KDM2A (lysine demethylase 2A) - Rat Genome Database

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Gene: KDM2A (lysine demethylase 2A) Homo sapiens
Analyze
Symbol: KDM2A
Name: lysine demethylase 2A
RGD ID: 1319753
HGNC Page HGNC
Description: Enables histone demethylase activity (H3-K36 specific); unmethylated CpG binding activity; and zinc ion binding activity. Involved in double-strand break repair via nonhomologous end joining; regulation of circadian rhythm; and regulation of gene expression. Acts upstream of or within histone H3-K36 demethylation. Located in nucleoplasm. Implicated in lung non-small cell carcinoma. Biomarker of lung non-small cell carcinoma.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: [Histone-H3]-lysine-36 demethylase 1A; CXXC-type zinc finger protein 8; CXXC8; DKFZp434M1735; F-box and leucine-rich repeat protein 11; F-box protein FBL11; F-box protein FBL7; F-box protein Lilina; F-box/LRR-repeat protein 11; FBL11; FBL7; FBXL11; FLJ00115; FLJ46431; JHDM1A; jmjC domain-containing histone demethylation protein 1A; jumonji C domain-containing histone demethylase 1A; KIAA1004; LILINA; lysine (K)-specific demethylase 2A; lysine-specific demethylase 2A; SF-KDM2A
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1167,119,263 - 67,258,082 (+)EnsemblGRCh38hg38GRCh38
GRCh381167,119,263 - 67,258,082 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371166,886,734 - 67,025,553 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361166,644,074 - 66,781,717 (+)NCBINCBI36hg18NCBI36
Build 341166,644,073 - 66,781,717NCBI
Celera1164,216,493 - 64,358,014 (+)NCBI
Cytogenetic Map11q13.2NCBI
HuRef1163,214,819 - 63,354,668 (+)NCBIHuRef
CHM1_11166,769,756 - 66,908,574 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Human Phenotype
References

Additional References at PubMed
PMID:10231032   PMID:10531035   PMID:10531037   PMID:10945468   PMID:11214971   PMID:12168954   PMID:12477932   PMID:14702039   PMID:15070733   PMID:15231748   PMID:15489334   PMID:15635413  
PMID:16147992   PMID:16362057   PMID:17081983   PMID:17463251   PMID:19001877   PMID:19322201   PMID:19490893   PMID:19805303   PMID:20080798   PMID:20379134   PMID:20417597   PMID:20682791  
PMID:20936779   PMID:21029866   PMID:21187428   PMID:21251613   PMID:21609845   PMID:21873635   PMID:21988832   PMID:22083960   PMID:22100412   PMID:22635273   PMID:23074094   PMID:23414517  
PMID:23537643   PMID:23559091   PMID:24457600   PMID:24553073   PMID:24981860   PMID:25029110   PMID:25245333   PMID:25281560   PMID:25609649   PMID:25823024   PMID:26004508   PMID:26037310  
PMID:26207617   PMID:26344197   PMID:26416883   PMID:26496610   PMID:27029061   PMID:27074224   PMID:27114453   PMID:27497248   PMID:27537276   PMID:27705803   PMID:28180290   PMID:28242625  
PMID:28262558   PMID:28514442   PMID:28611215   PMID:28816576   PMID:29117863   PMID:29276034   PMID:29360266   PMID:29467282   PMID:29507755   PMID:29509190   PMID:29662616   PMID:30033217  
PMID:30118678   PMID:30483744   PMID:30483796   PMID:30604066   PMID:30804502   PMID:30940825   PMID:31248990   PMID:31307234   PMID:31586073   PMID:32238831   PMID:32416067   PMID:32694731  
PMID:32780723   PMID:32901907   PMID:33024266   PMID:33050392   PMID:33155208   PMID:33536335   PMID:33854235   PMID:33961781   PMID:34079125  


Genomics

Comparative Map Data
KDM2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1167,119,263 - 67,258,082 (+)EnsemblGRCh38hg38GRCh38
GRCh381167,119,263 - 67,258,082 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371166,886,734 - 67,025,553 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361166,644,074 - 66,781,717 (+)NCBINCBI36hg18NCBI36
Build 341166,644,073 - 66,781,717NCBI
Celera1164,216,493 - 64,358,014 (+)NCBI
Cytogenetic Map11q13.2NCBI
HuRef1163,214,819 - 63,354,668 (+)NCBIHuRef
CHM1_11166,769,756 - 66,908,574 (+)NCBICHM1_1
Kdm2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39194,366,172 - 4,448,749 (-)NCBIGRCm39mm39
GRCm39 Ensembl194,364,447 - 4,448,313 (-)Ensembl
GRCm38194,316,144 - 4,398,721 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl194,314,419 - 4,398,285 (-)EnsemblGRCm38mm10GRCm38
MGSCv37194,316,144 - 4,397,077 (-)NCBIGRCm37mm9NCBIm37
MGSCv36194,317,806 - 4,398,266 (-)NCBImm8
Celera194,187,040 - 4,267,780 (-)NCBICelera
Cytogenetic Map19ANCBI
Kdm2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21201,612,427 - 201,682,359 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1201,612,453 - 201,680,787 (-)Ensembl
Rnor_6.01219,566,130 - 219,642,294 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1219,566,156 - 219,640,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01226,436,243 - 226,509,594 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41206,903,426 - 206,972,100 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11207,057,263 - 207,125,981 (-)NCBI
Celera1199,156,169 - 199,224,605 (-)NCBICelera
Cytogenetic Map1q43NCBI
Kdm2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542218,200,758 - 18,308,163 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542218,201,243 - 18,308,163 (-)NCBIChiLan1.0ChiLan1.0
KDM2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11165,793,464 - 65,930,509 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1165,793,464 - 65,930,498 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01162,470,549 - 62,616,135 (+)NCBIMhudiblu_PPA_v0panPan3
KDM2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11850,178,511 - 50,294,097 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1850,181,024 - 50,291,127 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1848,788,733 - 48,940,137 (-)NCBI
ROS_Cfam_1.01851,127,518 - 51,280,575 (-)NCBI
UMICH_Zoey_3.11850,313,570 - 50,464,719 (-)NCBI
UNSW_CanFamBas_1.01849,888,074 - 50,039,414 (-)NCBI
UU_Cfam_GSD_1.01850,682,691 - 50,834,402 (-)NCBI
Kdm2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049476,024,717 - 6,134,274 (-)NCBI
SpeTri2.0NW_0049365992,466,427 - 2,576,623 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl25,240,287 - 5,357,164 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.125,238,690 - 5,357,799 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.224,021,430 - 4,050,212 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.224,143,872 - 4,182,749 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.117,004,109 - 7,152,072 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl17,003,784 - 7,082,720 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666038104,292,429 - 104,442,261 (-)NCBIVero_WHO_p1.0
Kdm2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476719,247,009 - 19,365,520 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH44634  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371166,894,751 - 66,894,905UniSTSGRCh37
Build 361166,651,327 - 66,651,481RGDNCBI36
Celera1164,223,914 - 64,224,068RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,222,829 - 63,222,983UniSTS
GeneMap99-GB4 RH Map11253.3UniSTS
RH45252  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371166,950,800 - 66,950,989UniSTSGRCh37
Build 361166,707,376 - 66,707,565RGDNCBI36
Celera1164,280,266 - 64,280,455RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,277,856 - 63,278,045UniSTS
GeneMap99-GB4 RH Map11252.91UniSTS
RH124989  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371167,024,313 - 67,024,448UniSTSGRCh37
Build 361166,780,889 - 66,781,024RGDNCBI36
Celera1164,356,774 - 64,356,909RGD
HuRef1163,353,428 - 63,353,563UniSTS
G09895  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371167,004,727 - 67,004,967UniSTSGRCh37
Build 361166,761,303 - 66,761,543RGDNCBI36
Celera1164,337,190 - 64,337,430RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,333,856 - 63,334,096UniSTS
RH18199  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371167,023,551 - 67,023,691UniSTSGRCh37
Build 361166,780,127 - 66,780,267RGDNCBI36
Celera1164,356,012 - 64,356,152RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,352,666 - 63,352,806UniSTS
GeneMap99-GB4 RH Map11253.3UniSTS
RH12099  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371167,024,888 - 67,025,028UniSTSGRCh37
Build 361166,781,464 - 66,781,604RGDNCBI36
Celera1164,357,349 - 64,357,489RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,354,003 - 63,354,143UniSTS
GeneMap99-GB4 RH Map11253.3UniSTS
RH65398  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371166,952,119 - 66,952,247UniSTSGRCh37
Build 361166,708,695 - 66,708,823RGDNCBI36
Celera1164,281,585 - 64,281,713RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,279,175 - 63,279,303UniSTS
GeneMap99-GB4 RH Map11255.53UniSTS
STS-N24829  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371166,954,458 - 66,954,612UniSTSGRCh37
Build 361166,711,034 - 66,711,188RGDNCBI36
Celera1164,283,923 - 64,284,077RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,281,514 - 63,281,668UniSTS
GeneMap99-GB4 RH Map11252.91UniSTS
D11S4540  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371166,958,352 - 66,958,517UniSTSGRCh37
Build 361166,714,928 - 66,715,093RGDNCBI36
Celera1164,287,816 - 64,287,981RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,285,400 - 63,285,565UniSTS
Stanford-G3 RH Map112968.0UniSTS
NCBI RH Map11582.0UniSTS
STS-Z40471  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371167,023,551 - 67,023,668UniSTSGRCh37
Build 361166,780,127 - 66,780,244RGDNCBI36
Celera1164,356,012 - 64,356,129RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,352,666 - 63,352,783UniSTS
GeneMap99-GB4 RH Map11255.21UniSTS
AFMA190YD5  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371166,920,174 - 66,920,460UniSTSGRCh37
Build 361166,676,750 - 66,677,036RGDNCBI36
Celera1164,249,697 - 64,249,972RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,247,267 - 63,247,549UniSTS
Whitehead-YAC Contig Map11 UniSTS
STS-R06543  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371166,894,774 - 66,894,929UniSTSGRCh37
Build 361166,651,350 - 66,651,505RGDNCBI36
Celera1164,223,937 - 64,224,092RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,222,852 - 63,223,007UniSTS
GeneMap99-GB4 RH Map11255.53UniSTS
STS-H69553  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371166,988,187 - 66,988,447UniSTSGRCh37
Build 361166,744,763 - 66,745,023RGDNCBI36
Celera1164,317,907 - 64,318,167RGD
Cytogenetic Map11q13.2UniSTS
HuRef1163,315,686 - 63,315,946UniSTS
GeneMap99-GB4 RH Map11254.49UniSTS
MARC_17215-17216:1023895331:5  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371167,012,830 - 67,013,499UniSTSGRCh37
Build 361166,769,406 - 66,770,075RGDNCBI36
Celera1164,345,293 - 64,345,962RGD
HuRef1163,341,957 - 63,342,626UniSTS
FBXL11  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371167,024,751 - 67,025,020UniSTSGRCh37
Celera1164,357,212 - 64,357,481UniSTS
HuRef1163,353,866 - 63,354,135UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:7853
Count of miRNA genes:1202
Interacting mature miRNAs:1568
Transcripts:ENST00000308783, ENST00000398645, ENST00000517637, ENST00000524657, ENST00000525041, ENST00000525379, ENST00000526258, ENST00000527157, ENST00000528380, ENST00000529006, ENST00000529124, ENST00000530342, ENST00000531696, ENST00000532436, ENST00000534486
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.


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2429 2647 1682 590 1879 432 4345 1963 2704 366 1446 1602 171 1204 2780 4
Low 9 343 44 33 72 33 11 233 1027 53 12 10 4 1 8 2 1
Below cutoff 1 3 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001256405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_027473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006718480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011544860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011544861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017017391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017017392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB023221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB490246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF179221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI185920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK022684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK024505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK128293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK299725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL117517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AP000729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AP001885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC001203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC027467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC047371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC047486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC056905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC064360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BE675843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DR001963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HF548043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ710741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ710742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ710743 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ710744 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000308783   ⟹   ENSP00000309302
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,121,269 - 67,255,062 (+)Ensembl
RefSeq Acc Id: ENST00000398645   ⟹   ENSP00000381640
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,119,269 - 67,257,665 (+)Ensembl
RefSeq Acc Id: ENST00000517637
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,240,301 - 67,243,816 (+)Ensembl
RefSeq Acc Id: ENST00000524657
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,252,338 - 67,257,670 (+)Ensembl
RefSeq Acc Id: ENST00000525041
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,231,765 - 67,248,379 (+)Ensembl
RefSeq Acc Id: ENST00000525379
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,217,543 - 67,219,688 (+)Ensembl
RefSeq Acc Id: ENST00000526258
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,207,602 - 67,257,661 (+)Ensembl
RefSeq Acc Id: ENST00000527157
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,119,976 - 67,180,453 (+)Ensembl
RefSeq Acc Id: ENST00000528380
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,207,568 - 67,215,673 (+)Ensembl
RefSeq Acc Id: ENST00000529006   ⟹   ENSP00000432786
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,119,263 - 67,258,082 (+)Ensembl
RefSeq Acc Id: ENST00000529124
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,245,078 - 67,248,605 (+)Ensembl
RefSeq Acc Id: ENST00000530342   ⟹   ENSP00000435776
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,240,047 - 67,256,373 (+)Ensembl
RefSeq Acc Id: ENST00000531696
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,215,911 - 67,256,374 (+)Ensembl
RefSeq Acc Id: ENST00000532436
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,119,891 - 67,149,207 (+)Ensembl
RefSeq Acc Id: ENST00000534486
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1167,245,539 - 67,248,368 (+)Ensembl
RefSeq Acc Id: NM_001256405   ⟹   NP_001243334
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,240,014 - 67,258,082 (+)NCBI
GRCh371166,886,740 - 67,025,553 (+)NCBI
HuRef1163,214,819 - 63,354,668 (+)NCBI
CHM1_11166,890,547 - 66,908,574 (+)NCBI
Sequence:
RefSeq Acc Id: NM_012308   ⟹   NP_036440
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,119,263 - 67,258,082 (+)NCBI
GRCh371166,886,740 - 67,025,553 (+)ENTREZGENE
Build 361166,644,074 - 66,781,717 (+)NCBI Archive
HuRef1163,214,819 - 63,354,668 (+)ENTREZGENE
CHM1_11166,769,756 - 66,908,574 (+)NCBI
Sequence:
RefSeq Acc Id: NR_027473
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,119,263 - 67,258,082 (+)NCBI
GRCh371166,886,740 - 67,025,553 (+)ENTREZGENE
HuRef1163,214,819 - 63,354,668 (+)ENTREZGENE
CHM1_11166,769,756 - 66,908,574 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006718480   ⟹   XP_006718543
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,186,393 - 67,258,075 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011544860   ⟹   XP_011543162
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,119,746 - 67,257,795 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011544861   ⟹   XP_011543163
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,207,602 - 67,258,075 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017017391   ⟹   XP_016872880
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,121,269 - 67,258,075 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017017392   ⟹   XP_016872881
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,179,394 - 67,258,075 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036440   ⟸   NM_012308
- Peptide Label: isoform a
- UniProtKB: Q9Y2K7 (UniProtKB/Swiss-Prot),   I3VM53 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001243334   ⟸   NM_001256405
- Peptide Label: isoform b
- UniProtKB: Q9Y2K7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006718543   ⟸   XM_006718480
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_011543162   ⟸   XM_011544860
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_011543163   ⟸   XM_011544861
- Peptide Label: isoform X4
- UniProtKB: Q9Y2K7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_016872880   ⟸   XM_017017391
- Peptide Label: isoform X1
- UniProtKB: I3VM54 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_016872881   ⟸   XM_017017392
- Peptide Label: isoform X1
- UniProtKB: I3VM54 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000381640   ⟸   ENST00000398645
RefSeq Acc Id: ENSP00000309302   ⟸   ENST00000308783
RefSeq Acc Id: ENSP00000435776   ⟸   ENST00000530342
RefSeq Acc Id: ENSP00000432786   ⟸   ENST00000529006
Protein Domains
CXXC-type   F-box   JmjC   PHD-type

Promoters
RGD ID:6789031
Promoter ID:HG_KWN:13445
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_012308,   NR_027473
Position:
Human AssemblyChrPosition (strand)Source
Build 361166,642,326 - 66,643,422 (+)MPROMDB
RGD ID:6810036
Promoter ID:HG_ACW:12803
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   Lymphoblastoid,   NB4
Transcripts:FBXL11.LAPR07
Position:
Human AssemblyChrPosition (strand)Source
Build 361166,644,311 - 66,645,162 (+)MPROMDB
RGD ID:6810032
Promoter ID:HG_ACW:12815
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:FBXL11.EAPR07,   FBXL11.MAPR07
Position:
Human AssemblyChrPosition (strand)Source
Build 361166,763,834 - 66,764,334 (+)MPROMDB
RGD ID:6789036
Promoter ID:HG_KWN:13450
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lymphoblastoid
Transcripts:UC001OJZ.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361166,769,161 - 66,769,661 (+)MPROMDB
RGD ID:6789035
Promoter ID:HG_KWN:13451
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   K562,   Lymphoblastoid,   NB4
Transcripts:UC001OKA.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361166,775,716 - 66,776,902 (+)MPROMDB
RGD ID:6814974
Promoter ID:HG_MRA:2859
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:AL117517,   CR613662
Position:
Human AssemblyChrPosition (strand)Source
Build 361166,779,271 - 66,779,771 (+)MPROMDB
RGD ID:7221203
Promoter ID:EPDNEW_H16347
Type:initiation region
Name:KDM2A_2
Description:lysine demethylase 2A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H16348  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,119,263 - 67,119,323EPDNEW
RGD ID:7221205
Promoter ID:EPDNEW_H16348
Type:initiation region
Name:KDM2A_1
Description:lysine demethylase 2A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H16347  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381167,240,014 - 67,240,074EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q13.2(chr11:66885910-67698250)x1 copy number loss See cases [RCV000052682] Chr11:66885910..67698250 [GRCh38]
Chr11:66653381..67465721 [GRCh37]
Chr11:66409957..67222297 [NCBI36]
Chr11:11q13.2
pathogenic
GRCh38/hg38 11q13.2(chr11:66193502-67890770)x3 copy number gain See cases [RCV000053623] Chr11:66193502..67890770 [GRCh38]
Chr11:65960973..67658241 [GRCh37]
Chr11:65717549..67414817 [NCBI36]
Chr11:11q13.2
pathogenic
GRCh38/hg38 11q13.2(chr11:67016543-67256428)x3 copy number gain See cases [RCV000053624] Chr11:67016543..67256428 [GRCh38]
Chr11:66784014..67023899 [GRCh37]
Chr11:66540590..66780475 [NCBI36]
Chr11:11q13.2
pathogenic
GRCh38/hg38 11q13.2-13.3(chr11:67217264-69448598)x1 copy number loss See cases [RCV000135609] Chr11:67217264..69448598 [GRCh38]
Chr11:66984735..69263366 [GRCh37]
Chr11:66741311..68972547 [NCBI36]
Chr11:11q13.2-13.3
likely pathogenic
GRCh38/hg38 11q13.1-13.2(chr11:65741431-67705669)x1 copy number loss See cases [RCV000142881] Chr11:65741431..67705669 [GRCh38]
Chr11:65508902..67473140 [GRCh37]
Chr11:65265478..67229716 [NCBI36]
Chr11:11q13.1-13.2
pathogenic
GRCh37/hg19 11q13.2(chr11:66024774-67430781)x3 copy number gain See cases [RCV000240374] Chr11:66024774..67430781 [GRCh37]
Chr11:11q13.2
uncertain significance
GRCh37/hg19 11q13.1-13.2(chr11:64501919-67129258)x3 copy number gain See cases [RCV000511632] Chr11:64501919..67129258 [GRCh37]
Chr11:11q13.1-13.2
likely pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11q13.1-13.2(chr11:65138976-67574402) copy number gain not provided [RCV000767601] Chr11:65138976..67574402 [GRCh37]
Chr11:11q13.1-13.2
pathogenic
GRCh37/hg19 11q13.2(chr11:66662614-66975223)x3 copy number gain not provided [RCV000683330] Chr11:66662614..66975223 [GRCh37]
Chr11:11q13.2
uncertain significance
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25
pathogenic
GRCh37/hg19 11q13.2(chr11:66906392-66916559)x1 copy number loss not provided [RCV000750086] Chr11:66906392..66916559 [GRCh37]
Chr11:11q13.2
benign
GRCh37/hg19 11q13.2(chr11:66906392-66919278)x1 copy number loss not provided [RCV000750087] Chr11:66906392..66919278 [GRCh37]
Chr11:11q13.2
benign
GRCh37/hg19 11q13.2(chr11:66908750-66916559)x1 copy number loss not provided [RCV000750088] Chr11:66908750..66916559 [GRCh37]
Chr11:11q13.2
benign
GRCh37/hg19 11q13.2(chr11:66908750-66916676)x1 copy number loss not provided [RCV000750089] Chr11:66908750..66916676 [GRCh37]
Chr11:11q13.2
benign
GRCh37/hg19 11q13.2(chr11:66908750-66919278)x1 copy number loss not provided [RCV000750090] Chr11:66908750..66919278 [GRCh37]
Chr11:11q13.2
benign
NM_012308.3(KDM2A):c.3453C>T (p.Cys1151=) single nucleotide variant not provided [RCV000969605] Chr11:67255019 [GRCh38]
Chr11:67022490 [GRCh37]
Chr11:11q13.2
benign
NM_002047.4(GARS1):c.51G>A (p.Leu17=) single nucleotide variant not provided [RCV001720978] Chr11:67228132 [GRCh38]
Chr11:66995603 [GRCh37]
Chr11:11q13.2
benign
GRCh37/hg19 11q13.2(chr11:66820585-67979510)x3 copy number gain not provided [RCV001006414] Chr11:66820585..67979510 [GRCh37]
Chr11:11q13.2
uncertain significance
GRCh37/hg19 11q13.2(chr11:66760918-67015469)x3 copy number gain not provided [RCV001006413] Chr11:66760918..67015469 [GRCh37]
Chr11:11q13.2
uncertain significance
NC_000011.9:g.(?_59596957)_(68707199_?)dup duplication Epilepsy, familial temporal lobe, 8 [RCV001372442] Chr11:59596957..68707199 [GRCh37]
Chr11:11q12.1-13.3
uncertain significance
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:13606 AgrOrtholog
COSMIC KDM2A COSMIC
Ensembl Genes ENSG00000173120 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000309302 ENTREZGENE, UniProtKB/TrEMBL
  ENSP00000381640 UniProtKB/Swiss-Prot
  ENSP00000432786 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000435776 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000308783 ENTREZGENE, UniProtKB/TrEMBL
  ENST00000398645 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000526258 ENTREZGENE
  ENST00000529006 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000530342 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000173120 GTEx
HGNC ID HGNC:13606 ENTREZGENE
Human Proteome Map KDM2A Human Proteome Map
InterPro F-box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_Cys-con_subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CXXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:22992 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 22992 ENTREZGENE
OMIM 605657 OMIM
Pfam F-box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PHD_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-CXXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA164721195 PharmGKB
PROSITE JMJC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_CXXC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_CC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57903 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt I3VM53 ENTREZGENE, UniProtKB/TrEMBL
  I3VM54 ENTREZGENE, UniProtKB/TrEMBL
  KDM2A_HUMAN UniProtKB/Swiss-Prot
  L0R5B6_HUMAN UniProtKB/TrEMBL
  Q9Y2K7 ENTREZGENE
UniProt Secondary D4QA03 UniProtKB/Swiss-Prot
  E9PIL6 UniProtKB/Swiss-Prot
  I3VM55 UniProtKB/Swiss-Prot
  Q49A21 UniProtKB/Swiss-Prot
  Q4G0M3 UniProtKB/Swiss-Prot
  Q69YY8 UniProtKB/Swiss-Prot
  Q9BVH5 UniProtKB/Swiss-Prot
  Q9H7H5 UniProtKB/Swiss-Prot
  Q9UK66 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-16 KDM2A  lysine demethylase 2A    lysine (K)-specific demethylase 2A  Symbol and/or name change 5135510 APPROVED