Kdm4c (lysine demethylase 4C) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Kdm4c (lysine demethylase 4C) Rattus norvegicus
Analyze
Symbol: Kdm4c
Name: lysine demethylase 4C
RGD ID: 1307528
Description: Exhibits chromatin binding activity. Involved in positive regulation of gene expression and positive regulation of neuron differentiation. Localizes to 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 C60 fullerene; diuron; (-)-epigallocatechin 3-gallate (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2588,100,710 - 88,306,821 (+)NCBI
Rnor_6.0 Ensembl590,800,082 - 91,012,659 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0590,800,139 - 91,012,662 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0594,858,214 - 95,061,170 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4592,079,908 - 92,288,809 (+)NCBIRGSC3.4rn4RGSC3.4
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


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
2. Canova C, etal., Cancer Res. 2009 Apr 1;69(7):2956-65. doi: 10.1158/0008-5472.CAN-08-2604.
3. 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. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Hong Q, etal., Oncotarget. 2014 Jul 15;5(13):4779-87.
6. Hu N, etal., Cancer Res. 2005 Apr 1;65(7):2542-6.
7. Kantojarvi K, etal., Psychiatr Genet. 2010 Jun;20(3):102-8. doi: 10.1097/YPG.0b013e32833a2080.
8. 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. Liu G, etal., Oncogene. 2009 Dec 17;28(50):4491-500. doi: 10.1038/onc.2009.297. Epub 2009 Sep 28.
10. 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. MGD data from the GO Consortium
12. Northcott PA, etal., Nat Genet. 2009 Apr;41(4):465-72. doi: 10.1038/ng.336. Epub 2009 Mar 8.
13. RGD automated data pipeline
14. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. RGD automated import pipeline for gene-chemical interactions
16. Suikki HE, etal., Prostate. 2010 Jun 1;70(8):889-98. doi: 10.1002/pros.21123.
17. Sun LL, etal., Am J Cancer Res. 2013 Nov 1;3(5):509-17. eCollection 2013.
18. Wang KS, etal., J Neural Transm. 2012 Apr;119(4):425-33. doi: 10.1007/s00702-011-0729-z. Epub 2011 Nov 11.
19. Xu Y, etal., Zhonghua Yi Xue Za Zhi. 2013 Nov 12;93(42):3375-8.
20. 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  


Genomics

Comparative Map Data
Kdm4c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2588,100,710 - 88,306,821 (+)NCBI
Rnor_6.0 Ensembl590,800,082 - 91,012,659 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0590,800,139 - 91,012,662 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0594,858,214 - 95,061,170 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4592,079,908 - 92,288,809 (+)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl96,720,863 - 7,175,648 (+)EnsemblGRCh38hg38GRCh38
GRCh3896,720,863 - 7,175,648 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3796,720,863 - 7,175,648 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3696,747,654 - 7,165,648 (+)NCBINCBI36hg18NCBI36
Build 3496,748,082 - 7,165,647NCBI
Celera96,649,815 - 7,106,122 (+)NCBI
Cytogenetic Map9p24.1NCBI
HuRef96,675,237 - 7,130,973 (+)NCBIHuRef
CHM1_196,721,531 - 7,175,696 (+)NCBICHM1_1
Kdm4c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39474,160,734 - 74,324,101 (+)NCBIGRCm39mm39
GRCm39 Ensembl474,160,734 - 74,324,097 (+)Ensembl
GRCm38474,242,497 - 74,405,864 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl474,242,497 - 74,405,860 (+)EnsemblGRCm38mm10GRCm38
MGSCv37473,888,401 - 74,051,768 (+)NCBIGRCm37mm9NCBIm37
MGSCv36473,723,179 - 73,877,092 (+)NCBImm8
Celera472,763,879 - 72,927,310 (+)NCBICelera
Cytogenetic Map4C3NCBI
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
PanPan1.196,746,265 - 7,155,378 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl96,746,265 - 7,155,298 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v096,568,569 - 6,978,741 (+)NCBIMhudiblu_PPA_v0panPan3
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 (+)NCBI
ROS_Cfam_1.01128,552,268 - 28,967,726 (+)NCBI
UMICH_Zoey_3.11127,275,497 - 27,696,766 (+)NCBI
UNSW_CanFamBas_1.01127,094,962 - 27,512,380 (+)NCBI
UU_Cfam_GSD_1.01127,763,444 - 28,174,202 (+)NCBI
Kdm4c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947142,745,730 - 143,127,317 (+)NCBI
SpeTri2.0NW_0049365391,198,105 - 1,580,078 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM4C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1215,071,334 - 215,507,800 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11215,071,335 - 215,507,778 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
KDM4C
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11272,346,194 - 72,763,040 (-)NCBI
ChlSab1.1 Ensembl1272,347,071 - 72,761,666 (-)Ensembl
Kdm4c
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473611,254,125 - 11,711,498 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531926122136640934Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)535225432108092802Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)535661945117554267Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)544404276134502294Rat
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)547745646167946134Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54872203893587756Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)55180442696804426Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)55180442696804426Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55330956898309568Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)555903593100903593Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)556902367101902367Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)556991667137729065Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)560072951133313852Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)561086525149030144Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)56108665393273130Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)561086653117554114Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)561612600102331727Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
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)565696672129038896Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)568838385113838385Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)571154828108092802Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)571154828108092802Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)571154828108092802Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)571154828108092802Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)571154828108092802Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)583424556128424556Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)583424556128424556Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)583424556128424556Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)585800910100745614Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)589502294134502294Rat

