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Q62240 (KDM5D_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:Kdm5d
Synonyms:Hya, Jarid1d, Smcy
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length1548 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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. Ref.5 Ref.6

Cofactor

Ascorbate By similarity.

Binds 1 Fe2+ ion per subunit By similarity.

Subunit structure

Interacts with PCGF6 and MSH5 By similarity.

Subcellular location

Nucleus By similarity.

Domain

The JmjC domain is required for enzymatic activity By similarity.

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.

Sequence similarities

Belongs to the JARID1 histone demethylase family.

Contains 1 ARID domain.

Contains 1 JmjC domain.

Contains 1 JmjN domain.

Contains 2 PHD-type zinc fingers.

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q62240-1)

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.
Isoform 2 (identifier: Q62240-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-398: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q62240-3)

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.
Isoform 4 (identifier: Q62240-4)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 15481548Lysine-specific demethylase 5D
PRO_0000200589

Regions

Domain14 – 5542JmjN
Domain79 – 16991ARID
Domain467 – 633167JmjC
Zinc finger325 – 37147PHD-type 1
Zinc finger1182 – 124362PHD-type 2

Sites

Metal binding5131Iron; catalytic By similarity
Metal binding5161Iron; catalytic By similarity
Metal binding6011Iron; catalytic By similarity

Natural variations

Alternative sequence1 – 398398Missing in isoform 2.
VSP_026412
Alternative sequence583 – 5864VRTN → SIWK in isoform 3.
VSP_026413
Alternative sequence587 – 1548962Missing in isoform 3.
VSP_026414
Alternative sequence687 – 6915GITEA → LSLQA in isoform 4.
VSP_026415
Alternative sequence692 – 1548857Missing in isoform 4.
VSP_026416

Experimental info

Sequence conflict160 – 1623IIY → SFT in CAA82760. Ref.4
Sequence conflict1671F → S in CAA82760. Ref.4
Sequence conflict2151R → K in CAA82760. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 24, 2001. Version 2.
Checksum: 44AAB94708EA4A02

FASTA1,548177,018
        10         20         30         40         50         60 
MKPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV 

        70         80         90        100        110        120 
DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERKIL DLYSLNKIVM 

       130        140        150        160        170        180 
EEGGYEAICK DRRWARVAQR LNYPSGKNIG SLLRSHYERI IYPYEIFQSG ANLVQCNTDP 

       190        200        210        220        230        240 
FDSEERDKEY KPHSIPLRQS VQPSKFSCYS RRGKRLQPEP EPTEEDIEKN PELKKLQIYG 

       250        260        270        280        290        300 
AGPKMIGLGL KAKEKTLRKK DSKQPDKEEV TCPATIVVKG EASEFGKVTS AFSDKNLNHS 

       310        320        330        340        350        360 
FEPCMKMTMQ LRNNHSSTQF MNSYVCRICS RGDEVDKFLL CDGCSDNYHI FCLLPPLSEV 

       370        380        390        400        410        420 
PKGVWRCPKC ILAECKSPPE AFGFEQATQE YTLQSFGEMA DSFKADYFNM PVHMVPTEVV 

       430        440        450        460        470        480 
EKEFWRLVSS IEEDVTVEYG ADIHSKEFGS GFPVNNSKWD LSPEEKEYAA CGWNLNVMPV 

       490        500        510        520        530        540 
LDQSVLCHIN ADISGMKVPW LYVGMVFSAF CWHIEDHWSY SINYLHWGEP KTWYGVPSLA 

       550        560        570        580        590        600 
AEHLEDVMKR LTPELFDSQP DLLHQLVTLM NPNTLMSHGV PVVRTNQCAG EFVITFPRAY 

       610        620        630        640        650        660 
HSGFNQGYNF AEAVNFCTAD WLPVGRQCIE HYRRLRRYCV FSHEELICKM AAFPEKLDLN 

       670        680        690        700        710        720 
LAVAVHKEMF IMVQEERRLR KTLLEKGITE AEREAFELLP DDERQCIKCK TTCFLSALAC 

       730        740        750        760        770        780 
YDCPDSLVCL SHINDLCKCS RNRQYLRYRY TLDELPAMLQ KLKIRAESFD NWANKVQAAL 

       790        800        810        820        830        840 
EVEDGRKRSF EELRALESEA RDRRFPNSEL LQRLKKCLTE AEACISQVLG LISNSEDRLQ 

       850        860        870        880        890        900 
TPQITLTELQ LLLKQMGTLP CTMHQIDEVK DVLQQVESYQ IETREALTSL PYSLEILQSL 

