Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

UniProtKB - Q62240 (KDM5D_MOUSE)

Entry version 156 (11 Dec 2019)
Sequence version 2 (24 Oct 2001)
Previous versions | rss
Help videoAdd a publicationFeedback
Protein

Lysine-specific demethylase 5D

Gene

Kdm5d

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 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-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May play a role in spermatogenesis. Involved in transcriptional repression of diverse metastasis-associated genes; in this function seems to cooperate with ZMYND8. Suppresses prostate cancer cell invasion. Regulates androgen receptor (AR) transcriptional activity by demethylating H3K4me3 active transcription marks (By similarity).By similarity2 Publications

Miscellaneous

KDM5D encodes an H-Y epitope that is defined by the octamer peptide TENSGKDI; since no similar peptide was found in KDM5C, it is presumably the genetic basis for the antigenic difference between males and females that contributes toward a tissue transplant rejection response.

<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

Protein has several cofactor binding sites:

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 sitei4392-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 bindingi513Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi515Iron; catalyticBy similarity1
Binding sitei5212-oxoglutarateBy similarity1
Binding sitei5232-oxoglutarateBy similarity1
Binding sitei5312-oxoglutarateBy similarity1
Metal bindingi601Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 fingeri325 – 371PHD-type 1PROSITE-ProRule annotationAdd BLAST47
Zinc fingeri706 – 758C5HC2By similarityAdd BLAST53
Zinc fingeri1182 – 1243PHD-type 2PROSITE-ProRule annotationAdd BLAST62

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular 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-MMU-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 5D (EC:1.14.11.-)
Alternative name(s):
Histocompatibility Y antigen
Short name:
H-Y
Histone demethylase JARID1D
Jumonji/ARID domain-containing protein 1D
Protein SmcY
<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:Kdm5d
Synonyms:Hya, Jarid1d, Smcy
<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>OrganismiMus musculus (Mouse)
<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 identifieri10090 [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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_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
  • UP000000589 <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 Y

Organism-specific databases

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

More...MGIi		MGI:99780 Kdm5d

<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_00002005891 – 1548Lysine-specific demethylase 5DAdd BLAST1548

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki205Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki229Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki244Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki279Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
<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 residuei300PhosphoserineBy similarity1
Modified residuei316PhosphoserineBy similarity1
Modified residuei889PhosphoserineBy similarity1
Modified residuei893PhosphoserineBy similarity1
Cross-linki1123Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei1355PhosphoserineBy similarity1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

Encyclopedia of Proteome Dynamics

More...EPDi		Q62240

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

More...PaxDbi		Q62240

PeptideAtlas

More...PeptideAtlasi		Q62240

PRoteomics IDEntifications database

More...PRIDEi		Q62240

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		Q62240

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

More...PhosphoSitePlusi		Q62240

<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		ENSMUSG00000056673 Expressed in 220 organ(s), highest expression level in fibroblast

ExpressionAtlas, Differential and Baseline Expression

More...ExpressionAtlasi		Q62240 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...Genevisiblei		Q62240 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_section">'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_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Interacts withPCGF6, MSH5, ZMYND8, AR.

By similarity

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		203342, 3 interactors

STRING: functional protein association networks

More...STRINGi		10090.ENSMUSP00000061095

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...RNActi		Q62240 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

3D structure databases

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

More...SMRi		Q62240

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>Domaini14 – 55JmjNPROSITE-ProRule annotationAdd BLAST42
Domaini79 – 169ARIDPROSITE-ProRule annotationAdd BLAST91
Domaini467 – 633JmjCPROSITE-ProRule annotationAdd BLAST167

<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 JmjC domain is required for enzymatic activity.By similarity

<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 JARID1 histone demethylase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri325 – 371PHD-type 1PROSITE-ProRule annotationAdd BLAST47
Zinc fingeri706 – 758C5HC2By similarityAdd BLAST53
Zinc fingeri1182 – 1243PHD-type 2PROSITE-ProRule annotationAdd BLAST62

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG1246 Eukaryota
ENOG410XR9J LUCA

Ensembl GeneTree

More...GeneTreei		ENSGT00940000161236

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000290719

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q62240

KEGG Orthology (KO)

