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Entry version 88 (16 Oct 2019)
Sequence version 1 (23 Jan 2007)
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Protein

Lysine-specific demethylase 4D

Gene

Kdm4d

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score:

Annotation score:3 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 transcript 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 demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate (By similarity).By similarity

<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

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 sitei1332-oxoglutarateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 bindingi189Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi191Iron; catalyticPROSITE-ProRule annotation1
Binding sitei1992-oxoglutarateBy similarity1
Binding sitei2072-oxoglutarateBy similarity1
Metal bindingi235ZincBy similarity1
Metal bindingi241Zinc; via tele nitrogenBy similarity1
Binding sitei2422-oxoglutarateBy similarity1
Metal bindingi277Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi307ZincBy similarity1
Metal bindingi309ZincBy similarity1

<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 functionChromatin regulator, Dioxygenase, Oxidoreductase
Biological processTranscription, Transcription regulation
LigandIron, Metal-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-RNO-3214842 HDMs demethylate histones

<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
Recommended name:
Lysine-specific demethylase 4D (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing histone demethylation protein 3D
Jumonji domain-containing protein 2D
<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:Kdm4d
Synonyms:Jhdm3d, Jmjd2d
<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>OrganismiRattus norvegicus (Rat)
<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 identifieri10116 [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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
<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
  • UP000002494 <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 8

Organism-specific databases

Rat genome database

More...
RGDi
1591045 Kdm4d

<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

Nucleus

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003768241 – 510Lysine-specific demethylase 4DAdd BLAST510

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 residuei23PolyADP-ribosyl glutamic acidBy similarity1
Modified residuei24PolyADP-ribosyl glutamic acidBy similarity1

Keywords - PTMi

ADP-ribosylation

Proteomic databases

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

More...
PaxDbi
A1A5Q5

PRoteomics IDEntifications database

More...
PRIDEi
A1A5Q5

<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
ENSRNOG00000024726 Expressed in 4 organ(s), highest expression level in testis

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
A1A5Q5 RN

<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
10116.ENSRNOP00000067344

<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
A1A5Q5

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_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>Domaini15 – 57JmjNPROSITE-ProRule annotationAdd BLAST43
Domaini143 – 309JmjCPROSITE-ProRule annotationAdd BLAST167

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 biasi88 – 91Poly-Lys4

<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 JHDM3 histone demethylase family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG0958 Eukaryota
ENOG410XP0T LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000162152

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000231125

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
A1A5Q5

KEGG Orthology (KO)

More...
KOi
K06709

Identification of Orthologs from Complete Genome Data

More...
OMAi
PPHQNFE

Database of Orthologous Groups

More...
OrthoDBi
1186832at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
A1A5Q5

TreeFam database of animal gene trees

More...
TreeFami
TF106449

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003347 JmjC_dom
IPR003349 JmjN

Pfam protein domain database

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

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
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.

A1A5Q5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKTKSTCAQN PNCSIMIFRP TKEEFNDFDK YIAYMESQGA HRAGLAKVIP
60 70 80 90 100
PKEWRARQSY DNISNILIAT PLQQVVSGQA GVFTQYHKKK KAMTVGQYRH
110 120 130 140 150
LANSKKYQTP PHLDFEDLER KYWKNRLYES PIYGADVSGS LFDGKTQQWN
160 170 180 190 200
VGHLGTIQDL LEQECGIVIE GVNTPYLYFG MWKTSFAWHT EDMDLYSINY
210 220 230 240 250
LHFGQPKTWY AVPPEHGRRL ELLAKELFPG SSQGCQAFLR HKVALISPTV
260 270 280 290 300
LKENGIPFGR ITQEAGEFMV TFPYGYHAGF NHGFNCAEAI NFATPRWIDY
310 320 330 340 350
GKVASQCSCG EARVSFSMDA FVRILQPERY EMWKRGQDQA VVDHTEAMGP
360 370 380 390 400
TSQELTTWRV IQAPRKTWGL KHLRLRQVSR CLLPVATDSN IANNTQMCHT
410 420 430 440 450
SRQAADSKGD EVQESDPAIA PPYPLGLSSP GHMSTGKRGL GRRPCELGVQ
460 470 480 490 500
ESTNGAPVKR RLPEGRDDRS PSPELQSQSV TGDLIVNSDL VNPGPQHPVT
510
ASEGGLTSDP
Length:510
Mass (Da):57,188
Last modified:January 23, 2007 - 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:i3F312BF389E05560
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
BC128760 mRNA Translation: AAI28761.1

NCBI Reference Sequences

More...
RefSeqi
NP_001073180.1, NM_001079712.1
XP_017451454.1, XM_017595965.1
XP_017459055.1, XM_017603566.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSRNOT00000033932; ENSRNOP00000059913; ENSRNOG00000024726
ENSRNOT00000071532; ENSRNOP00000067344; ENSRNOG00000045905

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
108348070
689582

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
rno:108348070
rno:689582

UCSC genome browser

More...
UCSCi
RGD:1591045 rat

<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
BC128760 mRNA Translation: AAI28761.1
RefSeqiNP_001073180.1, NM_001079712.1
XP_017451454.1, XM_017595965.1
XP_017459055.1, XM_017603566.1

3D structure databases

SMRiA1A5Q5
ModBaseiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000067344

Proteomic databases

PaxDbiA1A5Q5
PRIDEiA1A5Q5

Genome annotation databases

EnsembliENSRNOT00000033932; ENSRNOP00000059913; ENSRNOG00000024726
ENSRNOT00000071532; ENSRNOP00000067344; ENSRNOG00000045905
GeneIDi108348070
689582
KEGGirno:108348070
rno:689582
UCSCiRGD:1591045 rat

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
55693
RGDi1591045 Kdm4d

Phylogenomic databases

eggNOGiKOG0958 Eukaryota
ENOG410XP0T LUCA
GeneTreeiENSGT00940000162152
HOGENOMiHOG000231125
InParanoidiA1A5Q5
KOiK06709
OMAiPPHQNFE
OrthoDBi1186832at2759
PhylomeDBiA1A5Q5
TreeFamiTF106449

Enzyme and pathway databases

ReactomeiR-RNO-3214842 HDMs demethylate histones

Miscellaneous databases

Protein Ontology

More...
PROi
PR:A1A5Q5

Gene expression databases

BgeeiENSRNOG00000024726 Expressed in 4 organ(s), highest expression level in testis
GenevisibleiA1A5Q5 RN

Family and domain databases

InterProiView protein in InterPro
IPR003347 JmjC_dom
IPR003349 JmjN
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
PF02375 JmjN, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00545 JmjN, 1 hit
PROSITEiView protein in PROSITE
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 nameiKDM4D_RAT
<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: A1A5Q5
<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/Swiss-Prot: June 16, 2009
Last sequence update: January 23, 2007
Last modified: October 16, 2019
This is version 88 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 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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