Kdm5b (lysine demethylase 5B) - Rat Genome Database

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Gene: Kdm5b (lysine demethylase 5B) Mus musculus
Analyze
Symbol: Kdm5b
Name: lysine demethylase 5B (Ensembl:lysine (K)-specific demethylase 5B)
RGD ID: 1557118
MGI Page MGI
Description: Enables histone H3K4 demethylase activity. Involved in negative regulation of DNA-templated transcription. Acts upstream of or within several processes, including cellular response to leukemia inhibitory factor; mammary gland duct morphogenesis; and positive regulation of mammary gland epithelial cell proliferation. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of chromatin. Predicted to be active in nucleus. Is expressed in several structures, including alimentary system; central nervous system; early conceptus; genitourinary system; and integumental system. Human ortholog(s) of this gene implicated in autosomal recessive intellectual developmental disorder 65; breast cancer; and high grade glioma. Orthologous to human KDM5B (lysine demethylase 5B).
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: 2010009J12Rik; 2210016I17Rik; [histone H3]-trimethyl-L-lysine(4) demethylase 5B; AW556288; D1Ertd202; D1Ertd202e; histone demethylase JARID1B; Jari; Jarid1b; jumonji, AT rich interactive domain 1B (Rbp2 like); jumonji/ARID domain-containing protein 1B; KIAA4034; lysine (K)-specific demethylase 5B; lysine-specific demethylase 5B; mKIAA4034; Pl; PLU; PLU-1; Plu1; PUT1; putative DNA/chromatin binding motif 1; Rb-B; Rb-Bp2; RBBP2H1A
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391134,487,916 - 134,560,621 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1134,487,909 - 134,563,023 (+)EnsemblGRCm39 Ensembl
GRCm381134,560,178 - 134,632,878 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1134,560,171 - 134,635,285 (+)EnsemblGRCm38mm10GRCm38
MGSCv371136,456,755 - 136,529,455 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361136,376,606 - 136,449,288 (+)NCBIMGSCv36mm8
Celera1137,167,324 - 137,243,758 (+)NCBICelera
Cytogenetic Map1E4NCBI
cM Map158.24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (EXP)
1,2-dimethylhydrazine  (EXP)
17alpha-ethynylestradiol  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
6-propyl-2-thiouracil  (ISO)
acetylsalicylic acid  (ISO)
all-trans-retinoic acid  (EXP,ISO)
amitrole  (ISO)
antimycin A  (ISO)
atrazine  (EXP)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (EXP)
berberine  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
cadmium atom  (ISO)
carbamazepine  (ISO)
carbon nanotube  (EXP)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (EXP,ISO)
cyclosporin A  (ISO)
deguelin  (ISO)
dioxygen  (ISO)
diuron  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
ethanol  (ISO)
fenpyroximate  (ISO)
folic acid  (EXP)
FR900359  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
hydrogen chloride  (ISO)
methimazole  (ISO)
nefazodone  (ISO)
niclosamide  (ISO)
oxaliplatin  (ISO)
parathion  (EXP)
PCB138  (EXP)
phenobarbital  (EXP)
picoxystrobin  (ISO)
pyrimidifen  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
sodium arsenate  (EXP)
sulfadimethoxine  (ISO)
tamibarotene  (ISO)
tamoxifen  (EXP)
tebufenpyrad  (ISO)
topotecan  (ISO)
triptonide  (EXP)
troglitazone  (ISO)
tungsten  (EXP)
uranium atom  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IBA)
cytosol  (ISO)
nucleoplasm  (ISO,TAS)
nucleus  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. PLU-1/JARID1B/KDM5B is required for embryonic survival and contributes to cell proliferation in the mammary gland and in ER+ breast cancer cells. Catchpole S, etal., Int J Oncol. 2011 May;38(5):1267-77. doi: 10.3892/ijo.2011.956. Epub 2011 Feb 28.
3. Overexpressed KDM5B is associated with the progression of glioma and promotes glioma cell growth via downregulating p21. Dai B, etal., Biochem Biophys Res Commun. 2014 Nov 7;454(1):221-7. doi: 10.1016/j.bbrc.2014.10.078. Epub 2014 Oct 22.
4. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, etal., Science 2004 Dec 24;306(5705):2255-7.
5. Overexpression of the JmjC histone demethylase KDM5B in human carcinogenesis: involvement in the proliferation of cancer cells through the E2F/RB pathway. Hayami S, etal., Mol Cancer. 2010 Mar 13;9:59. doi: 10.1186/1476-4598-9-59.
6. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
7. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Ko MS, etal., Development 2000 Apr;127(8):1737-49.
8. Histone demethylase JARID1B regulates proliferation and migration of pulmonary arterial smooth muscle cells in mice with chronic hypoxia-induced pulmonary hypertension via nuclear factor-kappa B (NFkB). Li Y, etal., Cardiovasc Pathol. 2018 Nov-Dec;37:8-14. doi: 10.1016/j.carpath.2018.07.004. Epub 2018 Aug 3.
9. A novel gene (PLU-1) containing highly conserved putative DNA/chromatin binding motifs is specifically up-regulated in breast cancer. Lu PJ, etal., J Biol Chem. 1999 May 28;274(22):15633-45.
10. Depletion of JARID1B induces cellular senescence in human colorectal cancer. Ohta K, etal., Int J Oncol. 2013 Apr;42(4):1212-8. doi: 10.3892/ijo.2013.1799. Epub 2013 Jan 25.
11. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
12. JARID1B protein expression and prognostic implications in uveal melanoma. Radberger P, etal., Invest Ophthalmol Vis Sci. 2012 Jul 3;53(8):4442-9. doi: 10.1167/iovs.11-9296.
13. Mouse MP Annotation Import Pipeline RGD automated import pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Overexpression of Jumonji AT-rich interactive domain 1B and PHD finger protein 2 is involved in the progression of esophageal squamous cell carcinoma. Sun LL, etal., Acta Histochem. 2013 Jan;115(1):56-62. doi: 10.1016/j.acthis.2012.04.001. Epub 2012 Apr 23.
17. Loss of KDM5B ameliorates pathological cardiac fibrosis and dysfunction by epigenetically enhancing ATF3 expression. Wang B, etal., Exp Mol Med. 2022 Dec;54(12):2175-2187. doi: 10.1038/s12276-022-00904-y. Epub 2022 Dec 8.
18. JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer. Xiang Y, etal., Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19226-31. Epub 2007 Nov 28.
Additional References at PubMed
PMID:7671812   PMID:10349636   PMID:10594239   PMID:10922068   PMID:11042159   PMID:11076861   PMID:12477932   PMID:12520002   PMID:12904583   PMID:14516692   PMID:14610273   PMID:14613977  
PMID:15201984   PMID:15741177   PMID:16141072   PMID:16141073   PMID:16325481   PMID:17302988   PMID:17310255   PMID:17320160   PMID:17967808   PMID:18022353   PMID:18287559   PMID:18591252  
PMID:18799693   PMID:20412781   PMID:20439489   PMID:21267068   PMID:21448134   PMID:21574959   PMID:21677750   PMID:21731673   PMID:21873635   PMID:21897363   PMID:21960634   PMID:21980403  
PMID:22020125   PMID:22223663   PMID:22988430   PMID:23637629   PMID:23777767   PMID:24100015   PMID:24183668   PMID:24619213   PMID:24778210   PMID:24802759   PMID:24859337   PMID:25655602  
PMID:26023081   PMID:26083387   PMID:26453309   PMID:26494787   PMID:26739753   PMID:27626377   PMID:28402433   PMID:30186101   PMID:30304676   PMID:30409806   PMID:30523048   PMID:30940185  
PMID:31077711   PMID:31467927   PMID:32325033   PMID:32868382   PMID:33245716   PMID:33627187   PMID:34321999   PMID:34368113   PMID:34671158   PMID:34709266   PMID:34713299   PMID:35468265  
PMID:36130801   PMID:36914768   PMID:37231097   PMID:38060382   PMID:38163400  


Genomics

Comparative Map Data
Kdm5b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391134,487,916 - 134,560,621 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1134,487,909 - 134,563,023 (+)EnsemblGRCm39 Ensembl
GRCm381134,560,178 - 134,632,878 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1134,560,171 - 134,635,285 (+)EnsemblGRCm38mm10GRCm38
MGSCv371136,456,755 - 136,529,455 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361136,376,606 - 136,449,288 (+)NCBIMGSCv36mm8
Celera1137,167,324 - 137,243,758 (+)NCBICelera
Cytogenetic Map1E4NCBI
cM Map158.24NCBI
KDM5B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381202,724,495 - 202,808,421 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1202,724,495 - 202,808,487 (-)EnsemblGRCh38hg38GRCh38
GRCh371202,693,623 - 202,777,549 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361200,963,155 - 201,044,172 (-)NCBINCBI36Build 36hg18NCBI36
Build 341199,428,188 - 199,509,206NCBI
Celera1175,824,418 - 175,906,769 (-)NCBICelera
Cytogenetic Map1q32.1NCBI
HuRef1173,862,355 - 173,943,136 (-)NCBIHuRef
CHM1_11204,118,752 - 204,199,788 (-)NCBICHM1_1
T2T-CHM13v2.01201,986,695 - 202,071,080 (-)NCBIT2T-CHM13v2.0
Kdm5b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81348,554,367 - 48,625,721 (+)NCBIGRCr8
mRatBN7.21346,001,589 - 46,073,868 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1346,002,542 - 46,073,872 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1348,608,619 - 48,679,295 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01349,896,685 - 49,967,365 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01347,162,325 - 47,233,666 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01351,384,371 - 51,455,392 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1351,384,389 - 51,455,357 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01356,438,019 - 56,509,593 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41347,502,602 - 47,576,946 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1346,328,788 - 46,400,255 (+)NCBICelera