More...KOi		K11446

Identification of Orthologs from Complete Genome Data

More...OMAi		EACISQV

Database of Orthologous Groups

More...OrthoDBi		664180at2759

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q62240

TreeFam database of animal gene trees

More...TreeFami		TF106476

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.150.60, 1 hit
3.30.40.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR001606 ARID_dom
IPR036431 ARID_dom_sf
IPR003347 JmjC_dom
IPR003349 JmjN
IPR013637 Lys_sp_deMease-like_dom
IPR019786 Zinc_finger_PHD-type_CS
IPR004198 Znf_C5HC2
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01388 ARID, 1 hit
PF02373 JmjC, 1 hit
PF02375 JmjN, 1 hit
PF00628 PHD, 1 hit
PF08429 PLU-1, 1 hit
PF02928 zf-C5HC2, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00501 BRIGHT, 1 hit
SM00558 JmjC, 1 hit
SM00545 JmjN, 1 hit
SM00249 PHD, 2 hits

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF46774 SSF46774, 1 hit
SSF57903 SSF57903, 2 hits

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51011 ARID, 1 hit
PS51184 JMJC, 1 hit
PS51183 JMJN, 1 hit
PS01359 ZF_PHD_1, 2 hits
PS50016 ZF_PHD_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_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>Sequences (4+)i

<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.

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 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q62240-1) [UniParc]FASTAAdd to basket

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

« Hide
        10         20         30         40         50
MKPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA 
        60         70         80         90        100
DWQPPFAVEV DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL 
       110        120        130        140        150
KIPNVERKIL DLYSLNKIVM EEGGYEAICK DRRWARVAQR LNYPSGKNIG 
       160        170        180        190        200
SLLRSHYERI IYPYEIFQSG ANLVQCNTDP FDSEERDKEY KPHSIPLRQS 
       210        220        230        240        250
VQPSKFSCYS RRGKRLQPEP EPTEEDIEKN PELKKLQIYG AGPKMIGLGL 
       260        270        280        290        300
KAKEKTLRKK DSKQPDKEEV TCPATIVVKG EASEFGKVTS AFSDKNLNHS 
       310        320        330        340        350
FEPCMKMTMQ LRNNHSSTQF MNSYVCRICS RGDEVDKFLL CDGCSDNYHI 
       360        370        380        390        400
FCLLPPLSEV PKGVWRCPKC ILAECKSPPE AFGFEQATQE YTLQSFGEMA 
       410        420        430        440        450
DSFKADYFNM PVHMVPTEVV EKEFWRLVSS IEEDVTVEYG ADIHSKEFGS 
       460        470        480        490        500
GFPVNNSKWD LSPEEKEYAA CGWNLNVMPV LDQSVLCHIN ADISGMKVPW 
       510        520        530        540        550
LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA AEHLEDVMKR 
       560        570        580        590        600
LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG EFVITFPRAY 
       610        620        630        640        650
HSGFNQGYNF AEAVNFCTAD WLPVGRQCIE HYRRLRRYCV FSHEELICKM 
       660        670        680        690        700
AAFPEKLDLN LAVAVHKEMF IMVQEERRLR KTLLEKGITE AEREAFELLP 
       710        720        730        740        750
DDERQCIKCK TTCFLSALAC YDCPDSLVCL SHINDLCKCS RNRQYLRYRY 
       760        770        780        790        800
TLDELPAMLQ KLKIRAESFD NWANKVQAAL EVEDGRKRSF EELRALESEA 
       810        820        830        840        850
RDRRFPNSEL LQRLKKCLTE AEACISQVLG LISNSEDRLQ TPQITLTELQ 
       860        870        880        890        900
LLLKQMGTLP CTMHQIDEVK DVLQQVESYQ IETREALTSL PYSLEILQSL 
       910        920        930        940        950
MEKGQQLRVE VPEAHQLEEL LEQAQWLDQV KQALAPSGQR HSLVIMKKLL 
       960        970        980        990       1000
VMGTKVASSP SVNKARAELQ ELLTIAECWE EKAHFCLKAS QKHSPATLEV 
      1010       1020       1030       1040       1050
IIREAENIPV YLPNIQSLKE ALTKAQAWIA DVNEIQNGDH YPCLDDLEGL 
      1060       1070       1080       1090       1100
VAVGRDLPVE LEELRQLENQ VLTAHSWKEK ASKTFLKKNS CYTLLEVLCP 
      1110       1120       1130       1140       1150
CADAGSVSTK RSRWIEKEMG LYKYDTELLG LSAQDLRDPG SVIMAFKEGE 
      1160       1170       1180       1190       1200
EKEKEGILHL RHINSAKPSP MSSSMNASAT SICICGQVCA GVESLQCDLC 
      1210       1220       1230       1240       1250
HDWFHGQCVT VPHLLSSVRA SHTSSQLLAW WEWDTKFLCP LCMRSRRPRL 
      1260       1270       1280       1290       1300
ETILSLLVGL QRLSVRLPEG EALQCLTERA IGWQGRARQA LASEDVTALL 
      1310       1320       1330       1340       1350
KQLEKSRQQL QDELRHKKPP TLPSGFAFDC LTENSGKDIL KEEEELVLNE 
      1360       1370       1380       1390       1400
ERIKSSEKIV PKESSCKGDK ELLPSLLSQL TGPVLELPEA TRAPLEELMM 
      1410       1420       1430       1440       1450
EGDLLEVTLD ENYSIWQLLQ AGQNPNLERI HTLLELEKPE NPGNWSEEQT 
      1460       1470       1480       1490       1500
PERRRQRRQK VVLSRKGEDF TQKELESKRV KSSRIKPKEE KFQKPILGDN 
      1510       1520       1530       1540 
VLYTHHTEHT NILKEHINSV QGKDPSPSSS FPSLTPLLHL SYFHQQKL
Length:1,548
Mass (Da):177,018
Last modified:October 24, 2001 - 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:i44AAB94708EA4A02
GO
Isoform 2 (identifier: Q62240-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-398: Missing.