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.


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_039109501 (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
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
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000009083   ⟹   ENSRNOP00000009083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl590,818,736 - 91,012,659 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093206   ⟹   ENSRNOP00000076133
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl590,800,166 - 90,888,305 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093480   ⟹   ENSRNOP00000076220
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl590,818,736 - 90,827,576 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093696   ⟹   ENSRNOP00000076322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl590,800,082 - 90,827,576 (+)Ensembl
RefSeq Acc Id: NM_001106663   ⟹   NP_001100133
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2588,100,711 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109497   ⟹   XP_038965425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2588,113,780 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109498   ⟹   XP_038965426
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2588,113,782 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109499   ⟹   XP_038965427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2588,113,786 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109500   ⟹   XP_038965428
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2588,121,785 - 88,306,821 (+)NCBI
RefSeq Acc Id: XM_039109501   ⟹   XP_038965429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2588,100,710 - 88,261,750 (+)NCBI
RefSeq Acc Id: XM_039109502   ⟹   XP_038965430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2588,100,712 - 88,258,056 (+)NCBI
RefSeq Acc Id: XM_039109503   ⟹   XP_038965431
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2588,202,581 - 88,306,821 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100133   ⟸   NM_001106663
- UniProtKB: B0BNJ6 (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_038965429   ⟸   XM_039109501
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038965424   ⟸   XM_039109496
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038965430   ⟸   XM_039109502
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038965425   ⟸   XM_039109497
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038965426   ⟸   XM_039109498
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038965427   ⟸   XM_039109499
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038965428   ⟸   XM_039109500
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038965431   ⟸   XM_039109503
- Peptide Label: isoform X6
Protein Domains
JmjC   JmjN

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307528 AgrOrtholog
Ensembl Genes ENSRNOG00000006644 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009083 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000076133 UniProtKB/TrEMBL
  ENSRNOP00000076220 UniProtKB/TrEMBL
  ENSRNOP00000076322 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009083 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000093206 UniProtKB/TrEMBL
  ENSRNOT00000093480 UniProtKB/TrEMBL
  ENSRNOT00000093696 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 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
Pfam JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  Tudor_2 UniProtKB/TrEMBL
PhenoGen Kdm4c PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  TUDOR UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt A0A1W2Q651_RAT UniProtKB/TrEMBL
  A0A1W2Q6C3_RAT UniProtKB/TrEMBL
  B0BNJ6 ENTREZGENE, UniProtKB/TrEMBL
  F1LS62_RAT 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 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