Kdm1a (lysine (K)-specific demethylase 1A) - Rat Genome Database

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Gene: Kdm1a (lysine (K)-specific demethylase 1A) Mus musculus
Analyze
Symbol: Kdm1a
Name: lysine (K)-specific demethylase 1A
RGD ID: 1558503
MGI Page MGI
Description: Enables several functions, including DNA-binding transcription factor binding activity; histone H3 demethylase activity; and transcription coregulator activity. Involved in several processes, including positive regulation of cell population proliferation; regulation of myeloid cell differentiation; and regulation of transcription by RNA polymerase II. Acts upstream of or within DNA repair-dependent chromatin remodeling; negative regulation of neurogenesis; and nervous system development. Located in chromatin and nucleus. Is expressed in several structures, including articular cartilage; brain; reproductive system; retina; and urinary system. Orthologous to human KDM1A (lysine demethylase 1A).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1810043O07Rik; AA408884; amine oxidase (flavin containing) domain 2; Ao; Aof2; BRAF35-HDAC complex protein BHC110; D4Ertd478e; flavin-containing amine oxidase domain-containing protein 2; Kdm1; LS; Lsd1; lysine (K)-specific demethylase 1; lysine-specific histone demethylase 1; lysine-specific histone demethylase 1A; mKIAA0601
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394136,277,844 - 136,330,127 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4136,277,851 - 136,330,034 (-)EnsemblGRCm39 Ensembl
GRCm384136,550,533 - 136,602,787 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4136,550,540 - 136,602,723 (-)EnsemblGRCm38mm10GRCm38
MGSCv374136,106,448 - 136,158,638 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364135,822,633 - 135,874,786 (-)NCBIMGSCv36mm8
Celera4134,744,880 - 134,796,951 (-)NCBICelera
Cytogenetic Map4D3NCBI
cM Map468.8NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (EXP)
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  (ISO)
all-trans-retinoic acid  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
berberine  (ISO)
biguanides  (ISO)
biphenyl-4-amine  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
choline  (EXP)
cisplatin  (EXP)
clofibrate  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
Cuprizon  (ISO)
cyclophosphamide  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (EXP)
dioxygen  (ISO)
doxorubicin  (ISO)
enzalutamide  (ISO)
ethanol  (EXP)
flutamide  (ISO)
folic acid  (EXP)
FR900359  (ISO)
fulvestrant  (ISO)
gentamycin  (ISO)
glucose  (ISO)
haloperidol  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
L-methionine  (EXP)
lead(0)  (ISO)
methyl methanesulfonate  (ISO)
methylazoxymethanol  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nitric oxide  (ISO)
paracetamol  (EXP)
pentachlorophenol  (EXP)
perfluorooctanoic acid  (ISO)
PhIP  (ISO)
rac-lactic acid  (ISO)
sodium arsenite  (EXP,ISO)
SP2509  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (ISO)
thiram  (ISO)
titanium dioxide  (EXP)
triphenyl phosphate  (ISO)
tungsten  (EXP)
valproic acid  (EXP,ISO)
vinclozolin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component
chromatin  (IBA,IDA,IEA,ISO)
chromosome, telomeric region  (IEA,ISO)
DNA repair complex  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA,ISO,ISS)
protein-containing complex  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal brain wave pattern  (IAGP)
abnormal cell cycle  (IAGP)
abnormal circadian behavior persistence  (IAGP)
abnormal circardian behavior entrainment  (IAGP)
abnormal common myeloid progenitor cell morphology  (IAGP)
abnormal definitive hematopoiesis  (IAGP)
abnormal erythropoiesis  (IAGP)
abnormal gastrulation  (IAGP)
