• Gene id: 8284

Gene Summary

• Gene Symbol: KDM5D   Gene   UCSC   Ensembl
• Aliases: HY, HYA, JARID1D, SMCY
• Gene name: lysine demethylase 5D
• Alternate names: lysine-specific demethylase 5D, H-Y, Jumonji, AT rich interactive domain 1D (RBP2-like), SMC homolog, Y chromosome, Smcy homolog, Y-linked, histocompatibility Y antigen, histone demethylase JARID1D, jumonji/ARID domain-containing protein 1D, lysine (K)-sp,
• Gene location: Yq11.223 (19745340: 19705414)     Exons: 28     NC_000024.10
• Gene summary(Entrez): This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multip
• OMIM: 426000

Protein Summary

• Protein general information: Q9BY66  
  • Name: Lysine specific demethylase 5D (EC 1.14.11. ) (Histocompatibility Y antigen) (H Y) (Histone demethylase JARID1D) (Jumonji/ARID domain containing protein 1D) (Protein SmcY)
  • Length: 1539  
  • Mass: 174,073
• Sequence:

  MEPGCDEFLPPPECPVFEPSWAEFQDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEVDNFRFTPRVQRLNEL
  EAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKNIG
  SLLRSHYERIIYPYEMFQSGANHVQCNTHPFDNEVKDKEYKPHSIPLRQSVQPSKFSSYSRRAKRLQPDPEPTEE
  DIEKHPELKKLQIYGPGPKMMGLGLMAKDKDKTVHKKVTCPPTVTVKDEQSGGGNVSSTLLKQHLSLEPCTKTTM
  QLRKNHSSAQFIDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILAECKQPPEAFGF
  EQATQEYSLQSFGEMADSFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVTVEYGADIHSKEFGSGFPVSNSKQ
  NLSPEEKEYATSGWNLNVMPVLDQSVLCHINADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWY
  GVPSLAAEHLEEVMKMLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYN
  FAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAAFPETLDLNLAVAVHKEMFIMVQEERRLRKALL
  EKGVTEAEREAFELLPDDERQCIKCKTTCFLSALACYDCPDGLVCLSHINDLCKCSSSRQYLRYRYTLDELPTML
  HKLKIRAESFDTWANKVRVALEVEDGRKRSFEELRALESEARERRFPNSELLQRLKNCLSEVEACIAQVLGLVSG
  QVARMDTPQLTLTELRVLLEQMGSLPCAMHQIGDVKDVLEQVEAYQAEAREALATLPSSPGLLRSLLERGQQLGV
  EVPEAHQLQQQVEQAQWLDEVKQALAPSAHRGSLVIMQGLLVMGAKIASSPSVDKARAELQELLTIAERWEEKAH
  FCLEARQKHPPATLEAIIRETENIPVHLPNIQALKEALTKAQAWIADVDEIQNGDHYPCLDDLEGLVAVGRDLPV
  GLEELRQLELQVLTAHSWREKASKTFLKKNSCYTLLEVLCPCADAGSDSTKRSRWMEKALGLYQCDTELLGLSAQ
  DLRDPGSVIVAFKEGEQKEKEGILQLRRTNSAKPSPLAPSLMASSPTSICVCGQVPAGVGVLQCDLCQDWFHGQC
  VSVPHLLTSPKPSLTSSPLLAWWEWDTKFLCPLCMRSRRPRLETILALLVALQRLPVRLPEGEALQCLTERAIGW
  QDRARKALASEDVTALLRQLAELRQQLQAKPRPEEASVYTSATACDPIREGSGNNISKVQGLLENGDSVTSPENM
  APGKGSDLELLSSLLPQLTGPVLELPEAIRAPLEELMMEGDLLEVTLDENHSIWQLLQAGQPPDLDRIRTLLELE
  KFEHQGSRTRSRALERRRRRQKVDQGRNVENLVQQELQSKRARSSGIMSQVGREEEHYQEKADRENMFLTPSTDH
  SPFLKGNQNSLQHKDSGSSAACPSLMPLLQLSYSDEQQL

• Structural information:
  • Protein Domains: JmjN. (14-55)
    ARID. (79-169)
    JmjC. (458-624)
  • Interpro: IPR001606  IPR036431  IPR003347  IPR003349  IPR013637   IPR019786  IPR004198  IPR011011  IPR001965  IPR019787  IPR013083  
  • Prosite: PS51011 PS51184 PS51183 PS01359 PS50016
  • PDB: 2E6R 2YQE
  • PDBsum: 2E6R 2YQE
  • STRING: ENSP00000444293
• Other Databases: GeneCards:  KDM5D  Malacards:  KDM5D

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0002457	T cell antigen processing and presentation	IEA	biological process
GO:0003677	DNA binding	IEA	molecular function
GO:0005575	cellular_component	ND	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0008270	zinc ion binding	IEA	molecular function
GO:0016706	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	IEA	molecular function
GO:0032452	histone demethylase activity	TAS	molecular function
GO:0032452	histone demethylase activity	TAS	molecular function
GO:0032453	histone demethylase activity (H3-K4 specific)	IDA	molecular function
GO:0034720	histone H3-K4 demethylation	IDA	biological process
GO:0055114	oxidation-reduction process	IEA	biological process
GO:0002457	T cell antigen processing and presentation	IEA	biological process
GO:0003677	DNA binding	IEA	molecular function
GO:0005575	cellular_component	ND	cellular component
GO:0005634	nucleus	IEA	cellular component
GO:0005634	nucleus	IEA	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0008270	zinc ion binding	IEA	molecular function
GO:0016491	oxidoreductase activity	IEA	molecular function
GO:0016706	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	IEA	molecular function
GO:0032452	histone demethylase activity	TAS	molecular function
GO:0032452	histone demethylase activity	TAS	molecular function
GO:0032453	histone demethylase activity (H3-K4 specific)	IDA	molecular function
GO:0034720	histone H3-K4 demethylation	IDA	biological process
GO:0046872	metal ion binding	IEA	molecular function
GO:0051213	dioxygenase activity	IEA	molecular function
GO:0055114	oxidation-reduction process	IEA	biological process
GO:0055114	oxidation-reduction process	IEA	biological process
GO:0005575	cellular_component	ND	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0032452	histone demethylase activity	TAS	molecular function
GO:0032452	histone demethylase activity	TAS	molecular function
GO:0032453	histone demethylase activity (H3-K4 specific)	IDA	molecular function
GO:0034720	histone H3-K4 demethylation	IDA	biological process

Diseases

Associated diseases	References
Male factor infertility	MIK: 17296183
Oligozoospermia	MIK: 8864744
Azoospermia	MIK: 8864744
Azoospermia	MIK: 8864744
Oligozoospermia	MIK: 8864744
Male infertility	MIK: 17296183
Role in spermatogenesis	MIK: 18459961
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
17296183	Male infertility			839 (627 infertile men, 212 fertile men)	Male infertility	USP9Y DBY SMCY  RBM1 and DAZ
8864744	Azoospermia, severe oligozoospermia			153 men with azoospermia or severe oligozoospermia whose Y chromosomes were cytogenetically normal	Male infertility	YRRM1 DAZ SMCY
18459961	Role in spermatogenesis				Male infertility
17327269	Teratozoospermia			13 (5 controls, 8 cases)	Male infertility	GSE6967 analyzed by GEO2R (cutoff 1.5 fold)