KDM5D

Protein-coding gene in the species Homo sapiens
KDM5D
Available structures
PDBOrtholog search: PDBe RCSB
List of PDB id codes

2E6R, 2YQE

Identifiers
AliasesKDM5D, HY, HYA, JARID1D, SMCY, lysine demethylase 5D
External IDsOMIM: 426000 MGI: 99780 HomoloGene: 55838 GeneCards: KDM5D
Gene location (Human)
Y chromosome (human)
Chr.Y chromosome (human)[1]
Y chromosome (human)
Genomic location for KDM5D
Genomic location for KDM5D
BandYq11.223Start19,703,865 bp[1]
End19,744,939 bp[1]
Gene location (Mouse)
Y chromosome (mouse)
Chr.Y chromosome (mouse)[2]
Y chromosome (mouse)
Genomic location for KDM5D
Genomic location for KDM5D
BandY|YpterStart897,788 bp[2]
End956,786 bp[2]
RNA expression pattern
Bgee
HumanMouse (ortholog)
Top expressed in
  • rectum

  • right lung

  • prostate

  • urethra

  • trabecular bone

  • Brodmann area 9

  • corpus callosum

  • seminal vesicula

  • right adrenal gland

  • mucosa of urinary bladder
Top expressed in
  • left lung lobe

  • internal carotid artery

  • external carotid artery

  • female urethra

  • male urethra

  • vas deferens

  • triceps brachii muscle

  • epithelium of stomach

  • digastric muscle

  • duodenum
More reference expression data
BioGPS
More reference expression data
Gene ontology
Molecular function
  • histone H3-methyl-lysine-4 demethylase activity
  • DNA binding
  • oxidoreductase activity
  • dioxygenase activity
  • metal ion binding
  • histone demethylase activity
  • androgen receptor binding
  • protein binding
  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • DNA-binding transcription repressor activity, RNA polymerase II-specific
  • chromatin binding
  • histone H3-tri/di/monomethyl-lysine-4 demethylase activity
  • methylated histone binding
Cellular component
  • nucleus
  • nucleoplasm
  • fibrillar center
  • cellular component
  • histone methyltransferase complex
Biological process
  • histone H3-K4 demethylation
  • T cell antigen processing and presentation
  • transcription, DNA-templated
  • regulation of transcription, DNA-templated
  • regulation of androgen receptor signaling pathway
  • chromatin organization
  • regulation of transcription by RNA polymerase II
  • negative regulation of transcription by RNA polymerase II
  • histone H3-K4 demethylation, trimethyl-H3-K4-specific
  • chromatin remodeling
Sources:Amigo / QuickGO
Orthologs
SpeciesHumanMouse
Entrez

8284

20592

Ensembl

ENSG00000012817

ENSMUSG00000056673

UniProt

Q9BY66

Q62240

RefSeq (mRNA)

NM_001146705
NM_001146706
NM_004653

NM_011419

RefSeq (protein)

NP_001140177
NP_001140178
NP_004644

NP_035549

Location (UCSC)Chr Y: 19.7 – 19.74 MbChr Y: 0.9 – 0.96 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Lysine-specific demethylase 5D is an enzyme that in humans is encoded by the KDM5D gene.[5][6][7] KDM5D belongs to the alpha-ketoglutarate-dependent hydroxylases superfamily.

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.[7]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000012817 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000056673 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ Froggatt P (Feb 1977). "The foundation of the "Inst" medical department and its association with the Belfast Fever Hospital". The Ulster Medical Journal. 45 (2): 107–45. PMC 2385577. PMID 795123.
  6. ^ Kent-First MG, Maffitt M, Muallem A, Brisco P, Shultz J, Ekenberg S, Agulnik AI, Agulnik I, Shramm D, Bavister B, Abdul-Mawgood A, VandeBerg J (October 1996). "Gene sequence and evolutionary conservation of human SMCY". Nature Genetics. 14 (2): 128–9. doi:10.1038/ng1096-128. PMID 8841177. S2CID 23054699.
  7. ^ a b "Entrez Gene: JARID1D jumonji, AT rich interactive domain 1D".

