KDM3B (lysine demethylase 3B) - Rat Genome Database

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Gene: KDM3B (lysine demethylase 3B) Pan paniscus
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Symbol: KDM3B
Name: lysine demethylase 3B
RGD ID: 11949452
Description: ENCODES a protein that exhibits antioxidant activity (ortholog); INVOLVED IN chromatin remodeling (inferred); demethylation (inferred); regulation of transcription by RNA polymerase II (inferred); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH acute lymphoblastic leukemia (ortholog); anxiety disorder (ortholog); autism spectrum disorder (ortholog); FOUND IN chromatin (inferred); histone deacetylase complex (inferred); nucleoplasm (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: lysine-specific demethylase 3B
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24133,627,936 - 133,712,447 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15131,767,490 - 131,852,004 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05133,732,400 - 133,816,988 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15139,863,961 - 139,947,895 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5139,863,922 - 139,947,895 (+)Ensemblpanpan1.1panPan2
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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


Genomics

Comparative Map Data
KDM3B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24133,627,936 - 133,712,447 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15131,767,490 - 131,852,004 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05133,732,400 - 133,816,988 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15139,863,961 - 139,947,895 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5139,863,922 - 139,947,895 (+)Ensemblpanpan1.1panPan2
KDM3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385138,352,685 - 138,437,027 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5138,352,685 - 138,437,028 (+)EnsemblGRCh38hg38GRCh38
GRCh375137,688,374 - 137,772,716 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365137,716,184 - 137,800,615 (+)NCBINCBI36Build 36hg18NCBI36
Build 345137,716,183 - 137,800,616NCBI
Celera5133,809,116 - 133,893,549 (+)NCBICelera
Cytogenetic Map5q31.2NCBI
HuRef5132,879,205 - 132,963,497 (+)NCBIHuRef
CHM1_15137,121,010 - 137,205,439 (+)NCBICHM1_1
T2T-CHM13v2.05138,878,903 - 138,963,243 (+)NCBIT2T-CHM13v2.0
Kdm3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391834,910,061 - 34,972,423 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1834,910,100 - 34,971,713 (+)EnsemblGRCm39 Ensembl
GRCm381834,777,008 - 34,839,370 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1834,777,047 - 34,838,660 (+)EnsemblGRCm38mm10GRCm38
MGSCv371834,936,662 - 34,999,024 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361834,902,982 - 34,965,344 (+)NCBIMGSCv36mm8
Celera1835,231,299 - 35,293,372 (+)NCBICelera
Cytogenetic Map18B1NCBI
cM Map1818.73NCBI
Kdm3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81826,655,004 - 26,710,814 (+)NCBIGRCr8
mRatBN7.21826,380,859 - 26,436,701 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1826,380,964 - 26,436,628 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01827,593,823 - 27,631,129 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1827,576,129 - 27,631,088 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01827,306,788 - 27,343,047 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1826,119,377 - 26,174,614 (+)NCBICelera
Cytogenetic Map18p12NCBI
Kdm3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554182,026,254 - 2,098,223 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554182,026,254 - 2,098,223 (-)NCBIChiLan1.0ChiLan1.0
KDM3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11125,954,352 - 26,024,919 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1125,943,864 - 26,023,866 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1124,717,936 - 24,794,255 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01126,804,754 - 26,881,233 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1126,804,369 - 26,881,233 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11125,517,476 - 25,588,205 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01125,334,621 - 25,411,002 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01125,998,804 - 26,075,210 (+)NCBIUU_Cfam_GSD_1.0
Kdm3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213154,011,186 - 154,094,889 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365317,516,125 - 7,600,347 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365317,517,810 - 7,600,319 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2140,346,223 - 140,418,527 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12140,346,145 - 140,418,556 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22146,045,537 - 146,115,232 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM3B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12341,027,490 - 41,111,560 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2341,062,020 - 41,112,469 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603436,775,963 - 36,860,235 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm3b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474331,148,098 - 31,225,992 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474331,148,051 - 31,224,896 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


RefSeq Acc Id: ENSPPAT00000054133   ⟹   ENSPPAP00000031269
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl5139,863,922 - 139,946,574 (+)Ensembl
RefSeq Acc Id: ENSPPAT00000054140   ⟹   ENSPPAP00000031277
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl5139,863,958 - 139,947,895 (+)Ensembl
RefSeq Acc Id: XM_008954713   ⟹   XP_008952961
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v24133,627,936 - 133,712,447 (+)NCBI
NHGRI_mPanPan15131,767,490 - 131,852,004 (+)NCBI
Mhudiblu_PPA_v05133,732,400 - 133,816,988 (+)NCBI
PanPan1.15139,863,961 - 139,947,895 (+)NCBI
Sequence:
RefSeq Acc Id: XM_034960580   ⟹   XP_034816471
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v24133,644,381 - 133,712,447 (+)NCBI
NHGRI_mPanPan15131,783,935 - 131,852,004 (+)NCBI
Mhudiblu_PPA_v05133,749,754 - 133,816,988 (+)NCBI
RefSeq Acc Id: XM_034960581   ⟹   XP_034816472
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v24133,627,976 - 133,712,447 (+)NCBI
NHGRI_mPanPan15131,767,562 - 131,852,004 (+)NCBI
Mhudiblu_PPA_v05133,732,567 - 133,816,988 (+)NCBI
Protein Sequences
Protein RefSeqs XP_008952961 (Get FASTA)   NCBI Sequence Viewer  
  XP_034816471 (Get FASTA)   NCBI Sequence Viewer  
  XP_034816472 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSPPAP00000031269.1
  ENSPPAP00000031277.1
RefSeq Acc Id: XP_008952961   ⟸   XM_008954713
- Peptide Label: isoform X1
- UniProtKB: A0A2R9BXN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_034816472   ⟸   XM_034960581
- Peptide Label: isoform X3
- UniProtKB: A0A2R9BXN8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_034816471   ⟸   XM_034960580
- Peptide Label: isoform X2
- UniProtKB: A0A2R9BXN8 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSPPAP00000031269   ⟸   ENSPPAT00000054133
RefSeq Acc Id: ENSPPAP00000031277   ⟸   ENSPPAT00000054140
Protein Domains
JmjC


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000038558 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000054133.1 UniProtKB/TrEMBL
  ENSPPAT00000054140.1 UniProtKB/TrEMBL
Gene3D-CATH Cupin UniProtKB/TrEMBL
InterPro JHDM2-like UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
NCBI Gene KDM3B ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE 3B 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 A0A2R9BPD8_PANPA UniProtKB/TrEMBL
  A0A2R9BXN8 ENTREZGENE, UniProtKB/TrEMBL