Kdm1a (lysine demethylase 1A) - Rat Genome Database

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Gene: Kdm1a (lysine demethylase 1A) Rattus norvegicus
Analyze
Symbol: Kdm1a
Name: lysine demethylase 1A
RGD ID: 1562975
Description: Enables chromatin binding activity. Involved in several processes, including cellular response to cAMP; nervous system development; and response to fungicide. Located in chromatin. Biomarker of breast cancer; diabetic retinopathy; schizophrenia; and transient cerebral ischemia. Orthologous to human KDM1A (lysine demethylase 1A); PARTICIPATES IN histone modification pathway; Notch signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; aldehydo-D-glucose; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: amine oxidase (flavin containing) domain 2; Aof2; Kdm1; LOC500569; Lsd1; lysine (K)-specific demethylase 1; lysine (K)-specific demethylase 1A; lysine-specific histone demethylase 1; lysine-specific histone demethylase 1A; neuroprotective protein 3; RGD1562975; similar to AOF2 protein
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
GRCr85154,066,436 - 154,121,913 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5154,065,543 - 154,121,775 (-)EnsemblGRCr8
mRatBN7.25148,782,976 - 148,838,319 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5148,782,976 - 148,838,319 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5151,480,546 - 151,535,814 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05153,254,833 - 153,310,100 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05153,236,837 - 153,292,108 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd5153,686,662 - 153,741,831 (-)NCBIDahl_SR_JrHsd
Lyon_Normotensive5155,675,163 - 155,730,383 (-)NCBILyon_Normotensive
Lyon_Hypertensive5154,852,169 - 154,907,577 (-)NCBILyon_Hypertensive
F344_StmMcwi5148,423,124 - 148,478,344 (-)NCBIF344_StmMcwi
Rnor_6.05154,909,003 - 154,965,171 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5154,909,003 - 154,965,171 (-)Ensemblrn6Rnor6.0
Rnor_5.05158,674,383 - 158,730,358 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45155,299,289 - 155,358,404 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5147,184,121 - 147,238,797 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
berberine  (ISO)
biguanides  (ISO)
biphenyl-4-amine  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
Cuprizon  (ISO)
cyclophosphamide  (ISO)
D-glucose  (EXP)
decabromodiphenyl ether  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (ISO)
dioxygen  (EXP,ISO)
doxorubicin  (EXP)
enzalutamide  (ISO)
ethanol  (ISO)
Evodiamine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP)
glucose  (EXP)
haloperidol  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
methyl methanesulfonate  (ISO)
methylazoxymethanol  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nitrates  (ISO)
nitric oxide  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (ISO)
PhIP  (ISO)
potassium chromate  (ISO)
rac-lactic acid  (ISO)
sodium arsenite  (EXP,ISO)
SP2509  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
triphenyl phosphate  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell differentiation  (ISO)
cellular response to cAMP  (IEP)
cellular response to gamma radiation  (ISO)
cellular response to UV  (ISO)
cerebral cortex development  (IEP)
chromatin organization  (IEA)
chromatin remodeling  (IEA)
DNA repair-dependent chromatin remodeling  (ISO)
DNA-templated transcription  (IEA)
granulocyte differentiation  (ISO)
guanine metabolic process  (IMP)
muscle cell development  (ISO)
negative regulation of DNA damage response, signal transduction by p53 class mediator  (ISO)
negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator  (ISO)
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator  (ISO)
negative regulation of neurogenesis  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription initiation-coupled chromatin remodeling  (ISO)
neuron maturation  (IEP,ISO)
neuron projection extension  (ISO)
neuron projection morphogenesis  (IMP)
pituitary gland development  (ISO)
positive regulation of chromatin binding  (IMP)
positive regulation of cold-induced thermogenesis  (ISO)