Further reading

  • Simpson E, Scott D, Chandler P (1997). "The male-specific histocompatibility antigen, H-Y: a history of transplantation, immune response genes, sex determination and expression cloning". Annual Review of Immunology. 15: 39–61. doi:10.1146/annurev.immunol.15.1.39. PMID 9143681.
  • Wolf U (1998). "The serologically detected H-Y antigen revisited". Cytogenetics and Cell Genetics. 80 (1–4): 232–5. doi:10.1159/000014986. PMID 9678364. S2CID 25908189.
  • Agulnik AI, Mitchell MJ, Lerner JL, Woods DR, Bishop CE (June 1994). "A mouse Y chromosome gene encoded by a region essential for spermatogenesis and expression of male-specific minor histocompatibility antigens". Human Molecular Genetics. 3 (6): 873–8. doi:10.1093/hmg/3.6.873. PMID 7524912.
  • Wang W, Meadows LR, den Haan JM, Sherman NE, Chen Y, Blokland E, Shabanowitz J, Agulnik AI, Hendrickson RC, Bishop CE (September 1995). "Human H-Y: a male-specific histocompatibility antigen derived from the SMCY protein". Science. 269 (5230): 1588–90. Bibcode:1995Sci...269.1588W. doi:10.1126/science.7667640. hdl:1887/2988. PMID 7667640.
  • Nagase T, Seki N, Ishikawa K, Ohira M, Kawarabayasi Y, Ohara O, Tanaka A, Kotani H, Miyajima N, Nomura N (October 1996). "Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain". DNA Research. 3 (5): 321–9, 341–54. doi:10.1093/dnares/3.5.321. PMID 9039502.
  • Agulnik AI, Bishop CE, Lerner JL, Agulnik SI, Solovyev VV (February 1997). "Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven". Mammalian Genome. 8 (2): 134–8. doi:10.1007/s003359900372. PMID 9060413. S2CID 8099911.
  • Rufer N, Wolpert E, Helg C, Tiercy JM, Gratwohl A, Chapuis B, Jeannet M, Goulmy E, Roosnek E (October 1998). "HA-1 and the SMCY-derived peptide FIDSYICQV (H-Y) are immunodominant minor histocompatibility antigens after bone marrow transplantation". Transplantation. 66 (7): 910–6. doi:10.1097/00007890-199810150-00016. PMID 9798702.
  • Lau YF, Zhang J (April 2000). "Expression analysis of thirty one Y chromosome genes in human prostate cancer". Molecular Carcinogenesis. 27 (4): 308–21. doi:10.1002/(SICI)1098-2744(200004)27:4<308::AID-MC9>3.0.CO;2-R. PMID 10747295. S2CID 23677925.
  • Shen P, Wang F, Underhill PA, Franco C, Yang WH, Roxas A, Sung R, Lin AA, Hyman RW, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ (June 2000). "Population genetic implications from sequence variation in four Y chromosome genes". Proceedings of the National Academy of Sciences of the United States of America. 97 (13): 7354–9. Bibcode:2000PNAS...97.7354S. doi:10.1073/pnas.97.13.7354. PMC 16549. PMID 10861003.
  • Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, Page DC (June 2003). "The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes". Nature. 423 (6942): 825–37. Bibcode:2003Natur.423..825S. doi:10.1038/nature01722. PMID 12815422.
  • Agate RJ, Choe M, Arnold AP (February 2004). "Sex differences in structure and expression of the sex chromosome genes CHD1Z and CHD1W in zebra finches". Molecular Biology and Evolution. 21 (2): 384–96. doi:10.1093/molbev/msh027. PMID 14660691.
  • Miklos DB, Kim HT, Miller KH, Guo L, Zorn E, Lee SJ, Hochberg EP, Wu CJ, Alyea EP, Cutler C, Ho V, Soiffer RJ, Antin JH, Ritz J (April 2005). "Antibody responses to H-Y minor histocompatibility antigens correlate with chronic graft-versus-host disease and disease remission". Blood. 105 (7): 2973–8. doi:10.1182/blood-2004-09-3660. PMC 1350982. PMID 15613541.
  • Piper KP, McLarnon A, Arrazi J, Horlock C, Ainsworth J, Kilby MD, Martin WL, Moss PA (January 2007). "Functional HY-specific CD8+ T cells are found in a high proportion of women following pregnancy with a male fetus". Biology of Reproduction. 76 (1): 96–101. doi:10.1095/biolreprod.106.055426. PMID 16988213.
  • Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y (March 2007). "The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases". Cell. 128 (6): 1077–88. doi:10.1016/j.cell.2007.02.017. PMID 17320160. S2CID 14729302.
  • Lee MG, Norman J, Shilatifard A, Shiekhattar R (March 2007). "Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein". Cell. 128 (5): 877–87. doi:10.1016/j.cell.2007.02.004. PMID 17320162. S2CID 6519228.

External links

  • JARID1D+protein,+human at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
  • Overview of all the structural information available in the PDB for UniProt: Q9BY66 (Lysine-specific demethylase 5D) at the PDBe-KB.

This article incorporates text from the United States National Library of Medicine, which is in the public domain.

  • v
  • t
  • e
(1) Basic domains
(1.1) Basic leucine zipper (bZIP)
(1.2) Basic helix-loop-helix (bHLH)
Group A
Group B
Group C
bHLH-PAS
Group D
Group E
Group F
bHLH-COE
(1.3) bHLH-ZIP
(1.4) NF-1
(1.5) RF-X
(1.6) Basic helix-span-helix (bHSH)
(2) Zinc finger DNA-binding domains
(2.1) Nuclear receptor (Cys4)
subfamily 1
subfamily 2
subfamily 3
subfamily 4
subfamily 5
subfamily 6
subfamily 0
(2.2) Other Cys4
(2.3) Cys2His2
(2.4) Cys6
(2.5) Alternating composition
(2.6) WRKY
(3) Helix-turn-helix domains
(3.1) Homeodomain
Antennapedia
ANTP class
protoHOX
Hox-like
metaHOX
NK-like
other
(3.2) Paired box
(3.3) Fork head / winged helix
(3.4) Heat shock factors
(3.5) Tryptophan clusters
(3.6) TEA domain
  • transcriptional enhancer factor
(4) β-Scaffold factors with minor groove contacts
(4.1) Rel homology region
(4.2) STAT
(4.3) p53-like
(4.4) MADS box
(4.6) TATA-binding proteins
(4.7) High-mobility group
(4.9) Grainyhead
(4.10) Cold-shock domain
(4.11) Runt
(0) Other transcription factors
(0.2) HMGI(Y)
(0.3) Pocket domain
(0.5) AP-2/EREBP-related factors
(0.6) Miscellaneous
see also transcription factor/coregulator deficiencies
  • v
  • t
  • e
1.14.11: 2-oxoglutarate
1.14.13: NADH or NADPH
1.14.14: reduced flavin or flavoprotein
1.14.15: reduced iron–sulfur protein
1.14.16: reduced pteridine (BH4 dependent)
1.14.17: reduced ascorbate
1.14.18-19: other
1.14.99 - miscellaneous
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