Kdm4c (lysine demethylase 4C) - Rat Genome Database

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Gene: Kdm4c (lysine demethylase 4C) Rattus norvegicus
Analyze
Symbol: Kdm4c
Name: lysine demethylase 4C
RGD ID: 1307528
Description: Enables chromatin binding activity. Involved in positive regulation of gene expression and positive regulation of neuron differentiation. Part of chromatin. Human ortholog(s) of this gene implicated in autistic disorder; breast cancer; carcinoma (multiple); head and neck cancer; and withdrawal disorder. Orthologous to human KDM4C (lysine demethylase 4C); PARTICIPATES IN histone modification pathway; INTERACTS WITH bisphenol A; C60 fullerene; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Jmjd2c; jumonji domain containing 2C; LOC108348059; LOC298144; lysine (K)-specific demethylase 4C; lysine-specific demethylase 4C; lysine-specific demethylase 4C-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8593,146,404 - 93,353,040 (+)NCBIGRCr8
mRatBN7.2588,100,710 - 88,306,821 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl588,100,733 - 88,306,818 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx590,550,808 - 90,743,411 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0592,379,831 - 92,572,427 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0592,361,586 - 92,554,190 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0590,800,139 - 91,012,662 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl590,800,082 - 91,012,659 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0594,858,214 - 95,061,170 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4592,079,908 - 92,288,809 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1592,086,392 - 92,293,919 (+)NCBI
Celera586,814,234 - 87,010,862 (+)NCBICelera
Cytogenetic Map5q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IBA,IDA,ISO)
nucleus  (IBA)
pericentric heterochromatin  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
2. Genetic associations of 115 polymorphisms with cancers of the upper aerodigestive tract across 10 European countries: the ARCAGE project. Canova C, etal., Cancer Res. 2009 Apr 1;69(7):2956-65. doi: 10.1158/0008-5472.CAN-08-2604.
3. Gene-Specific Methylation Control of H3K9 and H3K36 on Neurotrophic BDNF versus Astroglial GFAP Genes by KDM4A/C Regulates Neural Stem Cell Differentiation. Cascante A, etal., J Mol Biol. 2014 Oct 9;426(20):3467-77. doi: 10.1016/j.jmb.2014.04.008. Epub 2014 Apr 18.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. A polymorphism in JMJD2C alters the cleavage by caspase-3 and the prognosis of human breast cancer. Hong Q, etal., Oncotarget. 2014 Jul 15;5(13):4779-87.
6. Genome-wide association study in esophageal cancer using GeneChip mapping 10K array. Hu N, etal., Cancer Res. 2005 Apr 1;65(7):2542-6.
7. Analysis of 9p24 and 11p12-13 regions in autism spectrum disorders: rs1340513 in the JMJD2C gene is associated with ASDs in Finnish sample. Kantojarvi K, etal., Psychiatr Genet. 2010 Jun;20(3):102-8. doi: 10.1097/YPG.0b013e32833a2080.
8. Renal cell neoplasms contain shared tumor type-specific copy number variations. Krill-Burger JM, etal., Am J Pathol. 2012 Jun;180(6):2427-39. doi: 10.1016/j.ajpath.2012.01.044. Epub 2012 Apr 3.
9. Genomic amplification and oncogenic properties of the GASC1 histone demethylase gene in breast cancer. Liu G, etal., Oncogene. 2009 Dec 17;28(50):4491-500. doi: 10.1038/onc.2009.297. Epub 2009 Sep 28.
10. Histone demethylase JMJD2C is a coactivator for hypoxia-inducible factor 1 that is required for breast cancer progression. Luo W, etal., Proc Natl Acad Sci U S A. 2012 Dec 4;109(49):E3367-76. doi: 10.1073/pnas.1217394109. Epub 2012 Nov 5.
11. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
12. Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Northcott PA, etal., Nat Genet. 2009 Apr;41(4):465-72. doi: 10.1038/ng.336. Epub 2009 Mar 8.
13. GOA pipeline RGD automated data pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Genetic alterations and changes in expression of histone demethylases in prostate cancer. Suikki HE, etal., Prostate. 2010 Jun 1;70(8):889-98. doi: 10.1002/pros.21123.
