Kdm4b (lysine demethylase 4B) - Rat Genome Database

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Gene: Kdm4b (lysine demethylase 4B) Rattus norvegicus
Analyze
Symbol: Kdm4b
Name: lysine demethylase 4B
RGD ID: 1588576
Description: Predicted to enable histone H3K36 demethylase activity and histone H3K9me2/H3K9me3 demethylase activity. Predicted to be involved in brain development; chromatin remodeling; and regulation of gene expression. Predicted to be located in pericentric heterochromatin. Predicted to be active in chromatin and nucleus. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 65; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Orthologous to human KDM4B (lysine demethylase 4B); PARTICIPATES IN histone modification pathway; INTERACTS WITH bisphenol A; cobalt dichloride; fipronil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC301128; lysine (K)-specific demethylase 4B; lysine-specific demethylase 4B; similar to jumonji domain containing 2B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,245,885 - 1,324,384 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl91,245,899 - 1,324,384 (+)EnsemblGRCr8
mRatBN7.291,158,737 - 1,237,233 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,158,752 - 1,236,543 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx91,604,418 - 1,682,893 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,952,414 - 7,030,893 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,909,462 - 5,987,943 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,656,035 - 10,734,127 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,653,216 - 10,734,073 (-)Ensemblrn6Rnor6.0
Rnor_5.099,647,087 - 9,725,878 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera97,273,613 - 7,351,363 (-)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
calcitriol  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
coumarin  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
DDE  (ISO)
deoxynivalenol  (ISO)
diazinon  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
ethanol  (ISO)
fipronil  (EXP)
folic acid  (ISO)
glucose  (ISO)
hydrogen peroxide  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
methoxyacetic acid  (ISO)
methylmercury chloride  (ISO)
Monobutylphthalate  (ISO)
nickel dichloride  (ISO)
nitrates  (ISO)
nitric oxide  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP)
rac-lactic acid  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
theophylline  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
tungsten  (ISO)
uranium atom  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromatin  (IBA)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA)
pericentric heterochromatin  (IEA,ISO)

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. Jumonji domain-containing protein 2B silencing induces DNA damage response via STAT3 pathway in colorectal cancer. Chen L, etal., Br J Cancer. 2014 Feb 18;110(4):1014-26. doi: 10.1038/bjc.2013.808. Epub 2014 Jan 28.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein. Gray SG, etal., J Biol Chem. 2005 Aug 5;280(31):28507-18. Epub 2005 May 31.
6. Histone demethylase JMJD2B functions as a co-factor of estrogen receptor in breast cancer proliferation and mammary gland development. Kawazu M, etal., PLoS One. 2011 Mar 18;6(3):e17830. doi: 10.1371/journal.pone.0017830.
7. Histone demethylase JMJD2B is required for tumor cell proliferation and survival and is overexpressed in gastric cancer. Li W, etal., Biochem Biophys Res Commun. 2011 Dec 16;416(3-4):372-8. doi: 10.1016/j.bbrc.2011.11.045. Epub 2011 Nov 19.
8. An epigenetic role for PRL-3 as a regulator of H3K9 methylation in colorectal cancer. Liu Y, etal., Gut. 2013 Apr;62(4):571-81. doi: 10.1136/gutjnl-2011-301059. Epub 2012 Feb 16.
9. Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Northcott PA, etal., Nat Genet. 2009 Apr;41(4):465-72. doi: 10.1038/ng.336. Epub 2009 Mar 8.
10. Microarray comparative genomic hybridization detection of copy number changes in desmoplastic melanoma and malignant peripheral nerve sheath tumor. Pryor JG, etal., Am J Dermatopathol. 2011 Dec;33(8):780-5. doi: 10.1097/DAD.0b013e31820dfcbf.
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Comprehensive gene review and curation RGD comprehensive gene curation
15. The histone demethylase JMJD2B plays an essential role in human carcinogenesis through positive regulation of cyclin-dependent kinase 6. Toyokawa G, etal., Cancer Prev Res (Phila). 2011 Dec;4(12):2051-61. doi: 10.1158/1940-6207.CAPR-11-0290. Epub 2011 Sep 19.
16. JMJD2B promotes epithelial-mesenchymal transition by cooperating with beta-catenin and enhances gastric cancer metastasis. Zhao L, etal., Clin Cancer Res. 2013 Dec 1;19(23):6419-29. doi: 10.1158/1078-0432.CCR-13-0254. Epub 2013 Sep 27.
