Kdm4a (lysine demethylase 4A) - Rat Genome Database

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Gene: Kdm4a (lysine demethylase 4A) Rattus norvegicus
Analyze
Symbol: Kdm4a
Name: lysine demethylase 4A
RGD ID: 1306378
Description: Predicted to enable several functions, including histone H3 demethylase activity; histone H4K20me2 reader activity; and ubiquitin protein ligase binding activity. Involved in several processes, including apoptotic chromosome condensation; negative regulation of astrocyte differentiation; and positive regulation of neuron differentiation. Predicted to be located in pericentric heterochromatin. Predicted to be active in chromatin and nucleus. Orthologous to human KDM4A (lysine demethylase 4A); PARTICIPATES IN ataxia telangiectasia-mutated (ATM) signaling pathway; histone modification pathway; INTERACTS WITH 1,2-dimethylhydrazine; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Jmjd2a; jumonji domain containing 2A; LOC313539; lysine (K)-specific demethylase 4A; lysine-specific demethylase 4A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85136,958,178 - 137,004,942 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5136,958,178 - 137,004,951 (-)EnsemblGRCr8
mRatBN7.25131,672,754 - 131,719,534 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5131,672,754 - 131,719,501 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5134,380,901 - 134,427,756 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05136,135,538 - 136,182,398 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05136,157,943 - 136,204,803 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05136,967,650 - 137,014,402 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5136,967,650 - 137,014,430 (-)Ensemblrn6Rnor6.0
Rnor_5.05140,755,996 - 140,802,791 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45138,601,746 - 138,648,523 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5130,220,141 - 130,266,843 (-)NCBICelera
RGSC_v3.15138,611,767 - 138,673,033 (-)NCBI
Cytogenetic Map5q36NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
amitrole  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
berberine  (ISO)
beta-lapachone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
bisphenol F  (EXP)
buta-1,3-diene  (ISO)
caffeine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
clotrimazole  (EXP)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
desferrioxamine B  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
folic acid  (ISO)
FR900359  (ISO)
genistein  (EXP)
gentamycin  (EXP)
inulin  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methapyrilene  (ISO)
methimazole  (EXP)
methoxychlor  (EXP)
N,N-diethyl-m-toluamide  (EXP)
nitrates  (ISO)
nitric oxide  (ISO)
paracetamol  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (EXP)
progesterone  (ISO)
quercetin  (ISO)
rotenone  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
tetrachloromethane  (ISO)
thiram  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion. Bjorkman M, etal., Oncogene. 2012 Jul 19;31(29):3444-56. doi: 10.1038/onc.2011.512. Epub 2011 Nov 28.
2. 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.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein. Gray SG, etal., J Biol Chem. 2005 Aug 5;280(31):28507-18. Epub 2005 May 31.
7. JMJD2A predicts prognosis and regulates cell growth in human gastric cancer. Hu CE, etal., Biochem Biophys Res Commun. 2014 Jun 20;449(1):1-7. doi: 10.1016/j.bbrc.2014.04.126. Epub 2014 May 4.
8. Deregulation of the histone demethylase JMJD2A is involved in human carcinogenesis through regulation of the G(1)/S transition. Kogure M, etal., Cancer Lett. 2013 Aug 9;336(1):76-84. doi: 10.1016/j.canlet.2013.04.009. Epub 2013 Apr 18.
9. Tudor: a versatile family of histone methylation 'readers'. Lu R and Wang GG, Trends Biochem Sci. 2013 Nov;38(11):546-55. doi: 10.1016/j.tibs.2013.08.002. Epub 2013 Sep 10.
10. JMJD2A promotes cellular transformation by blocking cellular senescence through transcriptional repression of the tumor suppressor CHD5. Mallette FA and Richard S, Cell Rep. 2012 Nov 29;2(5):1233-43. doi: 10.1016/j.celrep.2012.09.033. Epub 2012 Nov 15.
11. Double-strand break repair: 53BP1 comes into focus. Panier S and Boulton SJ, Nat Rev Mol Cell Biol. 2014 Jan;15(1):7-18. doi: 10.1038/nrm3719. Epub 2013 Dec 11.
12. Push back to respond better: regulatory inhibition of the DNA double-strand break response. Panier S and Durocher D, Nat Rev Mol Cell Biol. 2013 Oct;14(10):661-72. doi: 10.1038/nrm3659. Epub 2013 Sep 4.
13. Histone-modifier gene expression profiles are associated with pathological and clinical outcomes in human breast cancer. Patani N, etal., Anticancer Res. 2011 Dec;31(12):4115-25.
14. Readout of epigenetic modifications. Patel DJ and Wang Z, Annu Rev Biochem. 2013;82:81-118. doi: 10.1146/annurev-biochem-072711-165700.
15. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Comprehensive gene review and curation RGD comprehensive gene curation
18. Maternal protein restriction elevates cholesterol in adult rat offspring due to repressive changes in histone modifications at the cholesterol 7alpha-hydroxylase promoter. Sohi G, etal., Mol Endocrinol. 2011 May;25(5):785-98. doi: 10.1210/me.2010-0395. Epub 2011 Mar 3.
19. The histone trimethyllysine demethylase JMJD2A promotes cardiac hypertrophy in response to hypertrophic stimuli in mice. Zhang QJ, etal., J Clin Invest. 2011 Jun;121(6):2447-56. doi: 10.1172/JCI46277. Epub 2011 May 9.
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:16024779   PMID:16738407   PMID:19144645   PMID:21914792   PMID:22373579   PMID:25660547   PMID:27214403   PMID:33187585   PMID:33402077   PMID:33499717   PMID:39136140  