abnormal heart development  (IAGP)
abnormal induced morbidity/mortality  (IAGP)
abnormal liver morphology  (IAGP)
abnormal luteinizing hormone level  (IAGP)
abnormal mitral valve morphology  (IAGP)
abnormal pituitary gland development  (IAGP)
abnormal pituitary hormone level  (IAGP)
abnormal proerythroblast morphology  (IAGP)
absence seizures  (IAGP)
absent egg cylinders  (IAGP)
anemia  (IAGP)
cardiac muscle degeneration  (IAGP)
decreased body size  (IAGP)
decreased bone marrow cell number  (IAGP)
decreased common myeloid progenitor cell number  (IAGP)
decreased embryo size  (IAGP)
decreased erythrocyte cell number  (IAGP)
decreased fetal derived definitive erythrocyte cell number  (IAGP)
decreased granulocyte number  (IAGP)
decreased grip strength  (IEA)
decreased growth hormone level  (IAGP)
decreased hematopoietic stem cell number  (IAGP)
decreased hemoglobin content  (IAGP)
decreased leukocyte cell number  (IAGP)
decreased locomotor activity  (IEA)
decreased neutrophil cell number  (IAGP)
decreased susceptibility to pharmacologically induced seizures  (IAGP)
decreased susceptibility to xenobiotic induced morbidity/mortality  (IAGP)
decreased thyroid-stimulating hormone level  (IAGP)
embryonic growth arrest  (IAGP)
embryonic lethality between implantation and placentation, incomplete penetrance  (IAGP)
embryonic lethality between implantation and somite formation, complete penetrance  (IAGP)
embryonic lethality during organogenesis, complete penetrance  (IAGP)
failure to gastrulate  (IAGP)
increased apoptosis  (IAGP)
increased basophil cell number  (IEA)
increased eosinophil cell number  (IEA)
increased hematopoietic stem cell number  (IAGP)
increased mean platelet volume  (IEA)
lethality during fetal growth through weaning, complete penetrance  (IAGP)
no abnormal phenotype detected  (IAGP)
pale liver  (IAGP)
pancytopenia  (IAGP)
perimembraneous ventricular septal defect  (IAGP)
perinatal lethality, complete penetrance  (IAGP)
postnatal lethality, incomplete penetrance  (IAGP)
prenatal lethality, complete penetrance  (IAGP)
preweaning lethality, complete penetrance  (IEA)
reticulocytopenia  (IAGP)
small heart  (IEA)
small kidney  (IEA)
small liver  (IEA)
small lung  (IEA)
small spleen  (IEA)
thrombocytopenia  (IAGP)
tonic-clonic seizures  (IAGP)
ventricular septal defect  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
2. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
3. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Ko MS, etal., Development 2000 Apr;127(8):1737-49.
4. 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.
5. 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.
6. MGDs mouse GO annotations MGD data from the GO Consortium
7. Prediction of the coding sequences of mouse homologues of KIAA gene: III. the complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, etal., DNA Res 2003 Aug 31;10(4):167-80.
8. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. 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.
11. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
12. Mouse MP Annotation Import Pipeline RGD automated import pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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.
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:12477932   PMID:12520002   PMID:14610273   PMID:15489334   PMID:15741177   PMID:15782199   PMID:16079795   PMID:16141072  
PMID:16141073   PMID:17277772   PMID:17296600   PMID:17392792   PMID:17634443   PMID:17707228   PMID:18022353   PMID:18454139   PMID:18573881   PMID:18799693   PMID:19098913   PMID:19124609  
PMID:19497860   PMID:19654328   PMID:19934284   PMID:20123967   PMID:20362541   PMID:20362542   PMID:20404188   PMID:20656681   PMID:20713442   PMID:20833138   PMID:21357675   PMID:21856776  