positive regulation of epithelial to mesenchymal transition  (ISO)
positive regulation of erythrocyte differentiation  (ISO)
positive regulation of megakaryocyte differentiation  (ISO)
positive regulation of neural precursor cell proliferation  (ISO)
positive regulation of neuroblast proliferation  (ISO)
positive regulation of protein ubiquitination  (ISO)
positive regulation of stem cell proliferation  (ISO)
positive regulation of transcription by RNA polymerase II  (IMP,ISO)
protein modification process  (IEP,IMP)
regulation of DNA-templated transcription  (IEA)
regulation of double-strand break repair via homologous recombination  (ISO)
regulation of neurogenesis  (ISO)
regulation of primitive erythrocyte differentiation  (ISO)
regulation of protein localization  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
response to fungicide  (IEP)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. LSD1-mediated demethylation of histone H3 lysine 4 triggers Myc-induced transcription. Amente S, etal., Oncogene. 2010 Jun 24;29(25):3691-702. doi: 10.1038/onc.2010.120. Epub 2010 Apr 26.
2. Coexpression of nuclear receptors and histone methylation modifying genes in the testis: implications for endocrine disruptor modes of action. Anderson AM, etal., PLoS One. 2012;7(4):e34158. doi: 10.1371/journal.pone.0034158. Epub 2012 Apr 4.
3. 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.
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. Lysine-specific demethylase 1 in breast cancer cells contributes to the production of endogenous formaldehyde in the metastatic bone cancer pain model of rats. Liu J, etal., PLoS One. 2013;8(3):e58957. doi: 10.1371/journal.pone.0058957. Epub 2013 Mar 14.
6. Prenatal MAM administration affects histone H3 methylation in postnatal life in the rat medial prefrontal cortex. Mackowiak M, etal., Eur Neuropsychopharmacol. 2014 Feb;24(2):271-89. doi: 10.1016/j.euroneuro.2013.05.013. Epub 2013 Aug 8.
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. 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.
9. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Insm1 controls development of pituitary endocrine cells and requires a SNAG domain for function and for recruitment of histone-modifying factors. Welcker JE, etal., Development. 2013 Dec;140(24):4947-58. doi: 10.1242/dev.097642. Epub 2013 Nov 13.
14. Lysine-specific demethylase 1 promotes brown adipose tissue thermogenesis via repressing glucocorticoid activation. Zeng X, etal., Genes Dev. 2016 Aug 15;30(16):1822-36. doi: 10.1101/gad.285312.116. Epub 2016 Aug 26.
15. Distribution of lysine-specific demethylase 1 in the brain of rat and its response in transient global cerebral ischemia. Zhang YZ, etal., Neurosci Res. 2010 Sep;68(1):66-72. doi: 10.1016/j.neures.2010.06.002. Epub 2010 Jun 11.
16. 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.
17. Overexpression of lysine specific demethylase 1 predicts worse prognosis in primary hepatocellular carcinoma patients. Zhao ZK, etal., World J Gastroenterol. 2012 Dec 7;18(45):6651-6. doi: 10.3748/wjg.v18.i45.6651.
18. Regulation of matrix metalloproteinase-9 by epigenetic modifications and the development of diabetic retinopathy. Zhong Q and Kowluru RA, Diabetes. 2013 Jul;62(7):2559-68. doi: 10.2337/db12-1141. Epub 2013 Feb 19.
19. Epigenetic modification of Sod2 in the development of diabetic retinopathy and in the metabolic memory: role of histone methylation. Zhong Q and Kowluru RA, Invest Ophthalmol Vis Sci. 2013 Jan 14;54(1):244-50. doi: 10.1167/iovs.12-10854.
20. Alternative splicing of the histone demethylase LSD1/KDM1 contributes to the modulation of neurite morphogenesis in the mammalian nervous system. Zibetti C, etal., J Neurosci. 2010 Feb 17;30(7):2521-32. doi: 10.1523/JNEUROSCI.5500-09.2010.
Additional References at PubMed
PMID:15620353   PMID:16079795   PMID:17277772   PMID:17392792   PMID:17707228   PMID:17805299   PMID:18066052   PMID:19497860   PMID:20123967   PMID:20228790   PMID:20833138   PMID:21124846  
PMID:22082260   PMID:23400681   PMID:24111946   PMID:24217620   PMID:24529708   PMID:24843136   PMID:25018020   PMID:25519973   PMID:27893888   PMID:28053041   PMID:29370269   PMID:31737960  
PMID:34958158  