Cytogenetic Map13q13NCBI
Kdm5b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540638,755,220 - 38,823,088 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540638,755,220 - 38,823,094 (-)NCBIChiLan1.0ChiLan1.0
KDM5B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2146,574,059 - 46,654,480 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1146,540,718 - 46,623,372 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01178,323,073 - 178,406,608 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11182,620,358 - 182,702,994 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1182,622,425 - 182,702,994 (-)Ensemblpanpan1.1panPan2
KDM5B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.17336,452 - 415,568 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl7330,705 - 412,386 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha7389,052 - 475,184 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.07343,885 - 430,080 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl7339,836 - 422,462 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.17332,707 - 418,792 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.07441,516 - 527,633 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.07464,790 - 550,918 (+)NCBIUU_Cfam_GSD_1.0
Kdm5b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934472,547,343 - 72,626,164 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365671,781,995 - 1,863,461 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365671,782,056 - 1,860,861 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM5B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1024,736,838 - 24,831,447 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11024,739,115 - 24,831,537 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21029,186,615 - 29,191,730 (-)NCBISscrofa10.2Sscrofa10.2susScr3
KDM5B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12526,599,740 - 26,685,256 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2526,600,736 - 26,683,632 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605527,379,047 - 27,463,383 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Kdm5b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248078,011,878 - 8,093,758 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248078,011,731 - 8,091,352 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Kdm5b
2476 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1103
Count of miRNA genes:606
Interacting mature miRNAs:747
Transcripts:ENSMUST00000047714, ENSMUST00000112197, ENSMUST00000112198, ENSMUST00000133725
Prediction methods: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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
13824984Twq5_mtestis weight QTL 5 (mouse)13069992184732197Mouse
11039528Ccc3_mcolitis susceptibility in the Collaborative Cross 3 (mouse)13680142195051546Mouse
1357753Kidq2_mkidney weight QTL 2 (mouse)Not determined134760138150193871Mouse
1357488Splq3_mspleen weight QTL 3 (mouse)Not determined134760138150193871Mouse
1558860W10q7_mweight 10 weeks QTL 7 (mouse)Not determined134760138150193871Mouse
1301722Cia9_mcollagen induced arthritis QTL 9 (mouse)Not determined145783900189303617Mouse
4142291Aec2_mautoimmune exocrinopathy 2 (mouse)Not determined52457737182250592Mouse
10412185Hcs9_mhepatocarcinogenesis susceptibility 9 (mouse)Not determined163854690189303617Mouse
1300841Ssial1_msusceptibility to sialadenitis 1 (mouse)Not determined163920002153557562Mouse
1300989Lrdg1_mlight induced retinal degeneration 1 (mouse)Not determined173755175147125370Mouse
4141914Gcsfis_mG-CSF induced splenomegaly (mouse)Not determined74516235148715579Mouse
27095928Pglq6_mpelvic girdle length QTL 6, 10 week (mouse)175976637148775742Mouse
26884448Sklq1_mskull length QTL 1, 5 week (mouse)175976637181327565Mouse
1301350Nidd4k_mNidd4 on KK-A (mouse)Not determined782291982147125370Mouse
1357439Popoa_mpremature ovulation and primary oocyte arrest (mouse)Not determined182643189135615379Mouse
27095913Scvln2_msacral vertebrae length 2, 5 week (mouse)194127725148775742Mouse
27095901Scvln8_msacral vertebrae length 2, 10 week (mouse)194127725172027567Mouse
27226779Tibl1_mtibia length 1, 5 week (mouse)195527725162027569Mouse
1301193Lxw3_mlupus BXSB x NZW 3 (mouse)Not determined1102968534136968667Mouse
10412162Nobq3_mNew Zealand obese QTL 3 (mouse)Not determined1103933405191225397Mouse
12790994Aaaq1_maortic arch angle QTL 1 (mouse)1109495943143495943Mouse
1301979Melm1_mmelanoma modifier 1 (mouse)Not determined1109638262143638479Mouse
