KDM5D (lysine demethylase 5D)

Gene Gene information from NCBI Gene database.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID 8284
Gene name Lysine demethylase 5D
Gene symbol KDM5D
Synonyms (NCBI Gene)
HYHYAJARID1DSMCY
Chromosome Y
Chromosome location Yq11.223
Summary 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.
15
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 (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
23
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (23)
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin IBA
GO:0001650 Component Fibrillar center IDA
GO:0002457 Process T cell antigen processing and presentation IEA
GO:0003677 Function DNA binding IEA
GO:0005515 Function Protein binding IPI 27185910
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
426000 11115 ENSG00000012817
Protein Protein information from UniProt database.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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 associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
3
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Show/Hide Unknown Diseases (3)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
AUTISM — GWAS catalog
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
SPERMATOGENIC FAILURE, NONOBSTRUCTIVE, Y-LINKED — CTD, Disgenet
CTD, Disgenet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
SPERMATOGENIC FAILURE, Y-LINKED, 2 — ClinVar, HPO
ClinVar, HPO
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Show/Hide Text Mining Associations (30)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Arteriosclerosis Arteriosclerosis BEFREE 29196750
★★★★★
★☆☆☆☆
Found in Text Mining only
Asthma Asthma Pubtator 33998076 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Atherosclerosis Atherosclerosis BEFREE 29196750
★★★★★
★☆☆☆☆
Found in Text Mining only
Azoospermia Azoospermia HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Bronchiolitis Bronchiolitis Pubtator 33851876 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Carcinoma Renal Cell Renal cell carcinoma Pubtator 21738768, 28332632, 36890610 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Carcinoma Squamous Cell Squamous cell carcinoma Pubtator 37974379 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Cardiovascular Diseases Cardiovascular Diseases BEFREE 30826357
★★★★★
★☆☆☆☆
Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma Renal Carcinoma BEFREE 21738768, 28332632
★★★★★
★☆☆☆☆
Found in Text Mining only
Coronary Artery Disease Coronary artery disease BEFREE 29196750
★★★★★
★☆☆☆☆
Found in Text Mining only