KDM3A (lysine demethylase 3A) - Rat Genome Database

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Gene: KDM3A (lysine demethylase 3A) Sus scrofa
Analyze
Symbol: KDM3A
Name: lysine demethylase 3A
RGD ID: 14162513
Description: ENCODES a protein that exhibits chromatin binding (inferred); chromatin DNA binding (inferred); histone H3K9 demethylase activity (inferred); INVOLVED IN cellular response to leukemia inhibitory factor (ortholog); male gonad development (ortholog); positive regulation of gene expression (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH CD8 Deficiency, Familial (ortholog); cervical cancer (ortholog); colon cancer (ortholog); FOUND IN chromatin (inferred); cytoplasm (inferred); histone deacetylase complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: lysine-specific demethylase 3A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:25966093   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
1052 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 7 2 1 5 6 1 3 3
Low 3 2 2 2 17 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000009003   ⟹   ENSSSCP00000008777
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl358,299,706 - 58,354,898 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000027376   ⟹   ENSSSCP00000022574
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl358,299,718 - 58,354,941 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000041997   ⟹   ENSSSCP00000036454
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl358,302,949 - 58,354,945 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000087657   ⟹   ENSSSCP00000073338
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl358,299,706 - 58,354,898 (-)Ensembl
RefSeq Acc Id: XM_003124935   ⟹   XP_003124983
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1358,300,109 - 58,355,000 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005662401   ⟹   XP_005662458
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1358,302,313 - 58,354,974 (-)NCBI
Sequence:
RefSeq Acc Id: XM_013995985   ⟹   XP_013851439
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1358,302,313 - 58,354,694 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021087280   ⟹   XP_020942939
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1358,302,313 - 58,354,945 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021087281   ⟹   XP_020942940
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1358,302,313 - 58,354,935 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_003124983   ⟸   XM_003124935
- Peptide Label: isoform X1
- UniProtKB: A0A8D2C8R8 (UniProtKB/TrEMBL),   A0A0B8RSQ5 (UniProtKB/TrEMBL),   A0A286ZY67 (UniProtKB/TrEMBL),   A0A8D1WS48 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005662458   ⟸   XM_005662401
- Peptide Label: isoform X1
- UniProtKB: A0A8D2C8R8 (UniProtKB/TrEMBL),   A0A0B8RSQ5 (UniProtKB/TrEMBL),   A0A286ZY67 (UniProtKB/TrEMBL),   A0A8D1WS48 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020942939   ⟸   XM_021087280
- Peptide Label: isoform X2
- UniProtKB: A0A480QRC5 (UniProtKB/TrEMBL),   A0A8D0LLG6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020942940   ⟸   XM_021087281
- Peptide Label: isoform X2
- UniProtKB: A0A480QRC5 (UniProtKB/TrEMBL),   A0A8D0LLG6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013851439   ⟸   XM_013995985
- Peptide Label: isoform X1
- UniProtKB: A0A8D2C8R8 (UniProtKB/TrEMBL),   A0A0B8RSQ5 (UniProtKB/TrEMBL),   A0A286ZY67 (UniProtKB/TrEMBL),   A0A8D1WS48 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000008777   ⟸   ENSSSCT00000009003
RefSeq Acc Id: ENSSSCP00000036454   ⟸   ENSSSCT00000041997
RefSeq Acc Id: ENSSSCP00000022574   ⟸   ENSSSCT00000027376
RefSeq Acc Id: ENSSSCP00000073338   ⟸   ENSSSCT00000087657
Protein Domains
JmjC


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000008221 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005019509 UniProtKB/TrEMBL
  ENSSSCG00035003301 UniProtKB/TrEMBL
  ENSSSCG00060073478 UniProtKB/TrEMBL
  ENSSSCG00065043581 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000041997 ENTREZGENE
  ENSSSCT00000041997.3 UniProtKB/TrEMBL
  ENSSSCT00005031119.1 UniProtKB/TrEMBL
  ENSSSCT00035004076.1 UniProtKB/TrEMBL
  ENSSSCT00035004082.1 UniProtKB/TrEMBL
  ENSSSCT00060100479.1 UniProtKB/TrEMBL
  ENSSSCT00065059825.1 UniProtKB/TrEMBL
  ENSSSCT00065059847.1 UniProtKB/TrEMBL
  ENSSSCT00065059853.1 UniProtKB/TrEMBL
Gene3D-CATH Cupin UniProtKB/TrEMBL
InterPro JHDM2-like UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
KEGG Report ssc:100517522 UniProtKB/TrEMBL
NCBI Gene KDM3A ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE 3A UniProtKB/TrEMBL
  PTHR12549 UniProtKB/TrEMBL
Pfam JmjC UniProtKB/TrEMBL
PROSITE JMJC UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
UniProt A0A0B8RSQ5 ENTREZGENE
  A0A286ZY67 ENTREZGENE, UniProtKB/TrEMBL
  A0A480QRC5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0LLG6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1WS48 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D2C875_PIG UniProtKB/TrEMBL
  A0A8D2C8R8 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:89411 ENTREZGENE