Show »
Length:1,150
Mass (Da):131,396
Checksum:i2920BEB66B2E98CF
GO
Isoform 3 (identifier: Q62240-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     583-586: VRTN → SIWK
     587-1548: Missing.

Note: May be due to an intron retention.Curated
Show »
Length:586
Mass (Da):67,244
Checksum:iA5764F58390D60F8
GO
Isoform 4 (identifier: Q62240-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     687-691: GITEA → LSLQA
     692-1548: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.Curated
Show »
Length:691
Mass (Da):79,525
Checksum:i40681B920A8B54FE
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 are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q8BQM3Q8BQM3_MOUSE
Lysine-specific demethylase 5D
Kdm5d Jarid1d
476Annotation score:

Annotation score:1 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>
A0A087WR43A0A087WR43_MOUSE
Lysine-specific demethylase 5D
Kdm5d
271Annotation score:

Annotation score:1 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 Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti160 – 162IIY → SFT in CAA82760 (PubMed:7524912).Curated3
Sequence conflicti167F → S in CAA82760 (PubMed:7524912).Curated1
Sequence conflicti215R → K in CAA82760 (PubMed:7524912).Curated1

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_0264121 – 398Missing in isoform 2. 1 PublicationAdd BLAST398
Alternative sequenceiVSP_026413583 – 586VRTN → SIWK in isoform 3. 1 Publication4
Alternative sequenceiVSP_026414587 – 1548Missing in isoform 3. 1 PublicationAdd BLAST962
Alternative sequenceiVSP_026415687 – 691GITEA → LSLQA in isoform 4. 1 Publication5
Alternative sequenceiVSP_026416692 – 1548Missing in isoform 4. 1 PublicationAdd BLAST857

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
AF127244 mRNA Translation: AAD53048.1
AK140971 mRNA Translation: BAE24534.1
BC059077 mRNA Translation: AAH59077.1
Z29652 mRNA Translation: CAA82760.1

The Consensus CDS (CCDS) project

More...CCDSi		CCDS30541.1 [Q62240-1]

Protein sequence database of the Protein Information Resource

More...PIRi		I48776

NCBI Reference Sequences

More...RefSeqi		NP_035549.1, NM_011419.3 [Q62240-1]