Genomics

Comparative Map Data
Kdm1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85154,066,436 - 154,121,913 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5154,065,543 - 154,121,775 (-)EnsemblGRCr8
mRatBN7.25148,782,976 - 148,838,319 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5148,782,976 - 148,838,319 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5151,480,546 - 151,535,814 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05153,254,833 - 153,310,100 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05153,236,837 - 153,292,108 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd5153,686,662 - 153,741,831 (-)NCBIDahl_SR_JrHsd
Lyon_Normotensive5155,675,163 - 155,730,383 (-)NCBILyon_Normotensive
Lyon_Hypertensive5154,852,169 - 154,907,577 (-)NCBILyon_Hypertensive
F344_StmMcwi5148,423,124 - 148,478,344 (-)NCBIF344_StmMcwi
Rnor_6.05154,909,003 - 154,965,171 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5154,909,003 - 154,965,171 (-)Ensemblrn6Rnor6.0
Rnor_5.05158,674,383 - 158,730,358 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45155,299,289 - 155,358,404 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5147,184,121 - 147,238,797 (-)NCBICelera
Cytogenetic Map5q36NCBI
KDM1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38123,019,468 - 23,083,689 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl123,019,395 - 23,083,693 (+)Ensemblhg38GRCh38
GRCh37123,345,961 - 23,410,182 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36123,218,533 - 23,282,771 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34123,091,251 - 23,155,490NCBI
Celera121,668,066 - 21,732,323 (+)NCBICelera
Cytogenetic Map1p36.12NCBI
HuRef121,590,111 - 21,655,045 (+)NCBIHuRef
CHM1_1123,458,660 - 23,522,895 (+)NCBICHM1_1
T2T-CHM13v2.0122,845,130 - 22,909,357 (+)NCBIT2T-CHM13v2.0
Kdm1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394136,277,844 - 136,330,127 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4136,277,851 - 136,330,034 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm384136,550,533 - 136,602,787 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4136,550,540 - 136,602,723 (-)Ensemblmm10GRCm38
MGSCv374136,106,448 - 136,158,638 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv364135,822,633 - 135,874,786 (-)NCBIMGSCv36mm8
Celera4134,744,880 - 134,796,951 (-)NCBICelera
Cytogenetic Map4D3NCBI
cM Map468.8NCBI
Kdm1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554523,044,264 - 3,104,418 (+)Ensembl
ChiLan1.0NW_0049554523,044,042 - 3,104,650 (+)NCBIChiLan1.0ChiLan1.0
KDM1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21203,863,445 - 203,927,430 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11202,966,436 - 203,030,428 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0122,205,624 - 22,269,571 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1123,153,066 - 23,217,693 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl123,153,066 - 23,217,692 (+)EnsemblpanPan2panpan1.1
KDM1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1276,313,742 - 76,375,716 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl276,156,434 - 76,375,632 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha272,818,576 - 72,880,479 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0276,872,072 - 76,934,039 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl276,872,072 - 76,934,863 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1273,694,139 - 73,755,941 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0274,702,184 - 74,764,063 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0275,705,895 - 75,767,600 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Kdm1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505842,426,557 - 42,494,307 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364748,262,885 - 8,319,092 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364748,262,913 - 8,319,089 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl680,903,424 - 80,971,873 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1680,903,407 - 80,971,875 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2675,060,275 - 75,073,680 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.2674,939,358 - 74,992,403 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120109,592,761 - 109,657,885 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20109,593,074 - 109,657,839 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660336,659,024 - 6,724,168 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247647,664,550 - 7,742,494 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Kdm1a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1121,632,018 - 21,686,694 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Kdm1a
250 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:239
Count of miRNA genes:170
Interacting mature miRNAs:187
Transcripts:ENSRNOT00000055992
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
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
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5141212838172190305Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149642129171146538Rat
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
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
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5149805999162987697Rat
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
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138002522170842766Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112142946157142946Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)5141764300172190305Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5148093485172129029Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
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
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111236572156236572Rat
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
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5149661912166600247Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116702075161702075Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112142946157142946Rat
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

