Kdm5b (lysine demethylase 5B) - Rat Genome Database

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Gene: Kdm5b (lysine demethylase 5B) Rattus norvegicus
Analyze
Symbol: Kdm5b
Name: lysine demethylase 5B
RGD ID: 1565602
Description: Predicted to enable several functions, including histone H3K4me/H3K4me2/H3K4me3 demethylase activity; transcription corepressor activity; and zinc ion binding activity. Involved in cellular response to fibroblast growth factor stimulus; lens fiber cell differentiation; and response to fungicide. Predicted to be located in chromatin; cytosol; and nucleoplasm. Predicted to be active in nucleus. 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); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Jarid1b; jumonji, AT rich interactive domain 1B; jumonji, AT rich interactive domain 1B (Rbp2 like); Jumonji, AT rich interactive domain 1B (RBP2-like); LOC304809; lysine (K)-specific demethylase 5B; lysine-specific demethylase 5B; RGD1565602; similar to PLU1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Gene Ontology Annotations     Click to see Annotation Detail View

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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Coexpression of nuclear receptors and histone methylation modifying genes in the testis: implications for endocrine disruptor modes of action. Anderson AM, etal., PLoS One. 2012;7(4):e34158. doi: 10.1371/journal.pone.0034158. Epub 2012 Apr 4.
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. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
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. 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.
16. 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.
17. Identification and characterization of FGF2-dependent mRNA: microRNA networks during lens fiber cell differentiation. Wolf L, etal., G3 (Bethesda). 2013 Dec 9;3(12):2239-55. doi: 10.1534/g3.113.008698.
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:12657635   PMID:15640446   PMID:17320160   PMID:20228790   PMID:20403335   PMID:20439489   PMID:21960634   PMID:22082260   PMID:24802759   PMID:24952722   PMID:27214403   PMID:28262558  
PMID:34960080  


Genomics

Comparative Map Data
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
(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
(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
(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
227 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:179
Count of miRNA genes:125
Interacting mature miRNAs:151
Transcripts:ENSRNOT00000006290
Prediction methods:Miranda, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133466346187525369Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)13931346554313465Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134372077062022792Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132230187567301875Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131491565559915655Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132320344868203448Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131769443653050594Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131192944946193066Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
4145117Mcs27Mammary carcinoma susceptibility QTL 270.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)134343790447841255Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132369296968692969Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133124133158363171Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132369296968692969Rat
12879472Bp399Blood pressure QTL 399arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134522835847841255Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)131515872260158722Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)13931346554313465Rat

Markers in Region
D13Mco9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21346,025,527 - 46,025,790 (+)MAPPERmRatBN7.2
Rnor_6.01351,407,374 - 51,407,636NCBIRnor6.0
Rnor_5.01356,461,941 - 56,462,203UniSTSRnor5.0
RGSC_v3.41347,525,586 - 47,525,849RGDRGSC3.4
RGSC_v3.41347,525,587 - 47,525,849UniSTSRGSC3.4
RGSC_v3.11347,539,629 - 47,539,892RGD
Celera1346,351,767 - 46,352,029UniSTS
Cytogenetic Map13q13UniSTS
RH132812  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21346,073,515 - 46,073,720 (+)MAPPERmRatBN7.2
Rnor_6.01351,455,032 - 51,455,236NCBIRnor6.0
Rnor_5.01356,509,241 - 56,509,445UniSTSRnor5.0
RGSC_v3.41347,576,594 - 47,576,798UniSTSRGSC3.4
Celera1346,399,903 - 46,400,107UniSTS
RH 3.4 Map13171.0UniSTS
Cytogenetic Map13q13UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000077928   ⟹   ENSRNOP00000073808
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1346,002,542 - 46,073,872 (+)Ensembl
Rnor_6.0 Ensembl1351,384,562 - 51,453,906 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000087025   ⟹   ENSRNOP00000072712
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1346,002,542 - 46,073,868 (+)Ensembl
Rnor_6.0 Ensembl1351,384,389 - 51,455,357 (+)Ensembl
RefSeq Acc Id: NM_001107177   ⟹   NP_001100647
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81348,554,397 - 48,625,713 (+)NCBI
mRatBN7.21346,002,542 - 46,073,868 (+)NCBI
Rnor_6.01351,384,396 - 51,455,384 (+)NCBI
Rnor_5.01356,438,019 - 56,509,593 (+)NCBI
RGSC_v3.41347,502,602 - 47,576,946 (+)RGD
Celera1346,328,788 - 46,400,255 (+)RGD
Sequence:
RefSeq Acc Id: XM_063272298   ⟹   XP_063128368
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81348,554,367 - 48,625,721 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100647 (Get FASTA)   NCBI Sequence Viewer  
  XP_063128368 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM09721 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000072712.2
  ENSRNOP00000073808.2
RefSeq Acc Id: NP_001100647   ⟸   NM_001107177
- UniProtKB: A6ICC6 (UniProtKB/TrEMBL),   A0A0G2K6G9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000072712   ⟸   ENSRNOT00000087025
Ensembl Acc Id: ENSRNOP00000073808   ⟸   ENSRNOT00000077928
RefSeq Acc Id: XP_063128368   ⟸   XM_063272298
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K3N6 (UniProtKB/TrEMBL)
Protein Domains
ARID   JmjC   JmjN   PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K6G9-F1-model_v2 AlphaFold A0A0G2K6G9 1-1545 view protein structure