PMID:21873498   PMID:21873635   PMID:21878487   PMID:21905163   PMID:22068596   PMID:22083510   PMID:22297846   PMID:22453831   PMID:22464800   PMID:22496869   PMID:22534796   PMID:22570500  
PMID:22801375   PMID:22802127   PMID:22922362   PMID:23028048   PMID:23576758   PMID:23592333   PMID:23592795   PMID:23595969   PMID:23637775   PMID:23795291   PMID:23870122   PMID:23892456  
PMID:24078251   PMID:24120133   PMID:24163373   PMID:24183668   PMID:24190971   PMID:24217620   PMID:24252778   PMID:24448552   PMID:24457600   PMID:24582500   PMID:24594919   PMID:24619213  
PMID:24735673   PMID:24752154   PMID:24828497   PMID:24843136   PMID:24912735   PMID:25018020   PMID:25255718   PMID:25437545   PMID:25473037   PMID:25519973   PMID:25545350   PMID:25561507  
PMID:25737280   PMID:26031919   PMID:26124638   PMID:26206133   PMID:26214369   PMID:26243864   PMID:26365490   PMID:26372689   PMID:26449473   PMID:26487685   PMID:26584622   PMID:26619147  
PMID:26626423   PMID:26795843   PMID:26806292   PMID:26814574   PMID:26836306   PMID:26947098   PMID:26974661   PMID:26976584   PMID:27112428   PMID:27264172   PMID:27501329   PMID:27566776  
PMID:27618650   PMID:27626377   PMID:27634040   PMID:27642069   PMID:27645313   PMID:27651463   PMID:27732873   PMID:27760309   PMID:28053041   PMID:28228264   PMID:28414096   PMID:28446510  
PMID:28461471   PMID:28498828   PMID:28597915   PMID:28671696   PMID:28687800   PMID:28899795   PMID:28993646   PMID:29233982   PMID:29263096   PMID:29281729   PMID:29370269   PMID:29371665  
PMID:29395062   PMID:29404406   PMID:29438700   PMID:29453291   PMID:29606613   PMID:29618057   PMID:29618580   PMID:29688375   PMID:29977079   PMID:30196744   PMID:30232138   PMID:30304676  
PMID:30400034   PMID:30457570   PMID:30538335   PMID:30659187   PMID:30679800   PMID:30894511   PMID:30995482   PMID:31138677   PMID:31152920   PMID:31364026   PMID:31492745   PMID:31606247  
PMID:31675426   PMID:31734274   PMID:31806371   PMID:31811020   PMID:31830521   PMID:32074399   PMID:32141088   PMID:32317082   PMID:32350257   PMID:32917713   PMID:33139560   PMID:33148658  
PMID:33385711   PMID:33393499   PMID:33457471   PMID:33596408   PMID:33664458   PMID:33788902   PMID:33811891   PMID:34050636   PMID:34078090   PMID:34078525   PMID:34082769   PMID:34161765  
PMID:34314389   PMID:34324630   PMID:34432529   PMID:34709266   PMID:34726730   PMID:34819502   PMID:34958158   PMID:35022775   PMID:35105672   PMID:35143753   PMID:35177789   PMID:35177822  
PMID:35255108   PMID:35296335   PMID:35688282   PMID:35775122   PMID:35856020   PMID:36162056   PMID:36321378   PMID:36335117   PMID:36357913   PMID:36401176   PMID:36610795   PMID:36689133  
PMID:36695573   PMID:36835016   PMID:36846208   PMID:37023372   PMID:37429639   PMID:38113337   PMID:38226173   PMID:38295985   PMID:38346162   PMID:38355793   PMID:38453932   PMID:38649356  
PMID:38670969   PMID:38723742   PMID:39154703   PMID:39237615  


Genomics

Comparative Map Data
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 Ensembl
GRCm384136,550,533 - 136,602,787 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4136,550,540 - 136,602,723 (-)EnsemblGRCm38mm10GRCm38
MGSCv374136,106,448 - 136,158,638 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364135,822,633 - 135,874,786 (-)NCBIMGSCv36mm8
Celera4134,744,880 - 134,796,951 (-)NCBICelera
Cytogenetic Map4D3NCBI
cM Map468.8NCBI
KDM1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38123,019,468 - 23,083,689 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl123,019,443 - 23,083,689 (+)EnsemblGRCh38hg38GRCh38
GRCh37123,345,961 - 23,410,182 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36123,218,533 - 23,282,771 (+)NCBINCBI36Build 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85154,066,436 - 154,121,913 (-)NCBIGRCr8