Genomics

Comparative Map Data
Kdm4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85136,958,178 - 137,004,942 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5136,958,178 - 137,004,951 (-)EnsemblGRCr8
mRatBN7.25131,672,754 - 131,719,534 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5131,672,754 - 131,719,501 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5134,380,901 - 134,427,756 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05136,135,538 - 136,182,398 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05136,157,943 - 136,204,803 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05136,967,650 - 137,014,402 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5136,967,650 - 137,014,430 (-)Ensemblrn6Rnor6.0
Rnor_5.05140,755,996 - 140,802,791 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45138,601,746 - 138,648,523 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5130,220,141 - 130,266,843 (-)NCBICelera
RGSC_v3.15138,611,767 - 138,673,033 (-)NCBI
Cytogenetic Map5q36NCBI
KDM4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38143,650,149 - 43,705,518 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl143,649,256 - 43,705,518 (+)Ensemblhg38GRCh38
GRCh37144,115,820 - 44,171,189 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36143,888,384 - 43,943,776 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34143,784,930 - 43,840,231NCBI
Celera142,397,631 - 42,453,018 (+)NCBICelera
Cytogenetic Map1p34.2-p34.1NCBI
HuRef142,236,372 - 42,291,619 (+)NCBIHuRef
CHM1_1144,232,091 - 44,287,481 (+)NCBICHM1_1
T2T-CHM13v2.0143,520,658 - 43,576,010 (+)NCBIT2T-CHM13v2.0
Kdm4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394117,994,154 - 118,037,216 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4117,994,154 - 118,037,240 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm384118,136,957 - 118,180,090 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4118,136,957 - 118,180,043 (-)Ensemblmm10GRCm38
MGSCv374117,809,609 - 117,852,648 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv364117,639,975 - 117,677,878 (-)NCBIMGSCv36mm8
Celera4116,859,945 - 116,902,916 (-)NCBICelera
Cytogenetic Map4D2.1NCBI
cM Map454.31NCBI
Kdm4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555373,199,394 - 3,255,945 (+)Ensembl
ChiLan1.0NW_0049555373,199,394 - 3,255,945 (+)NCBIChiLan1.0ChiLan1.0
KDM4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21183,105,784 - 183,161,620 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11182,247,190 - 182,303,016 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0142,949,977 - 43,005,684 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1144,325,218 - 44,380,163 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl144,325,624 - 44,380,163 (+)EnsemblpanPan2panpan1.1
KDM4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11516,521,760 - 16,570,965 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1516,521,700 - 16,571,000 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1516,644,941 - 16,693,693 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01516,678,695 - 16,727,479 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1516,678,747 - 16,727,458 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11516,477,445 - 16,526,326 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01516,545,705 - 16,594,652 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01516,619,222 - 16,667,917 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Kdm4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505859,177,719 - 59,231,860 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647425,002,509 - 25,056,642 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647425,002,527 - 25,056,642 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6167,597,956 - 167,642,333 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.16167,597,954 - 167,642,381 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
KDM4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12089,108,090 - 89,164,657 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2089,073,876 - 89,164,663 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603327,759,914 - 27,816,770 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248922,933,172 - 2,984,195 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248922,933,066 - 2,982,207 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Kdm4a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1138,841,799 - 38,884,163 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Kdm4a
185 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:405
Count of miRNA genes:238
Interacting mature miRNAs:288
Transcripts:ENSRNOT00000066165
Prediction methods:Microtar, Miranda, Rnahybrid
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)5102105698152749382Rat
2303586Gluco52Glucose level QTL 522blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)5100826632145826632Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)544924861153890773Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116702075161702075Rat
1354583Despr3Despair related QTL34.980.0002locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)5132930505172190305Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5130678987145274255Rat
7365049Bp359Blood pressure QTL 359arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133308734140009902Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)599905133172190305Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134369218156289444Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5133789363172190305Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)592583776137583776Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134369199172190305Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136631198172190305Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112142946157142946Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112142946157142946Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5110770739155770739Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133081618172190305Rat
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)551657967166600247Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112142946157142946Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)592583776137583776Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)598972960143972960Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125969677172190305Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)592583776137583776Rat
2303618Vencon1Ventilatory control QTL 13.8respiration trait (VT:0001943)oxygen consumption (CMO:0002169)5100826632145826632Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111236572156236572Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)594034903139034903Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5131708216172190305Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114131300159131300Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125969677156302135Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)560601597137492949Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112142946157142946Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116702075161702075Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112142946157142946Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116702075161702075Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)574335621156302135Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116702075161702075Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114131300159131300Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133081618172190305Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)592881678137881678Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)5104262817153890625Rat

