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Entry version 155 (16 Oct 2019)
Sequence version 2 (24 Oct 2001)
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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

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-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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
<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

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

<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.

Note: No experimental confirmation available.
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. No experimental confirmation available.
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: No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
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

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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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

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CCDSi
CCDS30541.1 [Q62240-1]

Protein sequence database of the Protein Information Resource

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PIRi
I48776

NCBI Reference Sequences

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

Genome annotation databases

Ensembl eukaryotic genome annotation project

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

Database of genes from NCBI RefSeq genomes

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GeneIDi
20592

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
mmu:20592

UCSC genome browser

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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

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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

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ChiTaRSi
Kdm5d mouse

Protein Ontology

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PROi
PR:Q62240

The Stanford Online Universal Resource for Clones and ESTs

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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

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ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

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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: October 16, 2019
This is version 155 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

Complete proteome, 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
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