mRatBN7.25148,782,976 - 148,838,319 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5148,782,976 - 148,838,319 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5151,480,546 - 151,535,814 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05153,254,833 - 153,310,100 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05153,236,837 - 153,292,108 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05154,909,003 - 154,965,171 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5154,909,003 - 154,965,171 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05158,674,383 - 158,730,358 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45155,299,289 - 155,358,404 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera5147,184,121 - 147,238,797 (-)NCBICelera
Cytogenetic Map5q36NCBI
Kdm1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554523,044,264 - 3,104,418 (+)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha272,818,576 - 72,880,479 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0276,872,072 - 76,934,039 (-)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Kdm1a
2531 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:814
Count of miRNA genes:393
Interacting mature miRNAs:454
Transcripts:ENSMUST00000046846, ENSMUST00000105847, ENSMUST00000116273, ENSMUST00000125111, ENSMUST00000139690, ENSMUST00000147886, ENSMUST00000155354, ENSMUST00000170979, ENSMUST00000171424
Prediction methods: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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301267Bcmd2_mB cell maturation defect 2 (mouse)Not determined4133154678150789451Mouse
4142139Adip12_madiposity 12 (mouse)Not determined4124621281156860686Mouse
10047132Albq19_malbuminuria QTL 19 (mouse)Not determined4112824389146824389Mouse
1301525Lmb1_mlupus in MRL and B6 F2 cross (mouse)Not determined4124264957150676858Mouse
14746982Manh56_mmandible shape 56 (mouse)4117815917151815917Mouse
4141623W6q13_mweight 6 weeks QTL 13 (mouse)Not determined88982069140468203Mouse
12910797Pwgrq4_mpre-weaning growth rate QTL 4 (mouse)4105835310141433838Mouse
25314312Syncl2_msynaptonemal complex length 2 (mouse)465718237146584457Mouse
12910794Pwbwq8_mpost-weaning body weight QTL 8 (mouse)4105835310141433838Mouse
1300743Skull6_mskull morphology 6 (mouse)Not determined4111009051145009280Mouse
1301382Arvm2_mautoimmune renal vasculitis 2 (mouse)Not determined4107791564141791756Mouse
1302149Tlsr2_mthymic lymphoma suppressor region 2 (mouse)Not determined4124264957142230960Mouse
12910813Pwbwq4_mpre-weaning body weight QTL 4 (mouse)4105835310141433838Mouse
1300874Gasa2_mgastritis type A susceptibility locus 2 (mouse)Not determined4133010494156860686Mouse
4141093W3q17_mweight 3 weeks QTL 17 (mouse)Not determined88982069140468203Mouse
27226757Femd1_mfemur midshaft diameter 1, 5 week (mouse)4123993793144326570Mouse
12910808Pwbwq9_mpost-weaning body weight QTL 9 (mouse)4105835310141433838Mouse
1300621Tpnr1_mthermal pain response 1 (mouse)Not determined4125230872156860686Mouse
11567249Elorr3_methanol induced loss of righting response 3 (mouse)43722677156268235Mouse
4142493Femwf13_mfemur work to failure 13 (mouse)Not determined116154678150154782Mouse
1301815Sles2_msystemic lupus erythmatosus suppressor 2 (mouse)Not determined494957579150676858Mouse
1300663Start2_mstartle response 2 (mouse)Not determined4107264957141265153Mouse
1300917Gasa1_mgastritis type A susceptibility locus 1 (mouse)Not determined4124055093142438020Mouse
1300537Ap3q_malcohol preference 3 QTL (mouse)Not determined4134654451156860686Mouse
1301823Bmd7_mbone mineral density 7 (mouse)Not determined488982069151654550Mouse
10412210Cypr6_mcytokine production 6 (mouse)Not determined4120617848154617995Mouse
1302078Sluc21_msusceptibility to lung cancer 21 (mouse)Not determined4117401141151401275Mouse
10045620Heal22_mwound healing/regeneration 22 (mouse)Not determined4125230872156860686Mouse
4142481Gct1_mgranulosa cell tumorigenesis 1 (mouse)Not determined4127784226156860686Mouse
1301793Tlsr3_mthymic lymphoma suppressor region 3 (mouse)Not determined4129465811136864536Mouse
4141065Shali2_msurvival time to hyperoxic acute lung injury 2 (mouse)Not determined124055093141572792Mouse
13503348Bntq18_mbone traits QTL 18 (mouse)4120617848154617995Mouse
13208562Wght7_mweight 7 (mouse)490888237148084457Mouse
4142082Psds2_mpsoriasis-like skin disease severity 2 (mouse)Not determined4133154678137617995Mouse
1300781Lith8_mlithogenic gene 8 (mouse)Not determined4107264957141265153Mouse
39128212Lwq21_mliver weight QTL 21 (mouse)488982069140468203Mouse
4142077Ignpq2_mIgA nephropathy QTL 2 (mouse)Not determined4133676733156860686Mouse
4141180Ssic1_msusceptibility to small intestinal cancer 1 (mouse)Not determined120674005154674151Mouse
1301584Lrdg2_mlight induced retinal degeneration 2 (mouse)Not determined4129465811151654550Mouse
1302102Bis1_mbeta-carboline-induced seizures 1 (mouse)Not determined4119864433153864536Mouse
10043996Gct5_mgranulosa cell tumorigenesis 5 (mouse)Not determined4127784226156860686Mouse
26884445Sklq7_mskull length QTL 7, 10 week (mouse)468018237150884457Mouse
10043985Stheal12_msoft tissue heal 12 (mouse)Not determined4121342649155342753Mouse
1301982Pltiq1_mphospholipid transfer protein inducibility QTL 1 (mouse)Not determined4124621281156860686Mouse
26884437Sklq13_mskull length QTL 13, 16 week (mouse)457700000155684457Mouse
1300803Sluc6_msusceptibility to lung cancer 6 (mouse)Not determined4120674005154674151Mouse
4141549W10q10_mweight 10 weeks QTL 10 (mouse)Not determined88982069140468203Mouse
4142061Chlq16_mcirculating hormone level QTL 16 (mouse)Not determined4121342649155342753Mouse
1357895Ctrcts_mcataract severity (mouse)Not determined445709925138342753Mouse
1300933Cdcs9_mcytokine deficiency colitis susceptibility 9 (mouse)Not determined4125230872156860686Mouse
1300809Ccrs2_mcorpus callosum hemisphere surface size 2 (mouse)Not determined4107264957141265153Mouse
4141154Nba1_mNew Zealand Black autoimmunity 1 (mouse)Not determined131650724140879275Mouse
1301964Bw8q2_mbody weight at 8 weeks QTL 2 (mouse)Not determined4119864433153864536Mouse
1301452Elsgp1_melevated serum gp70 1 (mouse)Not determined4121342649155342753Mouse
10755520Rbc1_mred blood cell count 1 (mouse)4108477692142477692Mouse
10755521Hct1_mhematocrit 1 (mouse)4108477692142477692Mouse
10755522Hgb1_mhemoglobin 1 (mouse)4108477692142477692Mouse
1301108Scon2_msucrose consumption 2 (mouse)Not determined4134654451156860686Mouse
1300858Tafat_mtally ho associated mesenteric fat pad weight (mouse)Not determined4124621281156860686Mouse
10755531Lymph3_mlymphocyte differential 3 (mouse)4124553483156860686Mouse
15039382Ltgq7_mliver triglyceride QTL 7 (mouse)4105705794139705794Mouse
11533916Mts1_mmammary tumor susceptibility 1 (mouse)4125289325156860686Mouse
15039377Bw45_mbody weight QTL 45 (mouse)4105705794139705794Mouse
1300839Dyscalc2_mdystrophic cardiac calcinosis 2 (mouse)Not determined4111009051145009280Mouse
4141001Tgq17_mtriglyceride QTL 17 (mouse)Not determined112523489146523489Mouse
15039378Adip30_madiposity 30 (mouse)4105705794139705794Mouse
1357800Tgq3_mtriglyceride QTL 3 (mouse)Not determined4107055093141055180Mouse
15039385Mvlq3_mmacrovesicular liver lesion QTL 3 (mouse)4112182386146182386Mouse

Markers in Region
AA408884  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm384136,550,738 - 136,550,951UniSTSGRCm38