Markers in Region
BE102827  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,693,813 - 131,693,990 (+)MAPPERmRatBN7.2
Rnor_6.05136,988,696 - 136,988,872NCBIRnor6.0
Rnor_5.05140,777,042 - 140,777,218UniSTSRnor5.0
RGSC_v3.45138,622,795 - 138,622,971UniSTSRGSC3.4
Celera5130,241,190 - 130,241,366UniSTS
RH 3.4 Map5855.9UniSTS
Cytogenetic Map5q36UniSTS
RH137800  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,696,381 - 131,696,502 (+)MAPPERmRatBN7.2
Rnor_6.05136,991,264 - 136,991,384NCBIRnor6.0
Rnor_5.05140,779,610 - 140,779,730UniSTSRnor5.0
RGSC_v3.45138,625,363 - 138,625,483UniSTSRGSC3.4
Celera5130,243,758 - 130,243,878UniSTS
RH 3.4 Map5854.9UniSTS
Cytogenetic Map5q36UniSTS
UniSTS:495405  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25131,693,710 - 131,695,138 (+)MAPPERmRatBN7.2
Rnor_6.05136,988,593 - 136,990,020NCBIRnor6.0
Rnor_5.05140,776,939 - 140,778,366UniSTSRnor5.0
RGSC_v3.45138,622,692 - 138,624,119UniSTSRGSC3.4
Celera5130,241,087 - 130,242,514UniSTS
Cytogenetic Map5q36UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000066165   ⟹   ENSRNOP00000061752
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5136,958,178 - 137,004,912 (-)Ensembl
mRatBN7.2 Ensembl5131,672,754 - 131,719,501 (-)Ensembl
Rnor_6.0 Ensembl5136,967,650 - 137,014,375 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000091866   ⟹   ENSRNOP00000073442
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5136,958,178 - 137,004,951 (-)Ensembl
mRatBN7.2 Ensembl5131,672,754 - 131,719,463 (-)Ensembl
Rnor_6.0 Ensembl5136,967,895 - 137,014,430 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000169258   ⟹   ENSRNOP00000109491
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5136,958,178 - 137,004,667 (-)Ensembl
RefSeq Acc Id: NM_001107966   ⟹   NP_001101436
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,958,178 - 137,004,912 (-)NCBI
mRatBN7.25131,672,754 - 131,719,501 (-)NCBI
Rnor_6.05136,967,650 - 137,014,375 (-)NCBI
Rnor_5.05140,755,996 - 140,802,791 (-)NCBI
RGSC_v3.45138,601,746 - 138,648,523 (-)RGD
Celera5130,220,141 - 130,266,843 (-)RGD
Sequence:
RefSeq Acc Id: XM_006238668   ⟹   XP_006238730
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,958,221 - 137,004,588 (-)NCBI
mRatBN7.25131,672,773 - 131,719,155 (-)NCBI
Rnor_6.05136,967,652 - 137,014,058 (-)NCBI
Rnor_5.05140,755,996 - 140,802,791 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593391   ⟹   XP_017448880
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,958,221 - 137,004,942 (-)NCBI
mRatBN7.25131,672,773 - 131,719,534 (-)NCBI
Rnor_6.05136,967,652 - 137,014,402 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110001   ⟹   XP_038965929
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,958,221 - 137,002,102 (-)NCBI
mRatBN7.25131,672,773 - 131,713,553 (-)NCBI
RefSeq Acc Id: XM_063287740   ⟹   XP_063143810
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85136,958,221 - 137,002,096 (-)NCBI
RefSeq Acc Id: NP_001101436   ⟸   NM_001107966
- UniProtKB: D4A2N4 (UniProtKB/TrEMBL),   A6JZG4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238730   ⟸   XM_006238668
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448880   ⟸   XM_017593391
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000061752   ⟸   ENSRNOT00000066165
Ensembl Acc Id: ENSRNOP00000073442   ⟸   ENSRNOT00000091866
RefSeq Acc Id: XP_038965929   ⟸   XM_039110001
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063143810   ⟸   XM_063287740
- Peptide Label: isoform X2
- UniProtKB: A6JZG4 (UniProtKB/TrEMBL),   D4A2N4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000109491   ⟸   ENSRNOT00000169258
Protein Domains
JmjC   JmjN   PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K5I7-F1-model_v2 AlphaFold A0A0G2K5I7 1-1062 view protein structure