1357600Obq17_mobesity QTL 17 (mouse)Not determined1110553179144553298Mouse
10401248Bglu12_mblood glucose level 12 (mouse)Not determined1110553179144553298Mouse
1301149Lrnx12_mlearning-contextual 12 (mouse)Not determined1112008822168186402Mouse
1302098Eila1_methanol induced locomotor activity 1 (mouse)Not determined1112008822175468938Mouse
1301249Sbw1_msplenomegaly-NZB x NZW 1 (mouse)Not determined1112131005146131085Mouse
10045640Jckm4_mjuvenile cystic kidney modifier 4 (mouse)Not determined1116290836150290937Mouse
27095915Scvln13_msacral vertebrae length 2, 16 week (mouse)1117527730179827565Mouse
1302161Exq2_mexploratory and excitability QTL 2 (mouse)Not determined1118099720152099816Mouse
27226714Metcl1_mmetatarsal-calcaneal length 1, 5 week (mouse)1121727729139727738Mouse
27226740Metcl13_mmetatarsal-calcaneal length 13, 16 week (mouse)1121727729153775746Mouse
27226743Metcl7_mmetatarsal-calcaneal length 7, 10 week (mouse)1121727729153875746Mouse
27226767Tibl10_mtibia length 10, 10 week (mouse)1121727729164827569Mouse
27226799Feml5_mfemur length 5, 5 week (mouse)1122027729164827569Mouse
12880408V125Dq3_mvitamin D active form serum level QTL 3 (mouse)1122927738156927738Mouse
27095935Ulnl5_mulna length 5, 10 week (mouse)1128727737181327565Mouse
1301608Emo3_memotionality 3 (mouse)Not determined1129130858163130993Mouse
1302128Ity3_mimmunity to S. typhimurium 3 (mouse)Not determined11131156308165139464Mouse
13524520Bodwtq1_mbody wweight QTL 1 (mouse)1131191160135621161Mouse
13513913Heal51_mwound healing/ regeneration 51 (mouse)1131780648135499606Mouse
14746980Manh50_mmandible shape 50 (mouse)1134131564168131564Mouse
13504831Bacszq1_mbaculum size QTL 1 (mouse)1134331161148128608Mouse

Markers in Region
AW556288  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381134,632,503 - 134,632,641UniSTSGRCm38
MGSCv371136,529,080 - 136,529,218UniSTSGRCm37
Celera1137,243,383 - 137,243,521UniSTS
Cytogenetic Map1E4UniSTS
cM Map172.0UniSTS
Whitehead/MRC_RH11914.38UniSTS
RH126466  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381134,632,605 - 134,632,843UniSTSGRCm38
MGSCv371136,529,182 - 136,529,420UniSTSGRCm37
Celera1137,243,485 - 137,243,723UniSTS
Cytogenetic Map1E4UniSTS
cM Map172.0UniSTS
Whitehead/MRC_RH11906.72UniSTS


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_152895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011248090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017312616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017312617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC122771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK008164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK008738 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK041304 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK076888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK081306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK162760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK163481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK220451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY082429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY082430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC019446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC019629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC034189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC038625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC048180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC057318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466520 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CX206086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CX567343 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  W35764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000047714   ⟹   ENSMUSP00000038138
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1134,487,909 - 134,563,023 (+)Ensembl
GRCm38.p6 Ensembl1134,560,171 - 134,635,285 (+)Ensembl
RefSeq Acc Id: ENSMUST00000112197
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1134,487,945 - 134,534,529 (+)Ensembl
GRCm38.p6 Ensembl1134,560,207 - 134,606,791 (+)Ensembl
RefSeq Acc Id: ENSMUST00000112198   ⟹   ENSMUSP00000107817
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1134,487,930 - 134,559,260 (+)Ensembl
GRCm38.p6 Ensembl1134,560,192 - 134,631,522 (+)Ensembl
RefSeq Acc Id: ENSMUST00000133725
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1134,549,618 - 134,552,839 (+)Ensembl
GRCm38.p6 Ensembl1134,621,880 - 134,625,101 (+)Ensembl
RefSeq Acc Id: ENSMUST00000186128
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1134,515,715 - 134,518,424 (+)Ensembl
GRCm38.p6 Ensembl1134,587,977 - 134,590,686 (+)Ensembl
RefSeq Acc Id: ENSMUST00000191572
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1134,550,538 - 134,554,939 (+)Ensembl
