KDM5D (lysine demethylase 5D)

Gene
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
8284
Gene name Gene Name - the full gene name approved by the HGNC.
Lysine demethylase 5D
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
KDM5D
Synonyms (NCBI Gene) Gene synonyms aliases
HY, HYA, JARID1D, SMCY
Chromosome Chromosome number
Y
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
Yq11.223
Summary Summary of gene provided in NCBI Entrez Gene.
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
miRNA miRNA information provided by mirtarbase database.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(15)
miRTarBase ID miRNA Experiments Reference
MIRT018612 hsa-miR-335-5p Microarray 18185580
MIRT029979 hsa-miR-26b-5p Microarray 19088304
MIRT1084890 hsa-miR-1227 CLIP-seq
MIRT1084891 hsa-miR-4252 CLIP-seq
MIRT1084892 hsa-miR-4719 CLIP-seq
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(15)
GO ID Ontology Definition Evidence Reference
GO:0001650 Component Fibrillar center IDA
GO:0003677 Function DNA binding IEA
GO:0005515 Function Protein binding IPI 27185910
GO:0005634 Component Nucleus IBA 21873635
GO:0005654 Component Nucleoplasm TAS
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
426000 11115 ENSG00000012817
Protein
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID Q9BY66
Protein name Lysine-specific demethylase 5D (EC 1.14.11.67) (Histocompatibility Y antigen) (H-Y) (Histone demethylase JARID1D) (Jumonji/ARID domain-containing protein 1D) (Protein SmcY) ([histone H3]-trimethyl-L-lysine(4) demethylase 5D)
Protein 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 a
PDB 2E6R , 2YQE
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02375 JmjN 15 → 48 jmjN domain Family
PF01388 ARID 81 → 165 ARID/BRIGHT DNA binding domain Domain
PF00628 PHD 316 → 364 PHD-finger Domain
PF02373 JmjC 491 → 607 JmjC domain, hydroxylase Domain
PF02928 zf-C5HC2 697 → 749 C5HC2 zinc finger Domain
PF08429 PLU-1 762 → 1087 PLU-1-like protein Family
Tissue specificity TISSUE SPECIFICITY: Expression is highly down-regulated in metastatic prostate tumors. {ECO:0000269|PubMed:26747897}.
Sequence 
MEPGCDEFLPPPECPVFEPSWAEFQDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEV
DNFRFTPRVQRLNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERKILDLYSLSKIVI
EEGGYEAICKDRRWARVAQRLHYPPGKNIGSLLRSHYERIIYPYEMFQSGANHVQCNTHP
FDNEVKDKEYKPHSIPLRQSVQPSKFSSYSRRAKRLQPDPEPTEEDIEKHPELKKLQIYG
PGPKMMGLGLMAKDKDKTVHKKVTCPPTVTVKDEQSGGGNVSSTLLKQHLSLEPCTKTTM
QLRKNHSSAQFIDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPK
CILAECKQPPEAFGFEQATQEYSLQSFGEMADSFKSDYFNMPVHMVPTELVEKEFWRLVS
SIEEDVTVEYGADIHSKEFGSGFPVSNSKQNLSPEEKEYATSGWNLNVMPVLDQSVLCHI
NADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMK
MLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYN
FAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAAFPETLDLNLAVAVHKEM
FIMVQEERRLRKALLEKGVTEAEREAFELLPDDERQCIKCKTTCFLSALACYDCPDGLVC
LSHINDLCKCSSSRQYLRYRYTLDELPTMLHKLKIRAESFDTWANKVRVALEVEDGRKRS
FEELRALESEARERRFPNSELLQRLKNCLSEVEACIAQVLGLVSGQVARMDTPQLTLTEL
RVLLEQMGSLPCAMHQIGDVKDVLEQVEAYQAEAREALATLPSSPGLLRSLLERGQQLGV
EVPEAHQLQQQVEQAQWLDEVKQALAPSAHRGSLVIMQGLLVMGAKIASSPSVDKARAEL
QELLTIAERWEEKAHFCLEARQKHPPATLEAIIRETENIPVHLPNIQALKEALTKAQAWI
ADVDEIQNGDHYPCLDDLEGLVAVGRDLPVGLEELRQLELQVLTAHSWREKASKTFLKKN
SCYTLLEVLCPCADAGSDSTKRSRWMEKALGLYQCDTELLGLSAQDLRDPGSVIVAFKEG
EQKEKEGILQLRRTNSAKPSPLAPSLMASSPTSICVCGQVPAGVGVLQCDLCQDWFHGQC
VSVPHLLTSPKPSLTSSPLLAWWEWDTKFLCPLCMRSRRPRLETILALLVALQRLPVRLP
EGEALQCLTERAIGWQDRARKALASEDVTALLRQLAELRQQLQAKPRPEEASVYTSATAC
DPIREGSGNNISKVQGLLENGDSVTSPENMAPGKGSDLELLSSLLPQLTGPVLELPEAIR
APLEELMMEGDLLEVTLDENHSIWQLLQAGQPPDLDRIRTLLELEKFEHQGSRTRSRALE
RRRRRQKVDQGRNVENLVQQELQSKRARSSGIMSQVGREEEHYQEKADRENMFLTPSTDH
SPFLKGNQNSLQHKDSGSSAACPSLMPLLQLSYSDEQQL
Sequence length 1539
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
  Reactome
    HDMs demethylate histones
Associated diseases Disease information provided by ClinVar, GenCC, and GWAS databases.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (1)
Causal
Disease term Disease name dbSNP ID References
Azoospermia Azoospermia rs200969445, rs144567652, rs765353898
Show/Hide Text Mining Associations (16)
Associations from Text Mining
Disease Name Relationship Type References
Asthma Associate 33998076
Bronchiolitis Associate 33851876
Carcinoma Renal Cell Associate 21738768, 28332632, 36890610
Carcinoma Squamous Cell Associate 37974379
Coronary Disease Associate 36688193
Death Associate 34127738
Glioblastoma Associate 33470396
Guillain Barre Syndrome Associate 35388043
Heart Failure Associate 35346191
Lung Neoplasms Associate 34127738