Transcriptome

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

Promoters
RGD ID:13693962
Promoter ID:EPDNEW_R4486
Type:initiation region
Name:Kdm4a_1
Description:lysine demethylase 4A
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_6.05137,014,351 - 137,014,411EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306378 AgrOrtholog
BioCyc Gene G2FUF-40163 BioCyc
Ensembl Genes ENSRNOG00000019956 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066165 ENTREZGENE
  ENSRNOT00000066165.4 UniProtKB/TrEMBL
  ENSRNOT00000091866 ENTREZGENE
  ENSRNOT00000091866.3 UniProtKB/TrEMBL
  ENSRNOT00000169258 ENTREZGENE
  ENSRNOT00000169258.1 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
InterPro EPHD UniProtKB/TrEMBL
  ePHD_JMJD2A UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  KDM4_Tudor_2 UniProtKB/TrEMBL
  TF_JmjC_AAH UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
  Tudor_KDM4A_rpt1 UniProtKB/TrEMBL
  Tudor_KDM4A_rpt2 UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:313539 UniProtKB/TrEMBL
NCBI Gene 313539 ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 4A UniProtKB/TrEMBL
Pfam JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD_2 UniProtKB/TrEMBL
  Tudor_2 UniProtKB/TrEMBL
  zf-HC5HC2H_2 UniProtKB/TrEMBL
PhenoGen Kdm4a PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019956 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 A0A0G2K5I7 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LWS9_RAT UniProtKB/TrEMBL
  A6JZG4 ENTREZGENE, UniProtKB/TrEMBL
  D4A2N4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kdm4a  lysine demethylase 4A  Kdm4a  lysine (K)-specific demethylase 4A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-05-06 Kdm4a  lysine (K)-specific demethylase 4A  Jmjd2a  jumonji domain containing 2A   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Jmjd2a  jumonji domain containing 2A   Jmjd2a_predicted  jumonji domain containing 2A (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Jmjd2a_predicted  jumonji domain containing 2A (predicted)      Symbol and Name status set to approved 70820 APPROVED