GRCm38.p6 Ensembl1134,622,800 - 134,627,201 (+)Ensembl
RefSeq Acc Id: NM_152895   ⟹   NP_690855
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391134,487,916 - 134,560,616 (+)NCBI
GRCm381134,560,178 - 134,632,878 (+)NCBI
MGSCv371136,456,755 - 136,529,455 (+)RGD
Celera1137,167,324 - 137,243,758 (+)RGD
cM Map1 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_011248090   ⟹   XP_011246392
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391134,490,052 - 134,560,621 (+)NCBI
GRCm381134,562,314 - 134,632,193 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017312616   ⟹   XP_017168105
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391134,510,859 - 134,560,621 (+)NCBI
GRCm381134,583,115 - 134,632,379 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017312617   ⟹   XP_017168106
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391134,508,805 - 134,559,688 (+)NCBI
GRCm381134,581,339 - 134,632,379 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_690855   ⟸   NM_152895
- UniProtKB: Q8BLU1 (UniProtKB/Swiss-Prot),   Q5DTR9 (UniProtKB/Swiss-Prot),   Q8JZL8 (UniProtKB/Swiss-Prot),   Q80Y84 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011246392   ⟸   XM_011248090
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017168106   ⟸   XM_017312617
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017168105   ⟸   XM_017312616
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000107817   ⟸   ENSMUST00000112198
RefSeq Acc Id: ENSMUSP00000038138   ⟸   ENSMUST00000047714
Protein Domains
ARID   JmjC   JmjN   PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q80Y84-F1-model_v2 AlphaFold Q80Y84 1-1544 view protein structure

Promoters
RGD ID:6875032
Promoter ID:EPDNEW_M963
Type:initiation region
Name:Kdm5b_1
Description:Mus musculus lysine -specific demethylase 5B , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381134,560,226 - 134,560,286EPDNEW
RGD ID:6817994
Promoter ID:MM_KWN:2162
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000112198,   OTTMUST00000041390,   UC007CSF.1,   UC007CSH.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361136,456,574 - 136,457,074 (+)MPROMDB
RGD ID:6817980
Promoter ID:MM_KWN:2163
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day2,   MEF_B6
Transcripts:OTTMUST00000041393
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361136,517,464 - 136,517,964 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1922855 AgrOrtholog
Ensembl Genes ENSMUSG00000042207 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000047714 ENTREZGENE
  ENSMUST00000047714.14 UniProtKB/Swiss-Prot
  ENSMUST00000112198.3 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.150.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cupin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ARID_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARID_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/Swiss-Prot
  KDM5B_ARID UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KDM5B_PHD1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KDM5B_PHD3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lys_sp_deMease-like_dom UniProtKB/Swiss-Prot
  Spp1/CFP1 UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C5HC2 UniProtKB/Swiss-Prot
  Znf_FYVE_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:75605 UniProtKB/Swiss-Prot
MGD MGI:1922855 ENTREZGENE
NCBI Gene 75605 ENTREZGENE
PANTHER AT26187P-RELATED UniProtKB/TrEMBL
  CXXC-TYPE ZINC FINGER PROTEIN 1 UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 5B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ARID UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/Swiss-Prot
  PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLU-1 UniProtKB/Swiss-Prot
  zf-C5HC2 UniProtKB/Swiss-Prot
PhenoGen Kdm5b PhenoGen
PROSITE ARID UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JMJC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JMJN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ARID UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BRIGHT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  JmjN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Clavaminate synthase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF46774 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57903 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt KDM5B_MOUSE UniProtKB/Swiss-Prot
  Q3TQL9_MOUSE UniProtKB/TrEMBL
  Q5DTR9 ENTREZGENE
  Q80Y84 ENTREZGENE
  Q8BLU1 ENTREZGENE
  Q8C1P6_MOUSE UniProtKB/TrEMBL
  Q8JZL8 ENTREZGENE
  Q8VCQ4_MOUSE UniProtKB/TrEMBL
UniProt Secondary Q5DTR9 UniProtKB/Swiss-Prot
  Q8BLU1 UniProtKB/Swiss-Prot
  Q8JZL8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-06-20 Kdm5b  lysine demethylase 5B  Kdm5b  lysine (K)-specific demethylase 5B  Symbol and/or name change 5135510 APPROVED