SubmitCancel

Skip Header

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

Q62240

- KDM5D_MOUSE

UniProt

Q62240 - KDM5D_MOUSE

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

Lysine-specific demethylase 5D

Gene
Kdm5d, Hya, Jarid1d, Smcy
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at transcript leveli

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 By similarity.2 Publications

Cofactori

Ascorbate By similarity.
Binds 1 Fe2+ ion per subunit By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi513 – 5131Iron; catalytic By similarity
Metal bindingi516 – 5161Iron; catalytic By similarity
Metal bindingi601 – 6011Iron; catalytic By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri325 – 37147PHD-type 1Add
BLAST
Zinc fingeri1182 – 124362PHD-type 2Add
BLAST

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. histone demethylase activity (H3-K4 specific) Source: Ensembl
  3. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors Source: InterPro
  4. zinc ion binding Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding, Zinc

Names & Taxonomyi

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
Gene namesi
Name:Kdm5d
Synonyms:Hya, Jarid1d, Smcy
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome Y

Organism-specific databases

MGIiMGI:99780. Kdm5d.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 15481548Lysine-specific demethylase 5DPRO_0000200589Add
BLAST

Proteomic databases

PaxDbiQ62240.
PRIDEiQ62240.

PTM databases

PhosphoSiteiQ62240.

Expressioni

Gene expression databases

BgeeiQ62240.
GenevestigatoriQ62240.

Interactioni

Subunit structurei

Interacts with PCGF6 and MSH5 By similarity.

Protein-protein interaction databases

BioGridi203342. 3 interactions.
STRINGi10090.ENSMUSP00000061095.

Structurei

3D structure databases

ProteinModelPortaliQ62240.
SMRiQ62240. Positions 13-76, 79-171, 319-659, 1179-1248.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 5542JmjNAdd
BLAST
Domaini79 – 16991ARIDAdd
BLAST
Domaini467 – 633167JmjCAdd
BLAST

Domaini

The JmjC domain is required for enzymatic activity By similarity.

Sequence similaritiesi

Contains 1 ARID domain.
Contains 1 JmjC domain.
Contains 1 JmjN domain.

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri325 – 37147PHD-type 1Add
BLAST
Zinc fingeri1182 – 124362PHD-type 2Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG327026.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiQ62240.
KOiK11446.
OMAiILMNANV.
OrthoDBiEOG7D85VK.
PhylomeDBiQ62240.
TreeFamiTF106476.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProiIPR001606. ARID/BRIGHT_DNA-bd.
IPR003347. JmjC_dom.
IPR013637. Lys_sp_deMease_like_dom.
IPR003349. TF_JmjN.
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.
[Graphical view]
PfamiPF01388. 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.
[Graphical view]
SMARTiSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view]
SUPFAMiSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEiPS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. Align

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

This isoform has been chosen as the 'canonical' 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

MKPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA     50
DWQPPFAVEV DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL 100
KIPNVERKIL DLYSLNKIVM EEGGYEAICK DRRWARVAQR LNYPSGKNIG 150
SLLRSHYERI IYPYEIFQSG ANLVQCNTDP FDSEERDKEY KPHSIPLRQS 200
VQPSKFSCYS RRGKRLQPEP EPTEEDIEKN PELKKLQIYG AGPKMIGLGL 250
KAKEKTLRKK DSKQPDKEEV TCPATIVVKG EASEFGKVTS AFSDKNLNHS 300
FEPCMKMTMQ LRNNHSSTQF MNSYVCRICS RGDEVDKFLL CDGCSDNYHI 350
FCLLPPLSEV PKGVWRCPKC ILAECKSPPE AFGFEQATQE YTLQSFGEMA 400
DSFKADYFNM PVHMVPTEVV EKEFWRLVSS IEEDVTVEYG ADIHSKEFGS 450
GFPVNNSKWD LSPEEKEYAA CGWNLNVMPV LDQSVLCHIN ADISGMKVPW 500
LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA AEHLEDVMKR 550
LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG EFVITFPRAY 600
HSGFNQGYNF AEAVNFCTAD WLPVGRQCIE HYRRLRRYCV FSHEELICKM 650
AAFPEKLDLN LAVAVHKEMF IMVQEERRLR KTLLEKGITE AEREAFELLP 700
DDERQCIKCK TTCFLSALAC YDCPDSLVCL SHINDLCKCS RNRQYLRYRY 750
TLDELPAMLQ KLKIRAESFD NWANKVQAAL EVEDGRKRSF EELRALESEA 800
RDRRFPNSEL LQRLKKCLTE AEACISQVLG LISNSEDRLQ TPQITLTELQ 850
LLLKQMGTLP CTMHQIDEVK DVLQQVESYQ IETREALTSL PYSLEILQSL 900
MEKGQQLRVE VPEAHQLEEL LEQAQWLDQV KQALAPSGQR HSLVIMKKLL 950
VMGTKVASSP SVNKARAELQ ELLTIAECWE EKAHFCLKAS QKHSPATLEV 1000
IIREAENIPV YLPNIQSLKE ALTKAQAWIA DVNEIQNGDH YPCLDDLEGL 1050
VAVGRDLPVE LEELRQLENQ VLTAHSWKEK ASKTFLKKNS CYTLLEVLCP 1100
CADAGSVSTK RSRWIEKEMG LYKYDTELLG LSAQDLRDPG SVIMAFKEGE 1150
EKEKEGILHL RHINSAKPSP MSSSMNASAT SICICGQVCA GVESLQCDLC 1200
HDWFHGQCVT VPHLLSSVRA SHTSSQLLAW WEWDTKFLCP LCMRSRRPRL 1250
ETILSLLVGL QRLSVRLPEG EALQCLTERA IGWQGRARQA LASEDVTALL 1300
KQLEKSRQQL QDELRHKKPP TLPSGFAFDC LTENSGKDIL KEEEELVLNE 1350
ERIKSSEKIV PKESSCKGDK ELLPSLLSQL TGPVLELPEA TRAPLEELMM 1400
EGDLLEVTLD ENYSIWQLLQ AGQNPNLERI HTLLELEKPE NPGNWSEEQT 1450
PERRRQRRQK VVLSRKGEDF TQKELESKRV KSSRIKPKEE KFQKPILGDN 1500
VLYTHHTEHT NILKEHINSV QGKDPSPSSS FPSLTPLLHL SYFHQQKL 1548
Length:1,548
Mass (Da):177,018
Last modified:October 24, 2001 - v2
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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 398398Missing in isoform 2. VSP_026412Add
BLAST
Alternative sequencei583 – 5864VRTN → SIWK in isoform 3. VSP_026413
Alternative sequencei587 – 1548962Missing in isoform 3. VSP_026414Add
BLAST
Alternative sequencei687 – 6915GITEA → LSLQA in isoform 4. VSP_026415
Alternative sequencei692 – 1548857Missing in isoform 4. VSP_026416Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti160 – 1623IIY → SFT in CAA82760. 1 Publication
Sequence conflicti167 – 1671F → S in CAA82760. 1 Publication
Sequence conflicti215 – 2151R → K in CAA82760. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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]
UniGeneiMm.262676.