Markers in Region
D5Uwm55  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25148,807,519 - 148,807,749 (+)MAPPERmRatBN7.2
Rnor_6.05154,933,567 - 154,933,796NCBIRnor6.0
Rnor_5.05158,698,947 - 158,699,176UniSTSRnor5.0
RGSC_v3.45155,323,721 - 155,323,951RGDRGSC3.4
RGSC_v3.45155,323,722 - 155,323,951UniSTSRGSC3.4
Celera5147,208,530 - 147,208,761UniSTS
RGSC_v3.15155,333,760 - 155,333,990RGD
Cytogenetic Map5q36UniSTS
RH128773  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25148,783,066 - 148,783,260 (+)MAPPERmRatBN7.2
Rnor_6.05154,909,094 - 154,909,287NCBIRnor6.0
Rnor_5.05158,674,474 - 158,674,667UniSTSRnor5.0
RGSC_v3.45155,299,380 - 155,299,573UniSTSRGSC3.4
Celera5147,184,212 - 147,184,405UniSTS
RH 3.4 Map51008.3UniSTS
Cytogenetic Map5q36UniSTS
AA408884  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr85154,066,635 - 154,066,842 (+)Marker Load Pipeline
mRatBN7.25148,783,174 - 148,783,382 (+)MAPPERmRatBN7.2
Rnor_6.05154,909,202 - 154,909,409NCBIRnor6.0
Rnor_5.05158,674,582 - 158,674,789UniSTSRnor5.0
RGSC_v3.45155,299,488 - 155,299,695UniSTSRGSC3.4
Celera5147,184,320 - 147,184,527UniSTS
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
18 12 72 173 91 90 59 113 59 6 401 218 12 159 98 95 31 23 23

Sequence


Ensembl Acc Id: ENSRNOT00000055992   ⟹   ENSRNOP00000052846
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5154,066,436 - 154,121,775 (-)Ensembl
mRatBN7.2 Ensembl5148,782,976 - 148,838,319 (-)Ensembl
Rnor_6.0 Ensembl5154,909,003 - 154,965,171 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000080881   ⟹   ENSRNOP00000074048
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5154,066,436 - 154,121,775 (-)Ensembl
mRatBN7.2 Ensembl5148,782,976 - 148,838,319 (-)Ensembl
Rnor_6.0 Ensembl5154,909,306 - 154,965,027 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000115653   ⟹   ENSRNOP00000078937
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5154,066,436 - 154,121,775 (-)Ensembl
mRatBN7.2 Ensembl5148,782,976 - 148,838,319 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000164213   ⟹   ENSRNOP00000100516
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5154,065,543 - 154,121,775 (-)Ensembl
RefSeq Acc Id: NM_001130098   ⟹   NP_001123570
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85154,066,436 - 154,121,775 (-)NCBI
mRatBN7.25148,782,976 - 148,838,319 (-)NCBI
Dahl_SR_JrHsd5153,686,662 - 153,741,831 (-)NCBI
Lyon_Normotensive5155,675,163 - 155,730,383 (-)NCBI
Lyon_Hypertensive5154,852,169 - 154,907,577 (-)NCBI
F344_StmMcwi5148,423,124 - 148,478,344 (-)NCBI
Rnor_6.05154,909,003 - 154,965,171 (-)NCBI
Rnor_5.05158,674,383 - 158,730,358 (-)NCBI
RGSC_v3.45155,299,289 - 155,358,404 (-)RGD
Celera5147,184,121 - 147,238,797 (-)RGD
Sequence:
RefSeq Acc Id: XM_039110624   ⟹   XP_038966552
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85154,066,440 - 154,121,913 (-)NCBI
mRatBN7.25148,782,976 - 148,838,175 (-)NCBI
RefSeq Acc Id: NP_001123570   ⟸   NM_001130098
- UniProtKB: B3STT9 (UniProtKB/TrEMBL),   F1MA31 (UniProtKB/TrEMBL),   A6ITB7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000074048   ⟸   ENSRNOT00000080881
Ensembl Acc Id: ENSRNOP00000052846   ⟸   ENSRNOT00000055992
RefSeq Acc Id: XP_038966552   ⟸   XM_039110624
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G2K8 (UniProtKB/TrEMBL),   A6ITB7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000078937   ⟸   ENSRNOT00000115653
Ensembl Acc Id: ENSRNOP00000100516   ⟸   ENSRNOT00000164213
Protein Domains
SWIRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1MA31-F1-model_v2 AlphaFold F1MA31 1-867 view protein structure