17. Abnormal epigenetic modifications in peripheral blood mononuclear cells from patients with alopecia areata. Zhao M, etal., Br J Dermatol. 2012 Feb;166(2):226-73. doi: 10.1111/j.1365-2133.2011.10646.x. Epub 2012 Jan 9.
Additional References at PubMed
PMID:12477932   PMID:16738407   PMID:19144645   PMID:21914792   PMID:28262558   PMID:32594337  


Genomics

Comparative Map Data
Kdm4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr891,245,885 - 1,324,384 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl91,245,899 - 1,324,384 (+)EnsemblGRCr8
mRatBN7.291,158,737 - 1,237,233 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl91,158,752 - 1,236,543 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx91,604,418 - 1,682,893 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.096,952,414 - 7,030,893 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.095,909,462 - 5,987,943 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0910,656,035 - 10,734,127 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,653,216 - 10,734,073 (-)Ensemblrn6Rnor6.0
Rnor_5.099,647,087 - 9,725,878 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera97,273,613 - 7,351,363 (-)NCBICelera
Cytogenetic Map9q11NCBI
KDM4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38194,969,113 - 5,153,598 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl194,969,107 - 5,153,611 (+)Ensemblhg38GRCh38
GRCh37194,969,124 - 5,153,609 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,920,132 - 5,104,606 (+)NCBIBuild 36Build 36hg18NCBI36
Celera194,906,316 - 5,091,160 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef194,730,929 - 4,915,533 (+)NCBIHuRef
CHM1_1194,969,172 - 5,153,207 (+)NCBICHM1_1
T2T-CHM13v2.0194,954,509 - 5,140,176 (+)NCBIT2T-CHM13v2.0
Kdm4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,632,975 - 56,710,774 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,633,062 - 56,709,870 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381756,325,970 - 56,403,774 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,326,062 - 56,402,870 (+)Ensemblmm10GRCm38
MGSCv371756,465,473 - 56,542,296 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361755,959,801 - 56,036,572 (+)NCBIMGSCv36mm8
Celera1760,697,409 - 60,748,612 (+)NCBICelera
Cytogenetic Map17DNCBI
cM Map1729.27NCBI
Kdm4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,018,770 - 4,114,604 (-)Ensembl
ChiLan1.0NW_0049554954,019,066 - 4,101,577 (-)NCBIChiLan1.0ChiLan1.0
KDM4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2209,362,473 - 9,551,249 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1198,591,717 - 8,777,748 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0193,986,296 - 4,172,359 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1194,977,413 - 5,116,113 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,977,413 - 5,116,113 (+)EnsemblpanPan2panpan1.1
KDM4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12054,713,900 - 54,843,991 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2054,634,121 - 54,820,816 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2054,438,687 - 54,576,517 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02055,368,796 - 55,506,632 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2055,370,326 - 55,506,729 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12054,430,228 - 54,567,939 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02054,910,865 - 55,048,624 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,108,670 - 55,246,485 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Kdm4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,829,153 - 214,917,129 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,908,899 - 3,005,674 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365882,908,970 - 3,005,625 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl273,747,669 - 73,889,866 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1273,746,379 - 73,889,881 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2274,436,488 - 74,458,404 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,649,140 - 4,831,634 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl64,649,221 - 4,831,636 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660813,296,265 - 3,480,930 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248284,796,972 - 4,864,638 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248284,796,306 - 4,893,093 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Kdm4b
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1487,716,424 - 87,794,767 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Kdm4b