Genome annotation databases

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

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF127244 mRNA. Translation: AAD53048.1 .
AK140971 mRNA. Translation: BAE24534.1 .
BC059077 mRNA. Translation: AAH59077.1 .
Z29652 mRNA. Translation: CAA82760.1 .
CCDSi CCDS30541.1. [Q62240-1 ]
PIRi I48776.
RefSeqi NP_035549.1. NM_011419.3. [Q62240-1 ]
UniGenei Mm.262676.

3D structure databases

ProteinModelPortali Q62240.
SMRi Q62240. Positions 13-76, 79-171, 319-659, 1179-1248.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 203342. 3 interactions.
STRINGi 10090.ENSMUSP00000061095.

PTM databases

PhosphoSitei Q62240.

Proteomic databases

PaxDbi Q62240.
PRIDEi Q62240.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000055032 ; ENSMUSP00000061095 ; ENSMUSG00000056673 . [Q62240-1 ]
GeneIDi 20592.
KEGGi mmu:20592.
UCSCi uc009uyz.1. mouse. [Q62240-3 ]
uc009uzb.1. mouse. [Q62240-1 ]

Organism-specific databases

CTDi 8284.
MGIi MGI:99780. Kdm5d.

Phylogenomic databases

eggNOGi NOG327026.
GeneTreei ENSGT00530000063118.
HOGENOMi HOG000290719.
InParanoidi Q62240.
KOi K11446.
OMAi ILMNANV.
OrthoDBi EOG7D85VK.
PhylomeDBi Q62240.
TreeFami TF106476.

Miscellaneous databases

NextBioi 298905.
PROi Q62240.
SOURCEi Search...

Gene expression databases

Bgeei Q62240.
Genevestigatori Q62240.

Family and domain databases

Gene3Di 1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProi IPR001606. ARID/BRIGHT_DNA-bd.
IPR003347. JmjC_dom.
IPR013637. Lys_sp_deMease_like_dom.
IPR003349. TF_JmjN.
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.
[Graphical view ]
Pfami 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.
[Graphical view ]
SMARTi SM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view ]
SUPFAMi SSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEi PS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Mouse H-Y encoding Smcy gene and its X chromosomal homolog Smcx."
    Agulnik A.I., Longepied G., Ty M.T., Bishop C.E., Mitchell M.J.
    Mamm. Genome 10:926-929(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Strain: 129/SvJ.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
    Strain: C57BL/6J.
    Tissue: Head.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: C57BL/6.
    Tissue: Brain.
  4. "A mouse Y chromosome gene encoded by a region essential for spermatogenesis and expression of male-specific minor histocompatibility antigens."
    Agulnik A.I., Mitchell M.J., Lerner J.L., Woods D.R., Bishop C.E.
    Hum. Mol. Genet. 3:873-878(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 23-1548 (ISOFORM 3).
    Strain: BALB/c.
    Tissue: Testis.
  5. "Identification of a mouse male-specific transplantation antigen, H-Y."
    Scott D.M., Ehrmann I.E., Ellis P.S., Bishop C.E., Agulnik A.I., Simpson E., Mitchell M.J.
    Nature 376:695-698(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Spermatogenic failure in male mice lacking H-Y antigen."
    Burgoyne P.S., Levy E.R., McLaren A.
    Nature 320:170-172(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiKDM5D_MOUSE
AccessioniPrimary (citable) accession number: Q62240
Secondary accession number(s): Q3US03
, Q6PCX3, Q9QVR9, Q9R040
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 24, 2001
Last sequence update: October 24, 2001
Last modified: July 9, 2014
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi