KDM3A (lysine demethylase 3A) - Rat Genome Database

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Gene: KDM3A (lysine demethylase 3A) Homo sapiens
Analyze
Symbol: KDM3A
Name: lysine demethylase 3A
RGD ID: 1346048
HGNC Page HGNC:20815
Description: Enables histone H3K9me/H3K9me2 demethylase activity; iron ion binding activity; and nuclear androgen receptor binding activity. Involved in androgen receptor signaling pathway; formaldehyde biosynthetic process; and positive regulation of DNA-templated transcription. Located in nucleoplasm. Implicated in cervical cancer and colon cancer. Biomarker of Ewing sarcoma; hepatocellular carcinoma; nasopharynx carcinoma; and prostate cancer.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: [histone H3]-dimethyl-L-lysine(9) demethylase 3A; DKFZp686A24246; DKFZp686P07111; JHDM2A; JHMD2A; jmjC domain-containing histone demethylation protein 2A; JMJD1; JMJD1A; jumonji C domain-containing histone demethylase 2A; jumonji domain containing 1; jumonji domain containing 1A; jumonji domain-containing protein 1A; KIAA0742; lysine (K)-specific demethylase 3A; lysine-specific demethylase 3A; testis-specific protein A; TSGA
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: KDM3AP1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38286,437,044 - 86,492,716 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl286,440,647 - 86,492,716 (+)EnsemblGRCh38hg38GRCh38
GRCh37286,668,494 - 86,719,839 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36286,521,865 - 86,573,350 (+)NCBINCBI36Build 36hg18NCBI36
Build 34286,580,100 - 86,631,497NCBI
Celera286,496,309 - 86,547,889 (+)NCBICelera
Cytogenetic Map2p11.2NCBI
HuRef286,565,835 - 86,617,601 (+)NCBIHuRef
CHM1_1286,598,317 - 86,649,908 (+)NCBICHM1_1
T2T-CHM13v2.0286,439,057 - 86,494,729 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3H-1,2-dithiole-3-thione  (ISO)
6-propyl-2-thiouracil  (ISO)
acrolein  (EXP)
adefovir pivoxil  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (EXP)
allethrin  (ISO)
amitrole  (ISO)
ammonium chloride  (ISO)
antimycin A  (EXP)
apigenin  (ISO)
aristolochic acid A  (EXP)
arsenite(3-)  (EXP)
arsenous acid  (EXP)
azoxystrobin  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (EXP)
bisphenol A  (EXP,ISO)
butanal  (EXP)
cadmium dichloride  (EXP)
caffeine  (EXP)
carbamazepine  (EXP)
carbon nanotube  (ISO)
carbonyl sulfide  (ISO)
chloroacetaldehyde  (EXP)
cidofovir anhydrous  (EXP)
cisplatin  (EXP)
clodronic acid  (EXP)
cobalt dichloride  (EXP,ISO)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) chloride  (EXP)
copper(II) sulfate  (EXP)
coumestrol  (EXP)
crocidolite asbestos  (ISO)
cyclosporin A  (EXP)
cyhalothrin  (ISO)
cypermethrin  (ISO)
desferrioxamine B  (EXP)
diarsenic trioxide  (EXP)
diazinon  (EXP)
dicrotophos  (EXP)
dioxygen  (EXP,ISO)
doxorubicin  (EXP)
ethanol  (EXP,ISO)
fenpyroximate  (EXP)
fenvalerate  (ISO)
folic acid  (EXP)
folpet  (ISO)
FR900359  (EXP)
gallic acid  (EXP)
gentamycin  (ISO)
hydrogen peroxide  (EXP)
ifosfamide  (EXP)
iron atom  (EXP)
iron(0)  (EXP)
ketoconazole  (ISO)
L-ascorbic acid  (EXP)
leflunomide  (EXP)
menadione  (EXP)
methimazole  (ISO)
motexafin gadolinium  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (EXP,ISO)
nickel dichloride  (EXP,ISO)
nickel sulfate  (EXP)
nitric oxide  (EXP)
ozone  (EXP)
paracetamol  (ISO)
phenobarbital  (EXP,ISO)
picoxystrobin  (EXP)
propiconazole  (ISO)
pyrethrins  (ISO)
pyrimidifen  (EXP)
quercetin  (EXP)
quercitrin  (EXP)
rotenone  (EXP)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sodium fluoride  (ISO)
sunitinib  (EXP)
tanespimycin  (EXP)
tebufenpyrad  (EXP)
tert-butyl hydroperoxide  (EXP)
thioacetamide  (ISO)
troglitazone  (ISO)
urethane  (EXP)
valproic acid  (EXP)
vandetanib  (EXP)
vinclozolin  (ISO)
zinc acetate  (EXP)
zinc dichloride  (EXP)
zoledronic acid  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IBA,IEA)
cytoplasm  (IEA)
histone deacetylase complex  (IBA,IEA)
male germ cell nucleus  (IEA)
membrane  (HDA)
nucleoplasm  (IDA,TAS)
nucleus  (IDA,IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Systematic knockdown of epigenetic enzymes identifies a novel histone demethylase PHF8 overexpressed in prostate cancer with an impact on cell proliferation, migration and invasion. Bjorkman M, etal., Oncogene. 2012 Jul 19;31(29):3444-56. doi: 10.1038/onc.2011.512. Epub 2011 Nov 28.
2. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
3. Upregulation of MiR-155 in nasopharyngeal carcinoma is partly driven by LMP1 and LMP2A and downregulates a negative prognostic marker JMJD1A. Du ZM, etal., PLoS One. 2011 Apr 26;6(4):e19137. doi: 10.1371/journal.pone.0019137.
4. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
5. Regulation of the histone demethylase JMJD1A by hypoxia-inducible factor 1 alpha enhances hypoxic gene expression and tumor growth. Krieg AJ, etal., Mol Cell Biol. 2010 Jan;30(1):344-53. doi: 10.1128/MCB.00444-09. Epub .
6. Histone demethylase JHDM2A is involved in male infertility and obesity. Okada Y, etal., J Androl. 2010 Jan-Feb;31(1):75-8. doi: 10.2164/jandrol.109.008052. Epub 2009 Oct 29.
7. Inhibition of histone demethylase JMJD1A improves anti-angiogenic therapy and reduces tumor-associated macrophages. Osawa T, etal., Cancer Res. 2013 May 15;73(10):3019-28. doi: 10.1158/0008-5472.CAN-12-3231. Epub 2013 Mar 14.
8. The histone demethylase KDM3A is a microRNA-22-regulated tumor promoter in Ewing Sarcoma. Parrish JK, etal., Oncogene. 2013 Dec 23. doi: 10.1038/onc.2013.541.
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Genetic alterations and changes in expression of histone demethylases in prostate cancer. Suikki HE, etal., Prostate. 2010 Jun 1;70(8):889-98. doi: 10.1002/pros.21123.
12. Hypoxia upregulates the histone demethylase JMJD1A via HIF-1. Wellmann S, etal., Biochem Biophys Res Commun. 2008 Aug 8;372(4):892-7. doi: 10.1016/j.bbrc.2008.05.150. Epub 2008 Jun 4.
13. Role of the hypoxia-related gene, JMJD1A, in hepatocellular carcinoma: clinical impact on recurrence after hepatic resection. Yamada D, etal., Ann Surg Oncol. 2012 Jul;19 Suppl 3:S355-64. doi: 10.1245/s10434-011-1797-x. Epub 2011 May 24.
Additional References at PubMed
PMID:9872452   PMID:12477932   PMID:14702039   PMID:15302935   PMID:15489334   PMID:15815621   PMID:16344560   PMID:16603237   PMID:16619273   PMID:17991879   PMID:18713068   PMID:18984585  
PMID:19194461   PMID:19471969   PMID:19615732   PMID:19946888   PMID:20042601   PMID:20378615   PMID:20823141   PMID:21275466   PMID:21282530   PMID:21873635   PMID:22020899   PMID:22318714  
PMID:22645302   PMID:23455924   PMID:23546878   PMID:23576503   PMID:23583388   PMID:23593242   PMID:23891737   PMID:24214985   PMID:24742640   PMID:24981860   PMID:25071150   PMID:25148682  
PMID:25535969   PMID:25544563   PMID:25609425   PMID:25948511   PMID:26186194   PMID:26279298   PMID:26344197   PMID:26496610   PMID:26617828   PMID:26728187   PMID:26864203   PMID:26945572  
PMID:27027467   PMID:27034728   PMID:27270439   PMID:27472901   PMID:27488962   PMID:27692601   PMID:27694900   PMID:27807143   PMID:27835890   PMID:28262558   PMID:28263974   PMID:28319067  
PMID:28514442   PMID:28692045   PMID:28843785   PMID:29444873   PMID:29507755   PMID:29590186   PMID:29712835   PMID:29802196   PMID:30053768   PMID:30293567   PMID:30344098   PMID:30377265  
PMID:30415952   PMID:30531796   PMID:30578902   PMID:30649550   PMID:30716474   PMID:30890647   PMID:31054974   PMID:31442435   PMID:31629659   PMID:32238799   PMID:32457453   PMID:32513696  
PMID:32522824   PMID:32569864   PMID:32697014   PMID:32762126   PMID:33174020   PMID:33318475   PMID:33486545   PMID:33888871   PMID:33961781   PMID:34079125   PMID:34171978   PMID:34235877  
PMID:34321328   PMID:34350711   PMID:34479471   PMID:34795231   PMID:34857952   PMID:35020958   PMID:35271311   PMID:35439318   PMID:35545047   PMID:35563538   PMID:35579678   PMID:35914814  
PMID:36089195   PMID:36094735   PMID:37689310   PMID:37931956   PMID:38113892   PMID:38165573   PMID:38280479  


Genomics

Comparative Map Data
KDM3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38286,437,044 - 86,492,716 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl286,440,647 - 86,492,716 (+)EnsemblGRCh38hg38GRCh38
GRCh37286,668,494 - 86,719,839 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36286,521,865 - 86,573,350 (+)NCBINCBI36Build 36hg18NCBI36
Build 34286,580,100 - 86,631,497NCBI
Celera286,496,309 - 86,547,889 (+)NCBICelera
Cytogenetic Map2p11.2NCBI
HuRef286,565,835 - 86,617,601 (+)NCBIHuRef
CHM1_1286,598,317 - 86,649,908 (+)NCBICHM1_1
T2T-CHM13v2.0286,439,057 - 86,494,729 (+)NCBIT2T-CHM13v2.0
Kdm3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39671,565,954 - 71,609,963 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl671,565,956 - 71,609,974 (-)EnsemblGRCm39 Ensembl
GRCm38671,588,970 - 71,632,990 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl671,588,972 - 71,632,990 (-)EnsemblGRCm38mm10GRCm38
MGSCv37671,538,966 - 71,582,899 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36671,518,550 - 71,562,078 (-)NCBIMGSCv36mm8
Celera673,672,792 - 73,716,729 (-)NCBICelera
Cytogenetic Map6C1NCBI
cM Map632.18NCBI
Kdm3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84105,189,208 - 105,233,526 (-)NCBIGRCr8
mRatBN7.24103,630,907 - 103,675,073 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4103,630,908 - 103,675,073 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4109,015,136 - 109,059,356 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04104,790,259 - 104,834,479 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04103,400,828 - 103,444,990 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0499,503,160 - 99,547,315 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl499,503,176 - 99,546,905 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04164,282,422 - 164,326,579 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44104,866,501 - 104,911,355 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14105,110,981 - 105,155,233 (-)NCBI