17. Histone demethylase GASC1, a potential prognostic and predictive marker in esophageal squamous cell carcinoma. Sun LL, etal., Am J Cancer Res. 2013 Nov 1;3(5):509-17. eCollection 2013.
18. Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms. Wang KS, etal., J Neural Transm. 2012 Apr;119(4):425-33. doi: 10.1007/s00702-011-0729-z. Epub 2011 Nov 11.
19. [Expressions of Jumonji domain containing protein 2C and hypoxia-inducible factor-1alpha in gastric carcinoma and their clinical significance]. Xu Y, etal., Zhonghua Yi Xue Za Zhi. 2013 Nov 12;93(42):3375-8.
20. Abnormal epigenetic modifications in peripheral blood mononuclear cells from patients with alopecia areata. Zhao M, etal., Br J Dermatol. 2012 Feb;166(2):226-73. doi: 10.1111/j.1365-2133.2011.10646.x. Epub 2012 Jan 9.
Additional References at PubMed
PMID:12477932   PMID:16738407   PMID:17277772   PMID:17938240   PMID:18066052   PMID:19144645   PMID:19696013   PMID:21914792   PMID:28262558   PMID:34121556  


Genomics

Comparative Map Data
Kdm4c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8593,146,404 - 93,353,040 (+)NCBIGRCr8
mRatBN7.2588,100,710 - 88,306,821 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl588,100,733 - 88,306,818 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx590,550,808 - 90,743,411 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0592,379,831 - 92,572,427 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0592,361,586 - 92,554,190 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0590,800,139 - 91,012,662 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl590,800,082 - 91,012,659 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0594,858,214 - 95,061,170 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4592,079,908 - 92,288,809 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1592,086,392 - 92,293,919 (+)NCBI
Celera586,814,234 - 87,010,862 (+)NCBICelera
Cytogenetic Map5q31NCBI
KDM4C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3896,720,863 - 7,175,648 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl96,757,641 - 7,175,648 (+)EnsemblGRCh38hg38GRCh38
GRCh3796,720,863 - 7,175,648 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3696,747,654 - 7,165,648 (+)NCBINCBI36Build 36hg18NCBI36
Build 3496,748,082 - 7,165,647NCBI
Celera96,649,815 - 7,106,122 (+)NCBICelera
Cytogenetic Map9p24.1NCBI
HuRef96,675,237 - 7,130,973 (+)NCBIHuRef
CHM1_196,721,531 - 7,175,696 (+)NCBICHM1_1
T2T-CHM13v2.096,715,554 - 7,172,114 (+)NCBIT2T-CHM13v2.0
Kdm4c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39474,160,734 - 74,324,101 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl474,160,734 - 74,324,097 (+)EnsemblGRCm39 Ensembl
GRCm38474,242,497 - 74,405,864 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl474,242,497 - 74,405,860 (+)EnsemblGRCm38mm10GRCm38
MGSCv37473,888,401 - 74,051,768 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36473,723,179 - 73,877,092 (+)NCBIMGSCv36mm8
Celera472,763,879 - 72,927,310 (+)NCBICelera
Cytogenetic Map4C3NCBI
cM Map436.06NCBI
Kdm4c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543410,685,704 - 11,000,644 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543410,646,524 - 11,000,589 (+)NCBIChiLan1.0ChiLan1.0
KDM4C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v211117,411,246 - 117,821,826 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan19117,417,193 - 117,832,340 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v096,568,569 - 6,978,741 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.196,746,265 - 7,155,378 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl96,746,265 - 7,155,298 (+)Ensemblpanpan1.1panPan2
KDM4C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11127,662,764 - 28,101,432 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1127,693,536 - 28,101,801 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1126,475,828 - 26,885,738 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01128,552,268 - 28,967,726 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1128,552,287 - 28,968,436 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11127,275,497 - 27,696,766 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01127,094,962 - 27,512,380 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01127,763,444 - 28,174,202 (+)NCBIUU_Cfam_GSD_1.0
Kdm4c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947142,745,730 - 143,127,317 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365391,198,147 - 1,580,082 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365391,198,105 - 1,580,078 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM4C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1215,071,419 - 215,507,800 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11215,071,335 - 215,507,778 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