114 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:556
Count of miRNA genes:256
Interacting mature miRNAs:306
Transcripts:ENSRNOT00000071199
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631533Iresp3Immunoglobin response QTL316.2blood immunoglobulin E amount (VT:0002492)serum immunoglobulin E level (CMO:0002101)916094576Rat
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9121707400Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)9131250552Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat

Markers in Region
D9Got200  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr891,272,993 - 1,273,201 (+)Marker Load Pipeline
mRatBN7.291,185,844 - 1,186,050 (-)MAPPERmRatBN7.2
Rnor_6.0910,706,528 - 10,706,733NCBIRnor6.0
Rnor_5.099,698,263 - 9,698,468UniSTSRnor5.0
Celera97,324,093 - 7,324,298UniSTS
Cytogenetic Map9q11UniSTS
RH143752  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,159,057 - 1,159,161 (-)MAPPERmRatBN7.2
Rnor_6.0910,733,691 - 10,733,794NCBIRnor6.0
Rnor_5.099,725,463 - 9,725,566UniSTSRnor5.0
Celera97,350,981 - 7,351,084UniSTS
Cytogenetic Map9q11UniSTS
AW525135  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,206,978 - 1,207,146 (-)MAPPERmRatBN7.2
Rnor_6.0910,685,433 - 10,685,600NCBIRnor6.0
Rnor_5.099,677,168 - 9,677,335UniSTSRnor5.0
Celera97,303,010 - 7,303,177UniSTS
RH 3.4 Map8180.2UniSTS
Cytogenetic Map9q11UniSTS
RH135189  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,236,318 - 1,236,505 (-)MAPPERmRatBN7.2
Rnor_6.0910,656,075 - 10,656,261NCBIRnor6.0
Rnor_5.099,647,810 - 9,647,996UniSTSRnor5.0
Celera97,273,651 - 7,273,837UniSTS
Cytogenetic Map9q11UniSTS
RH141483  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,235,486 - 1,235,686 (-)MAPPERmRatBN7.2
Rnor_6.0910,656,894 - 10,657,093NCBIRnor6.0
Rnor_5.099,648,629 - 9,648,828UniSTSRnor5.0
Celera97,274,470 - 7,274,669UniSTS
Cytogenetic Map9q11UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001044236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001395633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244319 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596322 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083144 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063266827 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063266828 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063266829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010054572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC098860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC161813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000071199   ⟹   ENSRNOP00000066803
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl91,245,899 - 1,324,384 (+)Ensembl
mRatBN7.2 Ensembl91,158,779 - 1,236,543 (+)Ensembl
Rnor_6.0 Ensembl910,656,037 - 10,734,073 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000089374   ⟹   ENSRNOP00000070258
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl91,245,920 - 1,324,378 (+)Ensembl
mRatBN7.2 Ensembl91,158,779 - 1,236,543 (+)Ensembl
Rnor_6.0 Ensembl910,653,216 - 10,710,648 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000091450   ⟹   ENSRNOP00000073251
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl910,657,185 - 10,659,357 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000095576   ⟹   ENSRNOP00000093085
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,158,779 - 1,236,543 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000108055   ⟹   ENSRNOP00000083814
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,158,752 - 1,236,317 (+)Ensembl
RefSeq Acc Id: NM_001044236   ⟹   NP_001037701
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,903 - 1,324,384 (+)NCBI
mRatBN7.291,158,752 - 1,237,233 (+)NCBI
Rnor_6.0910,656,037 - 10,734,073 (-)NCBI
Rnor_5.099,647,087 - 9,725,878 (-)NCBI
Celera97,273,613 - 7,351,363 (-)RGD
Sequence:
RefSeq Acc Id: NM_001395633   ⟹   NP_001382562
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,903 - 1,324,384 (+)NCBI
mRatBN7.291,158,752 - 1,237,233 (+)NCBI
RefSeq Acc Id: XM_006244319   ⟹   XP_006244381
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,888 - 1,323,691 (+)NCBI
mRatBN7.291,158,737 - 1,237,228 (+)NCBI
Rnor_6.0910,656,035 - 10,734,124 (-)NCBI
Rnor_5.099,647,087 - 9,725,878 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244320   ⟹   XP_006244382
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,888 - 1,323,691 (+)NCBI
mRatBN7.291,158,737 - 1,237,228 (+)NCBI
Rnor_6.0910,656,035 - 10,734,124 (-)NCBI