Celera492,789,151 - 92,833,037 (-)NCBICelera
Cytogenetic Map4q32NCBI
Kdm3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554241,171,827 - 1,218,607 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554241,164,384 - 1,218,607 (-)NCBIChiLan1.0ChiLan1.0
KDM3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21239,887,164 - 39,938,601 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A39,889,925 - 39,941,362 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A86,497,531 - 86,548,772 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A88,043,712 - 88,094,244 (+)NCBIpanpan1.1PanPan1.1panPan2
KDM3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11738,690,962 - 38,744,507 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1738,690,979 - 38,743,739 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1738,374,227 - 38,430,299 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01739,421,459 - 39,477,555 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1739,423,705 - 39,477,460 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11738,587,497 - 38,643,573 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01738,623,889 - 38,679,943 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01738,971,898 - 39,027,987 (-)NCBIUU_Cfam_GSD_1.0
Kdm3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629279,760,595 - 79,805,238 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367121,053,210 - 1,096,961 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367121,053,210 - 1,097,845 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl358,302,949 - 58,354,945 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1358,300,109 - 58,355,000 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2361,060,319 - 61,116,654 (-)NCBISscrofa10.2Sscrofa10.2susScr3
KDM3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11420,668,215 - 20,721,854 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1420,668,821 - 20,720,759 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604591,765,741 - 91,830,044 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474916,784,538 - 16,829,365 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474916,784,538 - 16,829,784 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in KDM3A
44 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p11.2(chr2:86395172-86859284)x1 copy number loss See cases [RCV000054056] Chr2:86395172..86859284 [GRCh38]
Chr2:86622295..87086407 [GRCh37]
Chr2:86475806..86939918 [NCBI36]
Chr2:2p11.2		 pathogenic
NM_001146688.1(KDM3A):c.2655C>T (p.Leu885=) single nucleotide variant Malignant melanoma [RCV000065716] Chr2:86482072 [GRCh38]
Chr2:86709195 [GRCh37]
Chr2:86562706 [NCBI36]
Chr2:2p11.2		 not provided
NM_001146688.1(KDM3A):c.1000C>T (p.Pro334Ser) single nucleotide variant Malignant melanoma [RCV000060624] Chr2:86464209 [GRCh38]
Chr2:86691332 [GRCh37]
Chr2:86544843 [NCBI36]
Chr2:2p11.2		 not provided
NM_018433.6(KDM3A):c.2685+6TGTT[2] microsatellite Malignant tumor of prostate [RCV000149073] Chr2:86482108..86482111 [GRCh38]
Chr2:86709231..86709234 [GRCh37]
Chr2:2p11.2		 uncertain significance
GRCh38/hg38 2p12-11.2(chr2:77025216-90282666)x3 copy number gain See cases [RCV000134786] Chr2:77025216..90282666 [GRCh38]
Chr2:77252342..91619262 [GRCh37]
Chr2:77105850..90982989 [NCBI36]
Chr2:2p12-11.2		 pathogenic
GRCh38/hg38 2p16.3-11.2(chr2:47620388-86702722)x3 copy number gain See cases [RCV000137586] Chr2:47620388..86702722 [GRCh38]
Chr2:47847527..86929845 [GRCh37]
Chr2:47701031..86783356 [NCBI36]
Chr2:2p16.3-11.2		 uncertain significance
GRCh38/hg38 2p11.2(chr2:85014686-88826619)x1 copy number loss See cases [RCV000141948] Chr2:85014686..88826619 [GRCh38]
Chr2:85241809..89126132 [GRCh37]
Chr2:85095320..88907247 [NCBI36]
Chr2:2p11.2		 pathogenic
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign
GRCh37/hg19 2p15-11.2(chr2:62245236-86978895)x3 copy number gain See cases [RCV000448688] Chr2:62245236..86978895 [GRCh37]
Chr2:2p15-11.2		 pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) copy number gain See cases [RCV000512056] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 copy number gain See cases [RCV000511212] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p13.1-11.2(chr2:74365484-89129064)x1 copy number loss See cases [RCV000510763] Chr2:74365484..89129064 [GRCh37]
Chr2:2p13.1-11.2		 pathogenic
NM_018433.6(KDM3A):c.2482A>G (p.Thr828Ala) single nucleotide variant Inborn genetic diseases [RCV003292580] Chr2:86480332 [GRCh38]
Chr2:86707455 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.3647G>A (p.Arg1216Gln) single nucleotide variant Inborn genetic diseases [RCV003289623] Chr2:86490954 [GRCh38]
Chr2:86718077 [GRCh37]
Chr2:2p11.2		 uncertain significance
Single allele deletion not provided [RCV000714264] Chr2:40608411..146900718 [GRCh37]
Chr2:2p22.1-q22.3		 likely pathogenic
GRCh37/hg19 2p13.1-11.2(chr2:74527522-89125488)x1 copy number loss not provided [RCV000682167] Chr2:74527522..89125488 [GRCh37]
Chr2:2p13.1-11.2		 pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 copy number gain not provided [RCV000752802] Chr2:14238..243048760 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 copy number gain not provided [RCV000752804] Chr2:15672..243101834 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p11.2(chr2:86502663-87430727)x1 copy number loss not provided [RCV000740518] Chr2:86502663..87430727 [GRCh37]