MGSCv374136,106,653 - 136,106,866UniSTSGRCm37
Celera4134,745,087 - 134,745,300UniSTS
Cytogenetic Map4D3UniSTS
cM Map466.75UniSTS
Whitehead/MRC_RH41804.32UniSTS
D4Ertd478e  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm384136,550,592 - 136,550,791UniSTSGRCm38
MGSCv374136,106,507 - 136,106,706UniSTSGRCm37
Celera4134,744,941 - 134,745,140UniSTS
Cytogenetic Map4D3UniSTS
cM Map466.75UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000046846   ⟹   ENSMUSP00000035457
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,278,159 - 136,329,619 (-)Ensembl
GRCm38.p6 Ensembl4136,550,848 - 136,602,308 (-)Ensembl
Ensembl Acc Id: ENSMUST00000105847   ⟹   ENSMUSP00000101473
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,277,855 - 136,329,998 (-)Ensembl
GRCm38.p6 Ensembl4136,550,544 - 136,602,687 (-)Ensembl
Ensembl Acc Id: ENSMUST00000116273   ⟹   ENSMUSP00000111977
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,277,851 - 136,330,034 (-)Ensembl
GRCm38.p6 Ensembl4136,550,540 - 136,602,723 (-)Ensembl
Ensembl Acc Id: ENSMUST00000125111
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,280,432 - 136,282,635 (-)Ensembl
GRCm38.p6 Ensembl4136,553,121 - 136,555,324 (-)Ensembl
Ensembl Acc Id: ENSMUST00000139690
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,279,184 - 136,280,483 (-)Ensembl
GRCm38.p6 Ensembl4136,551,873 - 136,553,172 (-)Ensembl
Ensembl Acc Id: ENSMUST00000147886
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,282,518 - 136,288,812 (-)Ensembl
GRCm38.p6 Ensembl4136,555,207 - 136,561,501 (-)Ensembl
Ensembl Acc Id: ENSMUST00000155354   ⟹   ENSMUSP00000114268
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,282,546 - 136,295,918 (-)Ensembl
GRCm38.p6 Ensembl4136,555,235 - 136,568,607 (-)Ensembl
Ensembl Acc Id: ENSMUST00000170979   ⟹   ENSMUSP00000131385
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,285,843 - 136,304,469 (-)Ensembl
GRCm38.p6 Ensembl4136,558,532 - 136,577,158 (-)Ensembl
Ensembl Acc Id: ENSMUST00000171424
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl4136,278,188 - 136,279,853 (-)Ensembl
GRCm38.p6 Ensembl4136,550,877 - 136,552,542 (-)Ensembl
RefSeq Acc Id: NM_001347221   ⟹   NP_001334150
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394136,277,844 - 136,330,034 (-)NCBI
GRCm384136,550,533 - 136,602,723 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001356567   ⟹   NP_001343496
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394136,277,844 - 136,330,034 (-)NCBI
GRCm384136,550,533 - 136,602,723 (-)NCBI
Sequence:
RefSeq Acc Id: NM_133872   ⟹   NP_598633
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394136,277,844 - 136,330,034 (-)NCBI
GRCm384136,550,533 - 136,602,723 (-)NCBI
MGSCv374136,106,448 - 136,158,638 (-)RGD
Celera4134,744,880 - 134,796,951 (-)RGD
cM Map4 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006539329   ⟹   XP_006539392
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm394136,277,863 - 136,330,127 (-)NCBI
GRCm384136,550,552 - 136,602,787 (-)NCBI
Sequence:
RefSeq Acc Id: NP_598633   ⟸   NM_133872
- Peptide Label: isoform 2
- UniProtKB: Q8VEA1 (UniProtKB/Swiss-Prot),   A3KG94 (UniProtKB/Swiss-Prot),   Q6ZQ88 (UniProtKB/Swiss-Prot),   Q6PB53 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006539392   ⟸   XM_006539329
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001343496   ⟸   NM_001356567
- Peptide Label: isoform 3
RefSeq Acc Id: NP_001334150   ⟸   NM_001347221
- Peptide Label: isoform 1
- UniProtKB: A3KG93 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSMUSP00000035457   ⟸   ENSMUST00000046846
Ensembl Acc Id: ENSMUSP00000101473   ⟸   ENSMUST00000105847
Ensembl Acc Id: ENSMUSP00000131385   ⟸   ENSMUST00000170979
Ensembl Acc Id: ENSMUSP00000114268   ⟸   ENSMUST00000155354
Ensembl Acc Id: ENSMUSP00000111977   ⟸   ENSMUST00000116273
Protein Domains
SWIRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6ZQ88-F1-model_v2 AlphaFold Q6ZQ88 1-853 view protein structure

Promoters
RGD ID:6834900
Promoter ID:MM_KWN:40218
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6
Transcripts:OTTMUST00000022419
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv364136,108,491 - 136,110,047 (-)MPROMDB
RGD ID:6834897
Promoter ID:MM_KWN:40219
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney,   Liver,   MEF_B6
Transcripts:OTTMUST00000022418
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv364136,110,816 - 136,112,142 (-)MPROMDB
RGD ID:6834896
Promoter ID:MM_KWN:40220
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   Brain,   Kidney,   Liver,   Lung,   MEF_B6
Transcripts:OTTMUST00000022417
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv364136,117,066 - 136,118,342 (-)MPROMDB
RGD ID:6835530
Promoter ID:MM_KWN:40224
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day3,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6
Transcripts:ENSMUST00000105847,   NM_133872
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv364136,158,379 - 136,158,879 (-)MPROMDB
RGD ID:6885124
Promoter ID:EPDNEW_M6013
Type:initiation region
Name:Kdm1a_1
Description:Mus musculus lysine -specific demethylase 1A , transcript variant1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm384136,602,703 - 136,602,763EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1196256 AgrOrtholog
Ensembl Genes ENSMUSG00000036940 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000046846.14 UniProtKB/TrEMBL
  ENSMUST00000105847 ENTREZGENE
  ENSMUST00000105847.8 UniProtKB/TrEMBL
  ENSMUST00000116273 ENTREZGENE
  ENSMUST00000116273.9 UniProtKB/Swiss-Prot
  ENSMUST00000155354.8 UniProtKB/TrEMBL
  ENSMUST00000170979.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.50.50.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.660.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ATP synthase, gamma subunit, helix hairpin domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Amino_oxidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD/NAD-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Flavin_monoamine_oxidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hist_Lys-spec_deMease UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SWIRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:99982 UniProtKB/Swiss-Prot
MGD MGI:1196256 ENTREZGENE
NCBI Gene Kdm1a ENTREZGENE
PANTHER FLAVIN MONOAMINE OXIDASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Amino_oxidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SWIRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Kdm1a PhenoGen
PIRSF Histone_Lys-demethylase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SWIRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP FAD-linked reductases, C-terminal domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51905 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A3KG93 ENTREZGENE, UniProtKB/TrEMBL
  A3KG94 ENTREZGENE
  F6Z4I3_MOUSE UniProtKB/TrEMBL
  F6ZC60_MOUSE UniProtKB/TrEMBL
  G8JL40_MOUSE UniProtKB/TrEMBL
  KDM1A_MOUSE UniProtKB/Swiss-Prot
  Q6PB53 ENTREZGENE
  Q6ZQ88 ENTREZGENE
  Q8VEA1 ENTREZGENE
UniProt Secondary A3KG94 UniProtKB/Swiss-Prot
  Q6PB53 UniProtKB/Swiss-Prot
  Q8VEA1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-08-26 Kdm1a  lysine (K)-specific demethylase 1A  D4Ertd478e  DNA segment, Chr 4, ERATO Doi 478, expressed  Symbol and/or name updated 27372883 PROVISIONAL
2024-08-21 D4Ertd478e  DNA segment, Chr 4, ERATO Doi 478, expressed  Kdm1a  lysine (K)-specific demethylase 1A  Symbol and/or name change 5135510 APPROVED