KDM4C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11272,346,194 - 72,763,040 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1272,347,071 - 72,761,666 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603860,686,049 - 60,981,876 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm4c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473611,382,598 - 11,711,536 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473611,254,125 - 11,711,498 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Kdm4c
642 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:66
Count of miRNA genes:56
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000009083
Prediction methods:Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)579584860124584860Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)584132602129132602Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)587765973132765973Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)587468046132468046Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)587468046132468046Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)58384059897059958Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)579584860124584860Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)579584860124584860Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 4 26 10 19 10 2 2 70 28 33 11 2
Low 1 39 31 31 31 6 9 4 7 8 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001106663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010066353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC158850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CA338814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB582180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK476947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO557703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO567036 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000009083   ⟹   ENSRNOP00000009083
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl588,100,733 - 88,306,818 (+)Ensembl
Rnor_6.0 Ensembl590,818,736 - 91,012,659 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093206   ⟹   ENSRNOP00000076133
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl588,100,831 - 88,197,451 (+)Ensembl
Rnor_6.0 Ensembl590,800,166 - 90,888,305 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093480   ⟹   ENSRNOP00000076220
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl590,818,736 - 90,827,576 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093696   ⟹   ENSRNOP00000076322
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl590,800,082 - 90,827,576 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108118   ⟹   ENSRNOP00000085474
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl588,100,752 - 88,306,818 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110293   ⟹   ENSRNOP00000088229
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl588,101,105 - 88,306,818 (+)Ensembl
RefSeq Acc Id: NM_001106663   ⟹   NP_001100133
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,147,037 - 93,353,040 (+)NCBI
mRatBN7.2588,100,804 - 88,306,821 (+)NCBI
Rnor_6.0590,800,139 - 91,012,662 (+)NCBI
Rnor_5.0594,858,214 - 95,061,170 (+)NCBI
Celera586,814,234 - 87,010,862 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109496   ⟹   XP_038965424
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,146,947 - 93,353,037 (+)NCBI
mRatBN7.2588,100,711 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109497   ⟹   XP_038965425
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,160,010 - 93,353,037 (+)NCBI
mRatBN7.2588,113,780 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109498   ⟹   XP_038965426
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,160,006 - 93,353,037 (+)NCBI
mRatBN7.2588,113,782 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109499   ⟹   XP_038965427
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,160,007 - 93,353,037 (+)NCBI
mRatBN7.2588,113,786 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109500   ⟹   XP_038965428
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,168,016 - 93,353,037 (+)NCBI
mRatBN7.2588,121,785 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109502   ⟹   XP_038965430
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,146,947 - 93,304,278 (+)NCBI
mRatBN7.2588,100,712 - 88,258,056 (+)NCBI
RefSeq Acc Id: XM_039109503   ⟹   XP_038965431
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,248,813 - 93,353,037 (+)NCBI
mRatBN7.2588,202,581 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_063287361   ⟹   XP_063143431
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,146,404 - 93,353,037 (+)NCBI
RefSeq Acc Id: XM_063287362   ⟹   XP_063143432
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,248,813 - 93,353,037 (+)NCBI
RefSeq Acc Id: XM_063287363   ⟹   XP_063143433
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,146,947 - 93,243,672 (+)NCBI
RefSeq Acc Id: XM_063287364   ⟹   XP_063143434
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,146,946 - 93,225,766 (+)NCBI
RefSeq Acc Id: XR_010066353
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8593,146,945 - 93,271,514 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001100133   ⟸   NM_001106663
- UniProtKB: F1LS62 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009083   ⟸   ENSRNOT00000009083
RefSeq Acc Id: ENSRNOP00000076322   ⟸   ENSRNOT00000093696
RefSeq Acc Id: ENSRNOP00000076220   ⟸   ENSRNOT00000093480
RefSeq Acc Id: ENSRNOP00000076133   ⟸   ENSRNOT00000093206
RefSeq Acc Id: XP_038965424   ⟸   XM_039109496
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A8Y8 (UniProtKB/TrEMBL),   F1LS62 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965430   ⟸   XM_039109502
- Peptide Label: isoform X5
- UniProtKB: A6J816 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965425   ⟸   XM_039109497
- Peptide Label: isoform X2
- UniProtKB: A0A8I6A3B2 (UniProtKB/TrEMBL),   F1LS62 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965426   ⟸   XM_039109498
- Peptide Label: isoform X2
- UniProtKB: A0A8I6A3B2 (UniProtKB/TrEMBL),   F1LS62 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965427   ⟸   XM_039109499
- Peptide Label: isoform X4
- UniProtKB: F1LS62 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965428   ⟸   XM_039109500
- Peptide Label: isoform X4
- UniProtKB: F1LS62 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965431   ⟸   XM_039109503
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000088229   ⟸   ENSRNOT00000110293
RefSeq Acc Id: ENSRNOP00000085474   ⟸   ENSRNOT00000108118
RefSeq Acc Id: XP_063143431   ⟸   XM_063287361
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063143434   ⟸   XM_063287364
- Peptide Label: isoform X8
RefSeq Acc Id: XP_063143433   ⟸   XM_063287363
- Peptide Label: isoform X7
RefSeq Acc Id: XP_063143432   ⟸   XM_063287362
- Peptide Label: isoform X6
Protein Domains
JmjC   JmjN   PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LS62-F1-model_v2 AlphaFold F1LS62 1-1005 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13693816
Promoter ID:EPDNEW_R4338
Type:initiation region
Name:Kdm4c_1
Description:lysine demethylase 4C
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0590,800,099 - 90,800,159EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307528 AgrOrtholog
BioCyc Gene G2FUF-40963 BioCyc
Ensembl Genes ENSRNOG00000006644 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009083 ENTREZGENE
  ENSRNOT00000009083.9 UniProtKB/TrEMBL
  ENSRNOT00000093206.2 UniProtKB/TrEMBL
  ENSRNOT00000108118.1 UniProtKB/TrEMBL
  ENSRNOT00000110293.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.140 UniProtKB/TrEMBL
  3.10.330.70 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  Cupin UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7446605 IMAGE-MGC_LOAD
InterPro EPHD UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  KDM4_Tudor_2 UniProtKB/TrEMBL
  TF_JmjC_AAH UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:298144 UniProtKB/TrEMBL
MGC_CLONE MGC:188335 IMAGE-MGC_LOAD
NCBI Gene 298144 ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 4C UniProtKB/TrEMBL
Pfam JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD_2 UniProtKB/TrEMBL
  Tudor_2 UniProtKB/TrEMBL
  zf-HC5HC2H_2 UniProtKB/TrEMBL
PhenoGen Kdm4c PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006644 RatGTEx
SMART JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  TUDOR UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
  FYVE_PHD_ZnF UniProtKB/TrEMBL
  Tudor/PWWP/MBT UniProtKB/TrEMBL
UniProt A0A1W2Q651_RAT UniProtKB/TrEMBL
  A0A8I6A3B2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A8Y8 ENTREZGENE, UniProtKB/TrEMBL
  A6J816 ENTREZGENE, UniProtKB/TrEMBL
  B0BNJ6_RAT UniProtKB/TrEMBL
  F1LS62 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Kdm4c  lysine demethylase 4C  LOC108348059  lysine-specific demethylase 4C-like  Data merged from RGD:11379415 737654 PROVISIONAL
2016-08-02 LOC108348059  lysine-specific demethylase 4C-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2016-02-17 Kdm4c  lysine demethylase 4C  Kdm4c  lysine (K)-specific demethylase 4C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-05-06 Kdm4c  lysine (K)-specific demethylase 4C  Jmjd2c  jumonji domain containing 2C   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Jmjd2c  jumonji domain containing 2C   Jmjd2c_predicted  jumonji domain containing 2C (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Jmjd2c_predicted  jumonji domain containing 2C (predicted)      Symbol and Name status set to approved 70820 APPROVED