Chr2:2p11.2		 likely pathogenic
NM_018433.6(KDM3A):c.189G>T (p.Val63=) single nucleotide variant KDM3A-related condition [RCV003950445]|not provided [RCV000894834] Chr2:86449809 [GRCh38]
Chr2:86676932 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.3847C>T (p.Leu1283=) single nucleotide variant KDM3A-related condition [RCV003940567]|not provided [RCV000886949] Chr2:86491237 [GRCh38]
Chr2:86718360 [GRCh37]
Chr2:2p11.2		 benign|likely benign
NM_018433.6(KDM3A):c.3207T>C (p.Ile1069=) single nucleotide variant not provided [RCV000922981] Chr2:86485753 [GRCh38]
Chr2:86712876 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.453+5A>G single nucleotide variant not provided [RCV000828122] Chr2:86451218 [GRCh38]
Chr2:86678341 [GRCh37]
Chr2:2p11.2		 likely benign
GRCh37/hg19 2p12-11.2(chr2:77907114-87330965)x1 copy number loss not provided [RCV000846587] Chr2:77907114..87330965 [GRCh37]
Chr2:2p12-11.2		 pathogenic
NM_018433.6(KDM3A):c.2809C>T (p.Leu937=) single nucleotide variant KDM3A-related condition [RCV003915891]|not provided [RCV000955950] Chr2:86482581 [GRCh38]
Chr2:86709704 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.2512+19T>C single nucleotide variant not provided [RCV001598252] Chr2:86480381 [GRCh38]
Chr2:86707504 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.1022del (p.Ser341fs) deletion not provided [RCV001035813] Chr2:86466386 [GRCh38]
Chr2:86693509 [GRCh37]
Chr2:2p11.2		 uncertain significance
GRCh37/hg19 2p25.3-q37.3(chr2:1-243199373) copy number gain Mosaic trisomy 2 [RCV002280628] Chr2:1..243199373 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p12-11.2(chr2:81209244-86688030)x1 copy number loss not provided [RCV001537915] Chr2:81209244..86688030 [GRCh37]
Chr2:2p12-11.2		 pathogenic
GRCh37/hg19 2p12-11.2(chr2:82486900-87322042) copy number loss not specified [RCV002053172] Chr2:82486900..87322042 [GRCh37]
Chr2:2p12-11.2		 pathogenic
NC_000002.11:g.(?_86067267)_(87017948_?)del deletion Susceptibility to respiratory infections associated with CD8alpha chain mutation [RCV001928070] Chr2:86067267..87017948 [GRCh37]
Chr2:2p11.2		 uncertain significance
GRCh37/hg19 2p25.1-q13(chr2:11504318-111365996)x1 copy number loss See cases [RCV002287563] Chr2:11504318..111365996 [GRCh37]
Chr2:2p25.1-q13		 pathogenic
NM_018433.6(KDM3A):c.3763T>C (p.Tyr1255His) single nucleotide variant Inborn genetic diseases [RCV003256093] Chr2:86491153 [GRCh38]
Chr2:86718276 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.3410A>G (p.Lys1137Arg) single nucleotide variant Inborn genetic diseases [RCV003259954] Chr2:86489414 [GRCh38]
Chr2:86716537 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1099G>C (p.Gly367Arg) single nucleotide variant Inborn genetic diseases [RCV003285340] Chr2:86466463 [GRCh38]
Chr2:86693586 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.995A>G (p.Lys332Arg) single nucleotide variant Inborn genetic diseases [RCV003288182] Chr2:86464204 [GRCh38]
Chr2:86691327 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1778A>G (p.Asn593Ser) single nucleotide variant Inborn genetic diseases [RCV002729428] Chr2:86474829 [GRCh38]
Chr2:86701952 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.2675C>G (p.Ser892Cys) single nucleotide variant Inborn genetic diseases [RCV002905194] Chr2:86482092 [GRCh38]
Chr2:86709215 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.296G>A (p.Arg99Gln) single nucleotide variant Inborn genetic diseases [RCV002823274] Chr2:86449916 [GRCh38]
Chr2:86677039 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1658G>T (p.Ser553Ile) single nucleotide variant Inborn genetic diseases [RCV002758894] Chr2:86470342 [GRCh38]
Chr2:86697465 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.493A>C (p.Ile165Leu) single nucleotide variant Inborn genetic diseases [RCV002757363] Chr2:86455124 [GRCh38]
Chr2:86682247 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1373G>A (p.Gly458Asp) single nucleotide variant Inborn genetic diseases [RCV002821477] Chr2:86466737 [GRCh38]
Chr2:86693860 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.2441G>T (p.Cys814Phe) single nucleotide variant Inborn genetic diseases [RCV002844463] Chr2:86480291 [GRCh38]
Chr2:86707414 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1316A>G (p.His439Arg) single nucleotide variant Inborn genetic diseases [RCV002869926] Chr2:86466680 [GRCh38]
Chr2:86693803 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.3955G>C (p.Gly1319Arg) single nucleotide variant Inborn genetic diseases [RCV002821230] Chr2:86492108 [GRCh38]
Chr2:86719231 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.2818G>A (p.Asp940Asn) single nucleotide variant Inborn genetic diseases [RCV002661011] Chr2:86482590 [GRCh38]
Chr2:86709713 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.2950A>C (p.Lys984Gln) single nucleotide variant Inborn genetic diseases [RCV002744230] Chr2:86484014 [GRCh38]
Chr2:86711137 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.2221G>C (p.Val741Leu) single nucleotide variant Inborn genetic diseases [RCV003004164] Chr2:86478640 [GRCh38]
Chr2:86705763 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.304C>T (p.Pro102Ser) single nucleotide variant Inborn genetic diseases [RCV002664413] Chr2:86449924 [GRCh38]
Chr2:86677047 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.76A>G (p.Ser26Gly) single nucleotide variant Inborn genetic diseases [RCV002891838] Chr2:86442123 [GRCh38]
