KDM1A (lysine demethylase 1A) - Rat Genome Database

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Gene: KDM1A (lysine demethylase 1A) Chlorocebus sabaeus
Analyze
Symbol: KDM1A
Name: lysine demethylase 1A
RGD ID: 18504780
Description: ENCODES a protein that exhibits chromatin binding (ortholog); demethylase activity (ortholog); DNA-binding transcription factor binding (ortholog); INVOLVED IN cell differentiation (ortholog); cellular response to cAMP (ortholog); cellular response to gamma radiation (ortholog); PARTICIPATES IN histone modification pathway; Notch signaling pathway; ASSOCIATED WITH 3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency (ortholog); alopecia areata (ortholog); breast cancer (ortholog); FOUND IN chromatin (ortholog); chromosome, telomeric region (ortholog); DNA repair complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: lysine-specific histone demethylase 1A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell differentiation  (ISO)
cellular response to cAMP  (ISO)
cellular response to gamma radiation  (ISO)
cellular response to UV  (ISO)
cerebral cortex development  (ISO)
chromatin organization  (IEA)
chromatin remodeling  (IEA)
DNA repair-dependent chromatin remodeling  (ISO)
granulocyte differentiation  (ISO)
guanine metabolic process  (ISO)
muscle cell development  (ISO)
negative regulation of DNA damage response, signal transduction by p53 class mediator  (ISO)
negative regulation of DNA-templated transcription  (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  (IEA,ISO)
neuron maturation  (ISO)
neuron projection extension  (ISO)
pituitary gland development  (ISO)
positive regulation of cell size  (ISO)
positive regulation of chromatin binding  (ISO)
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 neuron projection development  (ISO)
positive regulation of protein ubiquitination  (ISO)
positive regulation of stem cell proliferation  (ISO)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
protein modification process  (ISO)
regulation of DNA methylation-dependent heterochromatin formation  (ISO)
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  (ISO)
response to organic cyclic compound  (ISO)
transcription by RNA polymerase II  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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


Expression


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

endocrine system hemolymphoid system nervous system
High
Medium 36 10 60
Low 10
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000017614   ⟹   ENSCSAP00000017088
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl20109,593,074 - 109,657,839 (-)Ensembl
RefSeq Acc Id: XM_007980095   ⟹   XP_007978286
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.120109,592,761 - 109,657,831 (-)NCBI
Vero_WHO_p1.0NW_0236660336,659,024 - 6,724,168 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007980096   ⟹   XP_007978287
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.120109,592,761 - 109,657,831 (-)NCBI
Vero_WHO_p1.0NW_0236660336,659,024 - 6,724,168 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007980097   ⟹   XP_007978288
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.120109,592,761 - 109,657,884 (-)NCBI
Vero_WHO_p1.0NW_0236660336,659,024 - 6,724,168 (+)NCBI
Sequence:
RefSeq Acc Id: XM_007980098   ⟹   XP_007978289
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.120109,592,761 - 109,657,885 (-)NCBI
Vero_WHO_p1.0NW_0236660336,659,024 - 6,724,168 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_007978286 (Get FASTA)   NCBI Sequence Viewer  
  XP_007978287 (Get FASTA)   NCBI Sequence Viewer  
  XP_007978288 (Get FASTA)   NCBI Sequence Viewer  
  XP_007978289 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000017088
  ENSCSAP00000017088.1
Reference Protein Sequences
RefSeq Acc Id: XP_007978289   ⟸   XM_007980098
- Peptide Label: isoform X1
RefSeq Acc Id: XP_007978288   ⟸   XM_007980097
- Peptide Label: isoform X4
RefSeq Acc Id: XP_007978287   ⟸   XM_007980096
- Peptide Label: isoform X3
RefSeq Acc Id: XP_007978286   ⟸   XM_007980095
- Peptide Label: isoform X2
- UniProtKB: A0A0D9S899 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000017088   ⟸   ENSCSAT00000017614


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000000919 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000017614.1 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
  Hist_Lys-spec_deMease UniProtKB/TrEMBL
  Homeobox-like_sf UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report csab:103225404 UniProtKB/TrEMBL
NCBI Gene KDM1A ENTREZGENE
PANTHER FLAVIN MONOAMINE OXIDASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A UniProtKB/TrEMBL
Pfam Amino_oxidase UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
PIRSF Histone_Lys-demethylase UniProtKB/TrEMBL
PROSITE SWIRM UniProtKB/TrEMBL
Superfamily-SCOP FAD-linked reductases, C-terminal domain UniProtKB/TrEMBL
  SSF46689 UniProtKB/TrEMBL
  SSF51905 UniProtKB/TrEMBL
UniProt A0A0D9S899 ENTREZGENE, UniProtKB/TrEMBL