Transcriptome

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

Promoters
RGD ID:13694172
Promoter ID:EPDNEW_R4696
Type:initiation region
Name:Kdm1a_1
Description:lysine demethylase 1A
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_6.05154,965,176 - 154,965,236EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562975 AgrOrtholog
BioCyc Gene G2FUF-39496 BioCyc
Ensembl Genes ENSRNOG00000022372 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055992 ENTREZGENE
  ENSRNOT00000055992.6 UniProtKB/TrEMBL
  ENSRNOT00000080881.3 UniProtKB/TrEMBL
  ENSRNOT00000115653 ENTREZGENE
  ENSRNOT00000115653.2 UniProtKB/TrEMBL
  ENSRNOT00000164213.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
  3.50.50.60 UniProtKB/TrEMBL
  3.90.660.10 UniProtKB/TrEMBL
  ATP synthase, gamma subunit, helix hairpin domain UniProtKB/TrEMBL
InterPro Amino_oxidase UniProtKB/TrEMBL
  FAD/NAD-bd_sf UniProtKB/TrEMBL
  Flavin_monoamine_oxidase UniProtKB/TrEMBL
  Hist_Lys-spec_deMease UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:500569 UniProtKB/TrEMBL
NCBI Gene 500569 ENTREZGENE
PANTHER FLAVIN MONOAMINE OXIDASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A UniProtKB/TrEMBL
Pfam Amino_oxidase UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
PhenoGen Kdm1a PhenoGen
PIRSF Histone_Lys-demethylase UniProtKB/TrEMBL
PROSITE SWIRM UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022372 RatGTEx
Superfamily-SCOP FAD-linked reductases, C-terminal domain UniProtKB/TrEMBL
  Homeodomain_like UniProtKB/TrEMBL
  SSF51905 UniProtKB/TrEMBL
UniProt A0A0G2K736_RAT UniProtKB/TrEMBL
  A0A8I6G2K8 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LI04_RAT UniProtKB/TrEMBL
  A6ITB7 ENTREZGENE, UniProtKB/TrEMBL
  B3STT9 ENTREZGENE, UniProtKB/TrEMBL
  F1MA31 ENTREZGENE
UniProt Secondary F1MA31 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kdm1a  lysine demethylase 1A  Kdm1a  lysine (K)-specific demethylase 1A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Kdm1a  lysine (K)-specific demethylase 1A  Kdm1  lysine (K)-specific demethylase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-05-06 Kdm1  lysine (K)-specific demethylase 1  Aof2  amine oxidase (flavin containing) domain 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Aof2  amine oxidase (flavin containing) domain 2  RGD1562975_predicted  similar to AOF2 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562975_predicted  similar to AOF2 protein (predicted)  LOC500569  similar to AOF2 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC500569  similar to AOF2 protein      Symbol and Name status set to provisional 70820 PROVISIONAL