Chr2:86669246 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.13C>G (p.Leu5Val) single nucleotide variant Inborn genetic diseases [RCV002744229] Chr2:86442060 [GRCh38]
Chr2:86669183 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1883A>G (p.His628Arg) single nucleotide variant Inborn genetic diseases [RCV002940960] Chr2:86474934 [GRCh38]
Chr2:86702057 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.350A>G (p.Lys117Arg) single nucleotide variant Inborn genetic diseases [RCV002959630] Chr2:86451110 [GRCh38]
Chr2:86678233 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1855A>C (p.Lys619Gln) single nucleotide variant Inborn genetic diseases [RCV002832498] Chr2:86474906 [GRCh38]
Chr2:86702029 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.320G>A (p.Arg107Gln) single nucleotide variant Inborn genetic diseases [RCV002808411] Chr2:86449940 [GRCh38]
Chr2:86677063 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1790A>G (p.Asn597Ser) single nucleotide variant Inborn genetic diseases [RCV002719881] Chr2:86474841 [GRCh38]
Chr2:86701964 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.2228C>T (p.Ala743Val) single nucleotide variant Inborn genetic diseases [RCV002831782] Chr2:86478647 [GRCh38]
Chr2:86705770 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1085A>G (p.Asp362Gly) single nucleotide variant Inborn genetic diseases [RCV002963929] Chr2:86466449 [GRCh38]
Chr2:86693572 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.3602C>A (p.Pro1201Gln) single nucleotide variant Inborn genetic diseases [RCV002714755] Chr2:86490909 [GRCh38]
Chr2:86718032 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.2563C>G (p.Pro855Ala) single nucleotide variant Inborn genetic diseases [RCV003218058] Chr2:86481980 [GRCh38]
Chr2:86709103 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.3335G>A (p.Arg1112Gln) single nucleotide variant Inborn genetic diseases [RCV003344711] Chr2:86489339 [GRCh38]
Chr2:86716462 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1736A>G (p.Asn579Ser) single nucleotide variant Inborn genetic diseases [RCV003348357] Chr2:86474787 [GRCh38]
Chr2:86701910 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.1226C>T (p.Ala409Val) single nucleotide variant Inborn genetic diseases [RCV003370972] Chr2:86466590 [GRCh38]
Chr2:86693713 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.2490G>C (p.Gly830=) single nucleotide variant not provided [RCV003427094] Chr2:86480340 [GRCh38]
Chr2:86707463 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.1250G>T (p.Cys417Phe) single nucleotide variant not provided [RCV003427093] Chr2:86466614 [GRCh38]
Chr2:86693737 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.3391G>A (p.Val1131Ile) single nucleotide variant KDM3A-related condition [RCV003939399] Chr2:86489395 [GRCh38]
Chr2:86716518 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.1239T>G (p.Leu413=) single nucleotide variant KDM3A-related condition [RCV003951681] Chr2:86466603 [GRCh38]
Chr2:86693726 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.3957C>G (p.Gly1319=) single nucleotide variant KDM3A-related condition [RCV003917119] Chr2:86492110 [GRCh38]
Chr2:86719233 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.3783T>G (p.Ala1261=) single nucleotide variant KDM3A-related condition [RCV003921956] Chr2:86491173 [GRCh38]
Chr2:86718296 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.754+9T>C single nucleotide variant KDM3A-related condition [RCV003981372] Chr2:86456886 [GRCh38]
Chr2:86684009 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.3610C>T (p.His1204Tyr) single nucleotide variant KDM3A-related condition [RCV003924461] Chr2:86490917 [GRCh38]
Chr2:86718040 [GRCh37]
Chr2:2p11.2		 uncertain significance
NM_018433.6(KDM3A):c.2340G>A (p.Pro780=) single nucleotide variant KDM3A-related condition [RCV003981994] Chr2:86480190 [GRCh38]
Chr2:86707313 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.275A>G (p.His92Arg) single nucleotide variant KDM3A-related condition [RCV003977195] Chr2:86449895 [GRCh38]
Chr2:86677018 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.3561A>G (p.Glu1187=) single nucleotide variant KDM3A-related condition [RCV003949321] Chr2:86489647 [GRCh38]
Chr2:86716770 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.1559T>A (p.Leu520His) single nucleotide variant KDM3A-related condition [RCV003929403] Chr2:86470243 [GRCh38]
Chr2:86697366 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.456T>C (p.Asp152=) single nucleotide variant KDM3A-related condition [RCV003942300] Chr2:86455087 [GRCh38]
Chr2:86682210 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.921A>G (p.Ala307=) single nucleotide variant KDM3A-related condition [RCV003959182] Chr2:86464130 [GRCh38]
Chr2:86691253 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.789G>A (p.Lys263=) single nucleotide variant KDM3A-related condition [RCV003973904] Chr2:86457017 [GRCh38]
Chr2:86684140 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.1339T>C (p.Ser447Pro) single nucleotide variant KDM3A-related condition [RCV003979858] Chr2:86466703 [GRCh38]
Chr2:86693826 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.3111A>G (p.Glu1037=) single nucleotide variant KDM3A-related condition [RCV003934068] Chr2:86484958 [GRCh38]
