Kdm1b (lysine demethylase 1B) - Rat Genome Database

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Gene: Kdm1b (lysine demethylase 1B) Heterocephalus glaber
Analyze
Symbol: Kdm1b
Name: lysine demethylase 1B
RGD ID: 18927084
Description: ENCODES a protein that exhibits FAD binding (ortholog); histone binding (ortholog); histone H3K4 demethylase activity (ortholog); INVOLVED IN chromatin remodeling (ortholog); epigenetic programing of female pronucleus (ortholog); genomic imprinting (ortholog); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH atrial fibrillation (ortholog); genetic disease (ortholog); retinoblastoma (ortholog); FOUND IN chromatin (ortholog); nucleoplasm (ortholog); nucleosome (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: lysine-specific histone demethylase 1B
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247568,449,585 - 8,506,858 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247568,447,780 - 8,506,870 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
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
chromatin  (ISO)
nucleoplasm  (ISO)
nucleosome  (ISO)
nucleus  (ISO)

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


Genomics

Comparative Map Data
Kdm1b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247568,449,585 - 8,506,858 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247568,447,780 - 8,506,870 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
KDM1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38618,155,422 - 18,223,854 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl618,155,329 - 18,223,854 (+)EnsemblGRCh38hg38GRCh38
GRCh37618,155,653 - 18,224,085 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36618,263,598 - 18,332,063 (+)NCBINCBI36Build 36hg18NCBI36
Build 34618,263,661 - 18,332,063NCBI
Celera619,393,595 - 19,462,052 (+)NCBICelera
Cytogenetic Map6p22.3NCBI
HuRef618,099,960 - 18,168,421 (+)NCBIHuRef
CHM1_1618,158,209 - 18,226,680 (+)NCBICHM1_1
T2T-CHM13v2.0618,027,575 - 18,095,996 (+)NCBIT2T-CHM13v2.0
Kdm1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391347,196,849 - 47,238,085 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1347,196,975 - 47,238,755 (+)EnsemblGRCm39 Ensembl
GRCm381347,043,373 - 47,085,279 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1347,043,499 - 47,085,279 (+)EnsemblGRCm38mm10GRCm38
MGSCv371347,138,908 - 47,179,982 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361347,054,542 - 47,095,572 (+)NCBIMGSCv36mm8
Celera1348,128,158 - 48,169,189 (+)NCBICelera
Cytogenetic Map13A5NCBI
cM Map1324.5NCBI
Kdm1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81717,809,232 - 17,850,141 (-)NCBIGRCr8
mRatBN7.21717,602,961 - 17,643,865 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1717,602,961 - 17,643,800 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1717,489,102 - 17,529,009 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01719,092,959 - 19,132,866 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01717,416,219 - 17,456,126 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01717,987,972 - 18,028,808 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1717,987,972 - 18,028,808 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01719,908,417 - 19,948,376 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41723,655,643 - 23,695,480 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11723,657,302 - 23,693,673 (-)NCBI
Celera1717,314,243 - 17,353,918 (-)NCBICelera
Cytogenetic Map17p14NCBI
Kdm1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554838,002,577 - 8,052,486 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554838,000,862 - 8,052,486 (-)NCBIChiLan1.0ChiLan1.0
KDM1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2532,814,158 - 32,883,255 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1628,799,692 - 28,868,520 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0618,002,763 - 18,071,598 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1618,355,907 - 18,425,552 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl618,355,907 - 18,425,552 (+)Ensemblpanpan1.1panPan2
KDM1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13516,954,483 - 17,014,261 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3516,921,095 - 17,012,527 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3516,903,851 - 16,963,895 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03517,060,757 - 17,120,956 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3517,026,903 - 17,120,943 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13516,873,877 - 16,933,805 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03516,931,039 - 16,991,036 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03518,262,308 - 18,322,552 (+)NCBIUU_Cfam_GSD_1.0
Kdm1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049467,766,660 - 7,809,496 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365523,921,490 - 3,962,648 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365523,921,217 - 3,964,281 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl713,845,942 - 13,901,255 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1713,846,283 - 13,902,912 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2714,587,984 - 14,642,979 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM1B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11753,919,859 - 53,987,326 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1753,921,702 - 53,987,124 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604418,379,457 - 18,447,162 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSHGLT00000010404   ⟹   ENSHGLP00000010289
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_0046247568,449,585 - 8,506,858 (-)Ensembl
RefSeq Acc Id: XM_021260838   ⟹   XP_021116497
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_0046247568,447,780 - 8,506,870 (-)NCBI
Protein Sequences
Protein RefSeqs XP_021116497 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000010289
Reference Protein Sequences
RefSeq Acc Id: XP_021116497   ⟸   XM_021260838
- UniProtKB: G5AXT9 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSHGLP00000010289   ⟸   ENSHGLT00000010404


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000007385 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000010404 ENTREZGENE
Gene3D-CATH 3.30.40.100 UniProtKB/TrEMBL
  3.90.660.10 UniProtKB/TrEMBL
  FAD/NAD(P)-binding domain UniProtKB/TrEMBL
  Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain UniProtKB/TrEMBL
InterPro Amino_oxidase UniProtKB/TrEMBL
  FAD/NAD-bd_sf UniProtKB/TrEMBL
  Homeobox-like_sf UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  Znf_CW UniProtKB/TrEMBL
NCBI Gene Kdm1b ENTREZGENE
PANTHER FLAVIN MONOAMINE OXIDASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC HISTONE DEMETHYLASE 1B UniProtKB/TrEMBL
Pfam Amino_oxidase UniProtKB/TrEMBL
  SWIRM UniProtKB/TrEMBL
  zf-CW UniProtKB/TrEMBL
PRINTS ADXRDTASE UniProtKB/TrEMBL
PROSITE SWIRM UniProtKB/TrEMBL
  ZF_CW UniProtKB/TrEMBL
Superfamily-SCOP FAD-linked reductases, C-terminal domain UniProtKB/TrEMBL
  FAD/NAD(P)-binding domain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
UniProt G5AXT9 ENTREZGENE, UniProtKB/TrEMBL