Transcriptome

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

Promoters
RGD ID:13698847
Promoter ID:EPDNEW_R9359
Type:initiation region
Name:Kdm5b_1
Description:lysine demethylase 5B
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_6.01351,384,449 - 51,384,509EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565602 AgrOrtholog
BioCyc Gene G2FUF-18225 BioCyc
Ensembl Genes ENSRNOG00000060544 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077928.2 UniProtKB/TrEMBL
  ENSRNOT00000087025.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.60 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  Cupin UniProtKB/TrEMBL
InterPro ARID/BRIGHT_DNA-bd UniProtKB/TrEMBL
  ARID_dom_sf UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/TrEMBL
  KDM5B_ARID UniProtKB/TrEMBL
  KDM5B_PHD1 UniProtKB/TrEMBL
  KDM5B_PHD3 UniProtKB/TrEMBL
  PLU-1 UniProtKB/TrEMBL
  TF_JmjC_AAH UniProtKB/TrEMBL
  TF_JmjN UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_C5HC2 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:304809 UniProtKB/TrEMBL
NCBI Gene 304809 ENTREZGENE
PANTHER LYSINE-SPECIFIC DEMETHYLASE UniProtKB/TrEMBL
  LYSINE-SPECIFIC DEMETHYLASE 5B UniProtKB/TrEMBL
Pfam ARID UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  KDM5_C-hel UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  PLU-1 UniProtKB/TrEMBL
  zf-C5HC2 UniProtKB/TrEMBL
PhenoGen Kdm5b PhenoGen
PROSITE ARID UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000060544 RatGTEx
SMART ARID UniProtKB/TrEMBL
  BRIGHT UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
Superfamily-SCOP ARID UniProtKB/TrEMBL
  Clavaminate synthase-like UniProtKB/TrEMBL
  FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt A0A0G2K3N6 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K6G9 ENTREZGENE, UniProtKB/TrEMBL
  A6ICC6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kdm5b  lysine demethylase 5B  Kdm5b  lysine (K)-specific demethylase 5B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-05-06 Kdm5b  lysine (K)-specific demethylase 5B  Jarid1b  jumonji, AT rich interactive domain 1B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-06 Jarid1b  jumonji, AT rich interactive domain 1B  Jarid1b  jumonji, AT rich interactive domain 1B (Rbp2 like)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Jarid1b  jumonji, AT rich interactive domain 1B (Rbp2 like)  RGD1565602_predicted  similar to PLU1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565602_predicted  similar to PLU1 (predicted)  LOC304809  similar to PLU1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC304809  similar to PLU1      Symbol and Name status set to provisional 70820 PROVISIONAL