Chr2:86712081 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.2475C>T (p.Ala825=) single nucleotide variant KDM3A-related condition [RCV003974407] Chr2:86480325 [GRCh38]
Chr2:86707448 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.557-6_557-4dup duplication KDM3A-related condition [RCV003959064] Chr2:86456416..86456417 [GRCh38]
Chr2:86683539..86683540 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.1698G>A (p.Val566=) single nucleotide variant KDM3A-related condition [RCV003971823] Chr2:86470382 [GRCh38]
Chr2:86697505 [GRCh37]
Chr2:2p11.2		 likely benign
NM_018433.6(KDM3A):c.1560C>T (p.Leu520=) single nucleotide variant KDM3A-related condition [RCV003914783] Chr2:86470244 [GRCh38]
Chr2:86697367 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.557-5_557-4del deletion KDM3A-related condition [RCV003922182] Chr2:86456417..86456418 [GRCh38]
Chr2:86683540..86683541 [GRCh37]
Chr2:2p11.2		 benign
NM_018433.6(KDM3A):c.1917T>G (p.Ala639=) single nucleotide variant KDM3A-related condition [RCV003904147] Chr2:86474968 [GRCh38]
Chr2:86702091 [GRCh37]
Chr2:2p11.2		 benign
miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR155hsa-miR-155-5pMirtarbaseexternal_infoIn situ hybridization//Luciferase reporter assay//Functional MTI21541331
MIR155hsa-miR-155-5pOncomiRDBexternal_infoNANA21541331

Predicted Target Of
Summary Value
Count of predictions:4930
Count of miRNA genes:1336
Interacting mature miRNAs:1759
Transcripts:ENST00000312912, ENST00000409064, ENST00000409556, ENST00000427678, ENST00000441719, ENST00000452034, ENST00000462197, ENST00000463013, ENST00000466058, ENST00000470160, ENST00000483866, ENST00000485171, ENST00000488971, ENST00000491383, ENST00000498528, ENST00000542128
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.

Markers in Region
RH69600  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37286,708,689 - 86,708,897UniSTSGRCh37
Build 36286,562,200 - 86,562,408RGDNCBI36
Celera286,536,738 - 86,536,946RGD
Cytogenetic Map2p11.2UniSTS
HuRef286,606,451 - 86,606,659UniSTS
GeneMap99-GB4 RH Map2304.55UniSTS
NCBI RH Map2460.4UniSTS
RH92486  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37286,679,371 - 86,679,560UniSTSGRCh37
Build 36286,532,882 - 86,533,071RGDNCBI36
Celera286,507,409 - 86,507,598RGD
Cytogenetic Map2p11.2UniSTS
HuRef286,577,126 - 86,577,315UniSTS
GeneMap99-GB4 RH Map2317.03UniSTS
RH77990  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37286,681,603 - 86,681,695UniSTSGRCh37
Build 36286,535,114 - 86,535,206RGDNCBI36
Celera286,509,641 - 86,509,733RGD
Cytogenetic MapXq24UniSTS
Cytogenetic Map2p11.2UniSTS
HuRef286,579,358 - 86,579,450UniSTS
GeneMap99-GB4 RH MapX298.19UniSTS
NCBI RH MapX608.9UniSTS


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 2141 2100 1234 258 1535 104 3827 1297 2187 246 1399 1553 171 1 1047 2291 4 1
Low 298 891 492 366 416 361 530 900 1547 173 61 59 4 157 497 2 1
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_047167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001146688 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_018433 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006712051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017004494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024452994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024452995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024452996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024452997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047445101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047445102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047445103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047445104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047445105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342998 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB018285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC068288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI911797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK074314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK125045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK304276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL832150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC038297 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BG723267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX537674 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX640698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX647271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX647752 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX648841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX649109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR749581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB087171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB453517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KT585051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC064769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000312912   ⟹   ENSP00000323659
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,441,371 - 86,492,716 (+)Ensembl
RefSeq Acc Id: ENST00000409064   ⟹   ENSP00000386516
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,441,461 - 86,492,716 (+)Ensembl
RefSeq Acc Id: ENST00000409556   ⟹   ENSP00000386660
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,440,801 - 86,492,716 (+)Ensembl
