGYHAGF NHGFNCAEST NFATLRWIDY GKMAAQCTCR KDMVKISMDV
410 420 430 440 450
FVRRLQPERY TQWKQGKDTM VLDHLKPTSL SSPELEHWRK NRVTFREKVL
460 470 480 490 500
RRAQAKMKQF RRLKPEDLKV LMEAGVELDM EEYQRKVEEH DEQRRQQRDE
510 520 530 540 550
RMAREAMLTL EALEREEQEQ AEAALRGGGV EEIKADFQDP PVENGEKKKK
560 570 580 590 600
KKKKLQLTDE MSFQEVFEQF TTASEMQNQS NGAAPLQTNP FTKLKKKVEV
610 620 630 640 650
KKSRRHPISK PPMRSPHSIV KQEASSDEEL YSGLPVGGGV THESKKPEDS
660 670 680 690 700
DLWQNRSPNF LAEKQFNAAM STIEPYCAIC TLFCPYTQSV KDPFHISDMS
710 720 730 740 750
GLVSRVGCRT RPLVPEMCFS AGAENMEPLS SNSHIADDGT SVLLSCSGCN
760 770 780 790 800
LQVHASCYGV NPQTKQEGWM CSRCTTVAWT AACCLCSLRG GALKKTTDER
810 820 830 840 850
WVHVICAIAV AEVRFVNAIE REPVDVTAVP ETRKSLKCVY CHKTTKQIFG
860 870 880 890 900
ACIQCSQDNC STSFHVTCAL LAGVVMKPAD WPYVVSVTCH KHKLTNQKAK
910 920 930 940 950
SGSRDLSLGQ EVIGRNSNGW FYRCVITGTG TQTYYEVNFD DGSYCDNIFP
960 970 980 990 1000
ENLLSHDCLR NGPPELGELV VVKTVDGRVL NASYIKEHVH RYYQVEFQDE
1010 1020 1030 1040 1050
TQLLLKRSEI HSLDQELPKR VMSRLATVNQ QQPQAQPSDE PLAAKRPRLP
1060 1070 1080 1090 1100
TPPPTLAIEP SALPPELVST FLPPSITANT STAPCLPPAA LPVSAPPEPS
1110 1120 1130
ESYTHSSSYI AYMESLLKSD FPAEDGEPGL EPMY
Length:1,134
Mass (Da):127,470
Last modified:May 30, 2006 - v1
<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:i306BC1B5D4E59EE4
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
BX927276 Genomic DNA No translation available.
CU074310 Genomic DNA No translation available.
BC171698 mRNA Translation: AAI71698.1
BC171700 mRNA Translation: AAI71700.1

NCBI Reference Sequences

More...
RefSeqi
NP_001076274.1, NM_001082805.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSDART00000162523; ENSDARP00000133766; ENSDARG00000099675
ENSDART00000181893; ENSDARP00000156548; ENSDARG00000099675

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
556504

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
dre:556504

<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
BX927276 Genomic DNA No translation available.
CU074310 Genomic DNA No translation available.
BC171698 mRNA Translation: AAI71698.1
BC171700 mRNA Translation: AAI71700.1
RefSeqiNP_001076274.1, NM_001082805.1

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000106448

Genome annotation databases

EnsembliENSDART00000162523; ENSDARP00000133766; ENSDARG00000099675
ENSDART00000181893; ENSDARP00000156548; ENSDARG00000099675
GeneIDi556504
KEGGidre:556504

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
23030
ZFINiZDB-GENE-060503-664 kdm4b

Phylogenomic databases

eggNOGiKOG0958 Eukaryota
COG5141 LUCA
GeneTreeiENSGT00940000159248
HOGENOMiHOG000231125
KOiK06709
OMAiCDNLHPE
OrthoDBi1186832at2759
TreeFamiTF106449

Enzyme and pathway databases

ReactomeiR-DRE-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-DRE-9018519 Estrogen-dependent gene expression

Gene expression databases

BgeeiENSDARG00000099675 Expressed in 29 organ(s), highest expression level in head

Family and domain databases

Gene3Di3.30.40.10, 2 hits
InterProiView protein in InterPro
IPR034732 EPHD
IPR003347 JmjC_dom
IPR003349 JmjN
IPR040477 KDM4_Tudor_2
IPR002999 Tudor
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
PF02375 JmjN, 1 hit
PF18104 Tudor_2, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00545 JmjN, 1 hit
SM00249 PHD, 2 hits
SM00333 TUDOR, 2 hits
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS51805 EPHD, 1 hit
PS51184 JMJC, 1 hit
PS51183 JMJN, 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 nameiQ1LUQ0_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: Q1LUQ0
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/TrEMBL: May 30, 2006
Last sequence update: May 30, 2006
Last modified: October 16, 2019
This is version 111 of the entry and version 1 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

Complete proteome, Proteomics identificationCombined sources, Reference proteomeImported
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