Rnor_5.099,647,087 - 9,725,878 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083143   ⟹   XP_038939071
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,888 - 1,323,691 (+)NCBI
mRatBN7.291,158,737 - 1,236,537 (+)NCBI
RefSeq Acc Id: XM_039083144   ⟹   XP_038939072
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,285,872 - 1,323,691 (+)NCBI
mRatBN7.291,197,987 - 1,237,228 (+)NCBI
RefSeq Acc Id: XM_063266827   ⟹   XP_063122897
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,888 - 1,323,691 (+)NCBI
RefSeq Acc Id: XM_063266828   ⟹   XP_063122898
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,887 - 1,305,763 (+)NCBI
RefSeq Acc Id: XM_063266829   ⟹   XP_063122899
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,887 - 1,294,295 (+)NCBI
RefSeq Acc Id: XR_010054572
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr891,245,885 - 1,289,303 (+)NCBI
RefSeq Acc Id: NP_001037701   ⟸   NM_001044236
- Peptide Label: isoform 1
- UniProtKB: M0RB75 (UniProtKB/TrEMBL),   A6KQY4 (UniProtKB/TrEMBL),   A0A0G2JXG2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244382   ⟸   XM_006244320
- Peptide Label: isoform X4
- UniProtKB: A0A8I5ZWQ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244381   ⟸   XM_006244319
- Peptide Label: isoform X2
- UniProtKB: A0A0G2JXG2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000070258   ⟸   ENSRNOT00000089374
Ensembl Acc Id: ENSRNOP00000073251   ⟸   ENSRNOT00000091450
Ensembl Acc Id: ENSRNOP00000066803   ⟸   ENSRNOT00000071199
RefSeq Acc Id: XP_038939071   ⟸   XM_039083143
- Peptide Label: isoform X1
- UniProtKB: M0RB75 (UniProtKB/TrEMBL),   A6KQY4 (UniProtKB/TrEMBL),   A0A0G2JXG2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038939072   ⟸   XM_039083144
- Peptide Label: isoform X5
Ensembl Acc Id: ENSRNOP00000093085   ⟸   ENSRNOT00000095576
Ensembl Acc Id: ENSRNOP00000083814   ⟸   ENSRNOT00000108055
RefSeq Acc Id: NP_001382562   ⟸   NM_001395633
- Peptide Label: isoform 2
- UniProtKB: A0A0G2JXG2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063122898   ⟸   XM_063266828
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063122899   ⟸   XM_063266829
- Peptide Label: isoform X7
RefSeq Acc Id: XP_063122897   ⟸   XM_063266827
- Peptide Label: isoform X3
- UniProtKB: A0A0G2JXG2 (UniProtKB/TrEMBL)
Protein Domains
JmjC   JmjN   PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RB75-F1-model_v2 AlphaFold M0RB75 1-1099 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696459
Promoter ID:EPDNEW_R6984
Type:initiation region
Name:Kdm4b_1
Description:lysine demethylase 4B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0910,734,095 - 10,734,155EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588576 AgrOrtholog
BioCyc Gene G2FUF-28533 BioCyc
Ensembl Genes ENSRNOG00000049221 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071199 ENTREZGENE
  ENSRNOT00000071199.4 UniProtKB/TrEMBL
  ENSRNOT00000089374 ENTREZGENE
  ENSRNOT00000089374.3 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.140 UniProtKB/TrEMBL
  3.10.330.70 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  Cupin UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8367824 IMAGE-MGC_LOAD
InterPro EPHD UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
  KDM4_Tudor_2 UniProtKB/TrEMBL
  TF_JmjN UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
  Tudor_KDM4B_rpt1 UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:301128 UniProtKB/TrEMBL
MGC_CLONE MGC:187252 IMAGE-MGC_LOAD
NCBI Gene 301128 ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 4B UniProtKB/TrEMBL
Pfam JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD_2 UniProtKB/TrEMBL
  Tudor_2 UniProtKB/TrEMBL
  zf-HC5HC2H_2 UniProtKB/TrEMBL
PhenoGen Kdm4b PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000049221 RatGTEx
SMART JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  TUDOR UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/TrEMBL
  SSF57903 UniProtKB/TrEMBL
  Tudor/PWWP/MBT UniProtKB/TrEMBL
UniProt A0A0G2JXG2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZWQ3 ENTREZGENE
  A6KQY4 ENTREZGENE, UniProtKB/TrEMBL
  M0RB75 ENTREZGENE, UniProtKB/TrEMBL
  Q4KM27_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kdm4b  lysine demethylase 4B  Kdm4b  lysine (K)-specific demethylase 4B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-09-17 Kdm4b  lysine (K)-specific demethylase 4B  LOC301128  similar to jumonji domain containing 2B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC301128  similar to jumonji domain containing 2B      Symbol and Name status set to provisional 70820 PROVISIONAL