RefSeq Acc Id: ENST00000427678   ⟹   ENSP00000397660
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,441,995 - 86,455,143 (+)Ensembl
RefSeq Acc Id: ENST00000441719   ⟹   ENSP00000394691
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,441,379 - 86,492,714 (+)Ensembl
RefSeq Acc Id: ENST00000452034   ⟹   ENSP00000396561
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,440,647 - 86,451,123 (+)Ensembl
RefSeq Acc Id: ENST00000462197
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,484,681 - 86,489,590 (+)Ensembl
RefSeq Acc Id: ENST00000463013
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,449,814 - 86,456,655 (+)Ensembl
RefSeq Acc Id: ENST00000466058
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,443,178 - 86,449,897 (+)Ensembl
RefSeq Acc Id: ENST00000470160
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,487,694 - 86,492,715 (+)Ensembl
RefSeq Acc Id: ENST00000483866
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,489,177 - 86,490,928 (+)Ensembl
RefSeq Acc Id: ENST00000485171
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,466,632 - 86,474,950 (+)Ensembl
RefSeq Acc Id: ENST00000488971
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,456,433 - 86,466,833 (+)Ensembl
RefSeq Acc Id: ENST00000491383
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,486,928 - 86,492,716 (+)Ensembl
RefSeq Acc Id: ENST00000498528
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl286,442,324 - 86,449,887 (+)Ensembl
RefSeq Acc Id: NM_001146688   ⟹   NP_001140160
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,441,461 - 86,492,716 (+)NCBI
GRCh37286,668,271 - 86,719,839 (+)ENTREZGENE
HuRef286,565,835 - 86,617,601 (+)ENTREZGENE
CHM1_1286,598,630 - 86,649,908 (+)NCBI
T2T-CHM13v2.0286,443,474 - 86,494,729 (+)NCBI
Sequence:
RefSeq Acc Id: NM_018433   ⟹   NP_060903
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,441,371 - 86,492,716 (+)NCBI
GRCh37286,668,271 - 86,719,839 (+)ENTREZGENE
Build 36286,521,865 - 86,573,350 (+)NCBI Archive
HuRef286,565,835 - 86,617,601 (+)ENTREZGENE
CHM1_1286,598,317 - 86,649,908 (+)NCBI
T2T-CHM13v2.0286,443,384 - 86,494,729 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006712051   ⟹   XP_006712114
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,474,926 - 86,492,716 (+)NCBI
Sequence:
RefSeq Acc Id: XM_047445101   ⟹   XP_047301057
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,441,371 - 86,492,716 (+)NCBI
RefSeq Acc Id: XM_047445102   ⟹   XP_047301058
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,437,044 - 86,492,716 (+)NCBI
RefSeq Acc Id: XM_047445103   ⟹   XP_047301059
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,441,670 - 86,492,716 (+)NCBI
RefSeq Acc Id: XM_047445104   ⟹   XP_047301060
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,441,478 - 86,492,716 (+)NCBI
RefSeq Acc Id: XM_047445105   ⟹   XP_047301061
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,457,038 - 86,492,716 (+)NCBI
RefSeq Acc Id: XM_054342993   ⟹   XP_054198968
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0286,443,335 - 86,494,729 (+)NCBI
RefSeq Acc Id: XM_054342994   ⟹   XP_054198969
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0286,439,057 - 86,494,729 (+)NCBI
RefSeq Acc Id: XM_054342995   ⟹   XP_054198970
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0286,443,683 - 86,494,729 (+)NCBI
RefSeq Acc Id: XM_054342996   ⟹   XP_054198971
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0286,443,491 - 86,494,729 (+)NCBI
RefSeq Acc Id: XM_054342997   ⟹   XP_054198972
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0286,459,051 - 86,494,729 (+)NCBI
RefSeq Acc Id: XM_054342998   ⟹   XP_054198973
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0286,476,943 - 86,494,729 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001140160 (Get FASTA)   NCBI Sequence Viewer  
  NP_060903 (Get FASTA)   NCBI Sequence Viewer  
  XP_006712114 (Get FASTA)   NCBI Sequence Viewer  
  XP_047301057 (Get FASTA)   NCBI Sequence Viewer  
  XP_047301058 (Get FASTA)   NCBI Sequence Viewer  
  XP_047301059 (Get FASTA)   NCBI Sequence Viewer  
  XP_047301060 (Get FASTA)   NCBI Sequence Viewer  
  XP_047301061 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198968 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198969 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198970 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198971 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198972 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198973 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAY24210 (Get FASTA)   NCBI Sequence Viewer  
  BAA34462 (Get FASTA)   NCBI Sequence Viewer  
  BAG65137 (Get FASTA)   NCBI Sequence Viewer  
  CAE45820 (Get FASTA)   NCBI Sequence Viewer  
  CAH18373 (Get FASTA)   NCBI Sequence Viewer  
  CAH18459 (Get FASTA)   NCBI Sequence Viewer  
  EAW99453 (Get FASTA)   NCBI Sequence Viewer  
  EAW99454 (Get FASTA)   NCBI Sequence Viewer  
  EAW99455 (Get FASTA)   NCBI Sequence Viewer  
  EAW99456 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000323659
  ENSP00000323659.5
  ENSP00000386516
  ENSP00000386516.1
  ENSP00000386660.1
  ENSP00000394691.1
  ENSP00000396561.1
  ENSP00000397660.1
GenBank Protein Q9Y4C1 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_060903   ⟸   NM_018433
- UniProtKB: Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot),   Q9Y4C1 (UniProtKB/Swiss-Prot),   B4E2H5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001140160   ⟸   NM_001146688
- UniProtKB: Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot),   Q9Y4C1 (UniProtKB/Swiss-Prot),   B4E2H5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006712114   ⟸   XM_006712051
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSP00000397660   ⟸   ENST00000427678
RefSeq Acc Id: ENSP00000396561   ⟸   ENST00000452034
RefSeq Acc Id: ENSP00000394691   ⟸   ENST00000441719
RefSeq Acc Id: ENSP00000323659   ⟸   ENST00000312912
RefSeq Acc Id: ENSP00000386660   ⟸   ENST00000409556
RefSeq Acc Id: ENSP00000386516   ⟸   ENST00000409064
RefSeq Acc Id: XP_047301058   ⟸   XM_047445102
- Peptide Label: isoform X1
- UniProtKB: Q9Y4C1 (UniProtKB/Swiss-Prot),   Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_047301057   ⟸   XM_047445101
- Peptide Label: isoform X1
- UniProtKB: Q9Y4C1 (UniProtKB/Swiss-Prot),   Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_047301060   ⟸   XM_047445104
- Peptide Label: isoform X1
- UniProtKB: Q9Y4C1 (UniProtKB/Swiss-Prot),   Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_047301059   ⟸   XM_047445103
- Peptide Label: isoform X1
- UniProtKB: Q9Y4C1 (UniProtKB/Swiss-Prot),   Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_047301061   ⟸   XM_047445105
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054198969   ⟸   XM_054342994
- Peptide Label: isoform X1
- UniProtKB: Q9Y4C1 (UniProtKB/Swiss-Prot),   Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054198968   ⟸   XM_054342993
- Peptide Label: isoform X1
- UniProtKB: Q9Y4C1 (UniProtKB/Swiss-Prot),   Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054198971   ⟸   XM_054342996
- Peptide Label: isoform X1
- UniProtKB: Q9Y4C1 (UniProtKB/Swiss-Prot),   Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054198970   ⟸   XM_054342995
- Peptide Label: isoform X1
- UniProtKB: Q9Y4C1 (UniProtKB/Swiss-Prot),   Q6N050 (UniProtKB/Swiss-Prot),   Q68UT9 (UniProtKB/Swiss-Prot),   Q68D47 (UniProtKB/Swiss-Prot),   Q53S72 (UniProtKB/Swiss-Prot),   D6W5M3 (UniProtKB/Swiss-Prot),   Q8IY08 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054198972   ⟸   XM_054342997
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054198973   ⟸   XM_054342998
- Peptide Label: isoform X3
Protein Domains
JmjC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9Y4C1-F1-model_v2 AlphaFold Q9Y4C1 1-1321 view protein structure

Promoters
RGD ID:6860944
Promoter ID:EPDNEW_H3637
Type:initiation region
Name:KDM3A_1
Description:lysine demethylase 3A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38286,441,371 - 86,441,431EPDNEW
RGD ID:6797698
Promoter ID:HG_KWN:33614
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:ENST00000409064,   ENST00000409556,   OTTHUMT00000329984,   OTTHUMT00000329989,   UC002SRI.2
Position:
Human AssemblyChrPosition (strand)Source
Build 36286,521,456 - 86,522,107 (+)MPROMDB
RGD ID:6797691
Promoter ID:HG_KWN:33615
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000329988,   OTTHUMT00000330010
Position:
Human AssemblyChrPosition (strand)Source
Build 36286,522,126 - 86,523,197 (+)MPROMDB
RGD ID:6797690
Promoter ID:HG_KWN:33616
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   K562,   Lymphoblastoid
Transcripts:OTTHUMT00000329990
Position:
Human AssemblyChrPosition (strand)Source
Build 36286,523,101 - 86,523,601 (+)MPROMDB
RGD ID:6797688
Promoter ID:HG_KWN:33621
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   K562,   Lymphoblastoid
Transcripts:OTTHUMT00000329985,   OTTHUMT00000329986,   OTTHUMT00000329994
Position:
Human AssemblyChrPosition (strand)Source
Build 36286,567,581 - 86,569,507 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:20815 AgrOrtholog
COSMIC KDM3A COSMIC
Ensembl Genes ENSG00000115548 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000312912 ENTREZGENE
  ENST00000312912.10 UniProtKB/Swiss-Prot
  ENST00000409064 ENTREZGENE
  ENST00000409064.5 UniProtKB/Swiss-Prot
  ENST00000409556.5 UniProtKB/Swiss-Prot
  ENST00000427678.1 UniProtKB/TrEMBL
  ENST00000441719.5 UniProtKB/TrEMBL
  ENST00000452034.5 UniProtKB/TrEMBL
Gene3D-CATH Cupin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000115548 GTEx
HGNC ID HGNC:20815 ENTREZGENE
Human Proteome Map KDM3A Human Proteome Map
InterPro JHDM2-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:55818 UniProtKB/Swiss-Prot
NCBI Gene 55818 ENTREZGENE
OMIM 611512 OMIM
PANTHER LYSINE-SPECIFIC DEMETHYLASE 3A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12549 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA164721293 PharmGKB
PROSITE JMJC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B4E2H5 ENTREZGENE, UniProtKB/TrEMBL
  C9J7Q7_HUMAN UniProtKB/TrEMBL
  C9JC73_HUMAN UniProtKB/TrEMBL
  D6W5M3 ENTREZGENE
  F8WE62_HUMAN UniProtKB/TrEMBL
  KDM3A_HUMAN UniProtKB/Swiss-Prot
  Q53S72 ENTREZGENE
  Q68D47 ENTREZGENE
  Q68UT9 ENTREZGENE
  Q6N050 ENTREZGENE
  Q8IY08 ENTREZGENE
  Q9Y4C1 ENTREZGENE
UniProt Secondary D6W5M3 UniProtKB/Swiss-Prot
  Q53S72 UniProtKB/Swiss-Prot
  Q68D47 UniProtKB/Swiss-Prot
  Q68UT9 UniProtKB/Swiss-Prot
  Q6N050 UniProtKB/Swiss-Prot
  Q8IY08 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-16 KDM3A  lysine demethylase 3A  KDM3A  lysine (K)-specific demethylase 3A  Symbol and/or name change 5135510 APPROVED