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSMUST00000055032; ENSMUSP00000061095; ENSMUSG00000056673 [Q62240-1]
ENSMUST00000186696; ENSMUSP00000140663; ENSMUSG00000056673 [Q62240-4]

Database of genes from NCBI RefSeq genomes

More...GeneIDi		20592

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		mmu:20592

UCSC genome browser

More...UCSCi		uc009uyz.1 mouse [Q62240-3]
uc009uzb.1 mouse [Q62240-1]

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
AF127244 mRNA Translation: AAD53048.1
AK140971 mRNA Translation: BAE24534.1
BC059077 mRNA Translation: AAH59077.1
Z29652 mRNA Translation: CAA82760.1
CCDSiCCDS30541.1 [Q62240-1]
PIRiI48776
RefSeqiNP_035549.1, NM_011419.3 [Q62240-1]

3D structure databases

SMRiQ62240
ModBaseiSearch...

Protein-protein interaction databases

BioGridi203342, 3 interactors
STRINGi10090.ENSMUSP00000061095

PTM databases

iPTMnetiQ62240
PhosphoSitePlusiQ62240

Proteomic databases

EPDiQ62240
PaxDbiQ62240
PeptideAtlasiQ62240
PRIDEiQ62240

Genome annotation databases

EnsembliENSMUST00000055032; ENSMUSP00000061095; ENSMUSG00000056673 [Q62240-1]
ENSMUST00000186696; ENSMUSP00000140663; ENSMUSG00000056673 [Q62240-4]
GeneIDi20592
KEGGimmu:20592
UCSCiuc009uyz.1 mouse [Q62240-3]
uc009uzb.1 mouse [Q62240-1]

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		8284
MGIiMGI:99780 Kdm5d

Phylogenomic databases

eggNOGiKOG1246 Eukaryota
ENOG410XR9J LUCA
GeneTreeiENSGT00940000161236
HOGENOMiHOG000290719
InParanoidiQ62240
KOiK11446
OMAiEACISQV
OrthoDBi664180at2759
PhylomeDBiQ62240
TreeFamiTF106476

Enzyme and pathway databases

ReactomeiR-MMU-3214842 HDMs demethylate histones

Miscellaneous databases

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

More...ChiTaRSi		Kdm5d mouse

Protein Ontology

More...PROi		PR:Q62240
RNActiQ62240 protein

The Stanford Online Universal Resource for Clones and ESTs

More...SOURCEi		Search...

Gene expression databases

BgeeiENSMUSG00000056673 Expressed in 220 organ(s), highest expression level in fibroblast
ExpressionAtlasiQ62240 baseline and differential
GenevisibleiQ62240 MM

Family and domain databases

Gene3Di1.10.150.60, 1 hit
3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR001606 ARID_dom
IPR036431 ARID_dom_sf
IPR003347 JmjC_dom
IPR003349 JmjN
IPR013637 Lys_sp_deMease-like_dom
IPR019786 Zinc_finger_PHD-type_CS
IPR004198 Znf_C5HC2
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF01388 ARID, 1 hit
PF02373 JmjC, 1 hit
PF02375 JmjN, 1 hit
PF00628 PHD, 1 hit
PF08429 PLU-1, 1 hit
PF02928 zf-C5HC2, 1 hit
SMARTiView protein in SMART
SM00501 BRIGHT, 1 hit
SM00558 JmjC, 1 hit
SM00545 JmjN, 1 hit
SM00249 PHD, 2 hits
SUPFAMiSSF46774 SSF46774, 1 hit
SSF57903 SSF57903, 2 hits
PROSITEiView protein in PROSITE
PS51011 ARID, 1 hit
PS51184 JMJC, 1 hit
PS51183 JMJN, 1 hit
PS01359 ZF_PHD_1, 2 hits
PS50016 ZF_PHD_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 nameiKDM5D_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: Q62240
Secondary accession number(s): Q3US03
, Q6PCX3, Q9QVR9, Q9R040
<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: October 24, 2001
Last sequence update: October 24, 2001
Last modified: December 11, 2019
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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again