       910        920        930        940        950        960 
MEKGQQLRVE VPEAHQLEEL LEQAQWLDQV KQALAPSGQR HSLVIMKKLL VMGTKVASSP 

       970        980        990       1000       1010       1020 
SVNKARAELQ ELLTIAECWE EKAHFCLKAS QKHSPATLEV IIREAENIPV YLPNIQSLKE 

      1030       1040       1050       1060       1070       1080 
ALTKAQAWIA DVNEIQNGDH YPCLDDLEGL VAVGRDLPVE LEELRQLENQ VLTAHSWKEK 

      1090       1100       1110       1120       1130       1140 
ASKTFLKKNS CYTLLEVLCP CADAGSVSTK RSRWIEKEMG LYKYDTELLG LSAQDLRDPG 

      1150       1160       1170       1180       1190       1200 
SVIMAFKEGE EKEKEGILHL RHINSAKPSP MSSSMNASAT SICICGQVCA GVESLQCDLC 

      1210       1220       1230       1240       1250       1260 
HDWFHGQCVT VPHLLSSVRA SHTSSQLLAW WEWDTKFLCP LCMRSRRPRL ETILSLLVGL 

      1270       1280       1290       1300       1310       1320 
QRLSVRLPEG EALQCLTERA IGWQGRARQA LASEDVTALL KQLEKSRQQL QDELRHKKPP 

      1330       1340       1350       1360       1370       1380 
TLPSGFAFDC LTENSGKDIL KEEEELVLNE ERIKSSEKIV PKESSCKGDK ELLPSLLSQL 

      1390       1400       1410       1420       1430       1440 
TGPVLELPEA TRAPLEELMM EGDLLEVTLD ENYSIWQLLQ AGQNPNLERI HTLLELEKPE 

      1450       1460       1470       1480       1490       1500 
NPGNWSEEQT PERRRQRRQK VVLSRKGEDF TQKELESKRV KSSRIKPKEE KFQKPILGDN 

      1510       1520       1530       1540 
VLYTHHTEHT NILKEHINSV QGKDPSPSSS FPSLTPLLHL SYFHQQKL 

« Hide

Isoform 2 [UniParc].

Checksum: 2920BEB66B2E98CF
Show »

FASTA1,150131,396
Isoform 3 [UniParc].

Checksum: A5764F58390D60F8
Show »

FASTA58667,244
Isoform 4 [UniParc].

Checksum: 40681B920A8B54FE
Show »

FASTA69179,525

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF127244 mRNA. Translation: AAD53048.1.
AK140971 mRNA. Translation: BAE24534.1.
BC059077 mRNA. Translation: AAH59077.1.
Z29652 mRNA. Translation: CAA82760.1.
PIRI48776.
RefSeqNP_035549.1. NM_011419.3.
UniGeneMm.262676.

3D structure databases

ProteinModelPortalQ62240.
SMRQ62240. Positions 13-171, 319-659, 1180-1245.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid203342. 3 interactions.
STRING10090.ENSMUSP00000061095.

PTM databases

PhosphoSiteQ62240.

Proteomic databases

PaxDbQ62240.
PRIDEQ62240.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000055032; ENSMUSP00000061095; ENSMUSG00000056673. [Q62240-1]
GeneID20592.
KEGGmmu:20592.
UCSCuc009uyz.1. mouse. [Q62240-3]
uc009uzb.1. mouse. [Q62240-1]

Organism-specific databases

CTD8284.
MGIMGI:99780. Kdm5d.

Phylogenomic databases

eggNOGNOG327026.
GeneTreeENSGT00530000063118.
HOGENOMHOG000290719.
InParanoidQ62240.
KOK11446.
OMAILMNANV.
OrthoDBEOG7D85VK.
PhylomeDBQ62240.
TreeFamTF106476.

Gene expression databases

BgeeQ62240.
GenevestigatorQ62240.

Family and domain databases

Gene3D1.10.150.60. 1 hit.
3.30.40.10. 2 hits.
InterProIPR001606. 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]
PfamPF01388. 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]
SMARTSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
[Graphical view]
SUPFAMSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 2 hits.
PROSITEPS51011. 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]
ProtoNetSearch...

Other

NextBio298905.
PROQ62240.
SOURCESearch...

Entry information

Entry nameKDM5D_MOUSE
AccessionPrimary (citable) accession number: Q62240
Secondary accession number(s): Q3US03 expand/collapse secondary AC list , Q6PCX3, Q9QVR9, Q9R040
Entry history
Integrated into UniProtKB/Swiss-Prot: October 24, 2001
Last sequence update: October 24, 2001
Last modified: April 16, 2014
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot