KDM5C

Protein-coding gene in the species Homo sapiens
KDM5C
Available structures
PDBOrtholog search: PDBe RCSB
List of PDB id codes

2JRZ, 5FWJ

Identifiers
AliasesKDM5C, DXS1272E, JARID1C, MRX13, MRXJ, MRXSCJ, MRXSJ, SMCX, XE169, lysine demethylase 5C
External IDsOMIM: 314690 MGI: 99781 HomoloGene: 79498 GeneCards: KDM5C
Gene location (Human)
X chromosome (human)
Chr.X chromosome (human)[1]
X chromosome (human)
Genomic location for KDM5C
Genomic location for KDM5C
BandXp11.22Start53,176,283 bp[1]
End53,225,422 bp[1]
Gene location (Mouse)
X chromosome (mouse)
Chr.X chromosome (mouse)[2]
X chromosome (mouse)
Genomic location for KDM5C
Genomic location for KDM5C
BandX F3|X 68.46 cMStart151,016,016 bp[2]
End151,057,531 bp[2]
RNA expression pattern
Bgee
HumanMouse (ortholog)
Top expressed in
  • sural nerve

  • stromal cell of endometrium

  • right uterine tube

  • skin of abdomen

  • canal of the cervix

  • left uterine tube

  • gastric mucosa

  • smooth muscle tissue

  • lymph node

  • gastrocnemius muscle
Top expressed in
  • yolk sac

  • pineal gland

  • fossa

  • condyle

  • substantia nigra

  • trigeminal ganglion

  • retinal pigment epithelium

  • hair follicle

  • lip

  • ureter
More reference expression data
BioGPS
More reference expression data
Gene ontology
Molecular function
  • DNA binding
  • oxidoreductase activity
  • dioxygenase activity
  • metal ion binding
  • histone demethylase activity
  • zinc ion binding
  • histone H3-methyl-lysine-4 demethylase activity
  • 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
  • cytosol
  • histone methyltransferase complex
Biological process
  • negative regulation of transcription, DNA-templated
  • regulation of transcription, DNA-templated
  • transcription, DNA-templated
  • rhythmic process
  • response to toxic substance
  • histone H3-K4 demethylation
  • 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

8242

20591

Ensembl

ENSG00000126012

ENSMUSG00000025332

UniProt

P41229

P41230

RefSeq (mRNA)
NM_001146702
NM_001282622
NM_004187
NM_001353978
NM_001353979

NM_001353981
NM_001353982
NM_001353984

NM_013668

RefSeq (protein)
NP_001140174
NP_001269551
NP_004178
NP_001340907
NP_001340908

NP_001340910
NP_001340911
NP_001340913

NP_038696
NP_001390000
NP_001390001
NP_001390002
NP_001390003

NP_001390004
NP_001390005

Location (UCSC)Chr X: 53.18 – 53.23 MbChr X: 151.02 – 151.06 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Lysine-specific demethylase 5C is an enzyme that in humans is encoded by the KDM5C gene.[5][6][7] KDM5C belongs to the alpha-ketoglutarate-dependent hydroxylase superfamily.

Function

This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motif suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked intellectual disability. Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined.[7]

See also

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000126012 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000025332 – 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. ^ Agulnik AI, Mitchell MJ, Mattei MG, Borsani G, Avner PA, Lerner JL, Bishop CE (Jun 1994). "A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human". Human Molecular Genetics. 3 (6): 879–84. doi:10.1093/hmg/3.6.879. PMID 7951230.
  6. ^ Wu J, Ellison J, Salido E, Yen P, Mohandas T, Shapiro LJ (Jan 1994). "Isolation and characterization of XE169, a novel human gene that escapes X-inactivation". Human Molecular Genetics. 3 (1): 153–60. doi:10.1093/hmg/3.1.153. PMID 8162017.
  7. ^ a b "Entrez Gene: JARID1C jumonji, AT rich interactive domain 1C".

Further reading

  • Agate RJ, Choe M, Arnold AP (Feb 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.
  • Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, Cohn MA, Cantley LC, Gygi SP (Aug 2004). "Large-scale characterization of HeLa cell nuclear phosphoproteins". Proceedings of the National Academy of Sciences of the United States of America. 101 (33): 12130–5. Bibcode:2004PNAS..10112130B. doi:10.1073/pnas.0404720101. PMC 514446. PMID 15302935.
  • Jensen LR, Amende M, Gurok U, Moser B, Gimmel V, Tzschach A, Janecke AR, Tariverdian G, Chelly J, Fryns JP, Van Esch H, Kleefstra T, Hamel B, Moraine C, Gecz J, Turner G, Reinhardt R, Kalscheuer VM, Ropers HH, Lenzner S (Feb 2005). "Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation". American Journal of Human Genetics. 76 (2): 227–36. doi:10.1086/427563. PMC 1196368. PMID 15586325.
  • Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, Ishii S, Sugiyama T, Saito K, Isono Y, Irie R, Kushida N, Yoneyama T, Otsuka R, Kanda K, Yokoi T, Kondo H, Wagatsuma M, Murakawa K, Ishida S, Ishibashi T, Takahashi-Fujii A, Tanase T, Nagai K, Kikuchi H, Nakai K, Isogai T, Sugano S (Jan 2006). "Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes". Genome Research. 16 (1): 55–65. doi:10.1101/gr.4039406. PMC 1356129. PMID 16344560.
  • Santos C, Rodriguez-Revenga L, Madrigal I, Badenas C, Pineda M, Milà M (May 2006). "A novel mutation in JARID1C gene associated with mental retardation". European Journal of Human Genetics. 14 (5): 583–6. doi:10.1038/sj.ejhg.5201608. PMID 16538222.
  • Tzschach A, Lenzner S, Moser B, Reinhardt R, Chelly J, Fryns JP, Kleefstra T, Raynaud M, Turner G, Ropers HH, Kuss A, Jensen LR (Apr 2006). "Novel JARID1C/SMCX mutations in patients with X-linked mental retardation". Human Mutation. 27 (4): 389. doi:10.1002/humu.9420. PMID 16541399. S2CID 25318561.
  • Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP (Oct 2006). "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". Nature Biotechnology. 24 (10): 1285–92. doi:10.1038/nbt1240. PMID 16964243. S2CID 14294292.
  • Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (Nov 2006). "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks". Cell. 127 (3): 635–48. doi:10.1016/j.cell.2006.09.026. PMID 17081983. S2CID 7827573.
  • Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y (Mar 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.
  • Tahiliani M, Mei P, Fang R, Leonor T, Rutenberg M, Shimizu F, Li J, Rao A, Shi Y (May 2007). "The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation". Nature. 447 (7144): 601–5. Bibcode:2007Natur.447..601T. doi:10.1038/nature05823. PMID 17468742. S2CID 34527537.

External links

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

  • v
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(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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