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Gene: Kdm5b (lysine demethylase 5B) Rattus norvegicus

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Symbol:

Kdm5b

Name:

lysine demethylase 5B

RGD ID:

1565602

Description:

Predicted to enable several functions, including histone H3K4me/H3K4me2/H3K4me3 demethylase activity; histone binding 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 cytosol and nucleoplasm. Predicted to be active in chromatin and 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

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	KDM5B (lysine demethylase 5B)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Kdm5b (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Kdm5b (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	KDM5B (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	KDM5B (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Kdm5b (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	KDM5B (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	KDM5B (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Kdm5b (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Kdm5b (lysine demethylase 5B)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	KDM5B (lysine demethylase 5B)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Kdm5b (lysine demethylase 5B)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	kdm5bb (lysine (K)-specific demethylase 5Bb)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	kdm5ba (lysine (K)-specific demethylase 5Ba)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	lid	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	rbr-2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	JHD2	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	JHD2	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	kdm5b	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	kdm5b	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	13	48,554,367 - 48,625,721 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	13	48,554,420 - 48,626,423 (+)	Ensembl				GRCr8
mRatBN7.2	13	46,001,589 - 46,073,868 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	46,002,542 - 46,073,872 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	13	48,608,619 - 48,679,295 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	49,896,685 - 49,967,365 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	47,162,325 - 47,233,666 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	51,384,371 - 51,455,392 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	51,384,389 - 51,455,357 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	13	56,438,019 - 56,509,593 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	13	47,502,602 - 47,576,946 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	13	46,328,788 - 46,400,255 (+)	NCBI		Celera
Cytogenetic Map	13	q13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISO)

autosomal recessive intellectual developmental disorder 65 (ISO)

bladder exstrophy-epispadias-cloacal exstrophy complex (ISO)

breast cancer (ISO)

Breast Neoplasms (ISO)

Colonic Neoplasms (ISO)

Colorectal Neoplasms (ISO)

Developmental Disease (ISO)

diffuse pediatric-type high-grade glioma, H3-wildtype and IDH-wildtype (ISO)

esophagus squamous cell carcinoma (ISO)

genetic disease (ISO)

high grade glioma (ISO)

intellectual disability (ISO)

myocardial infarction (ISO)

Neurodevelopmental Disorders (ISO)

prostate cancer (ISO)

pulmonary hypertension (ISO)

urinary bladder cancer (ISO)

uveal melanoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ISO)

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)

2,4,4'-trichlorobiphenyl (ISO)

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)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

Bufotalin (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

Biological Process

branching involved in mammary gland duct morphogenesis (ISO)

cellular response to fibroblast growth factor stimulus (IEP)

cellular response to leukemia inhibitory factor (ISO)

chromatin organization (IEA)

chromatin remodeling (IBA)

DNA-templated transcription (IEA)

lens fiber cell differentiation (IEP)

mammary duct terminal end bud growth (ISO)

negative regulation of DNA-templated transcription (IEA,ISO)

positive regulation of gene expression (ISO)

positive regulation of mammary gland epithelial cell proliferation (ISO)

post-embryonic development (ISO)

regulation of DNA-templated transcription (IBA)

regulation of estradiol secretion (ISO)

response to fungicide (IEP)

rhythmic process (IEA)

single fertilization (ISO)

uterus morphogenesis (ISO)

Cellular Component

chromatin (IBA)

nucleoplasm (IEA,ISO)

nucleus (IBA,IEA,ISO)

ribonucleoprotein complex (IEA,ISO)

Molecular Function

dioxygenase activity (IEA)

DNA binding (IEA,ISO)

histone binding (IEA,ISO)

histone H3K4 demethylase activity (IEA,ISO)

histone H3K4me/H3K4me2/H3K4me3 demethylase activity (IBA,IEA,ISO)

metal ion binding (IEA)

nucleic acid binding (IEA,ISO)

oxidoreductase activity (IEA)

protein binding (ISO)

sequence-specific double-stranded DNA binding (IEA,ISO)

transcription corepressor activity (IEA,ISO)

zinc ion binding (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

histone modification pathway (ISO)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	13	48,554,367 - 48,625,721 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	13	48,554,420 - 48,626,423 (+)	Ensembl				GRCr8
mRatBN7.2	13	46,001,589 - 46,073,868 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	46,002,542 - 46,073,872 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	13	48,608,619 - 48,679,295 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	49,896,685 - 49,967,365 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	47,162,325 - 47,233,666 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	51,384,371 - 51,455,392 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	51,384,389 - 51,455,357 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	13	56,438,019 - 56,509,593 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	13	47,502,602 - 47,576,946 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	13	46,328,788 - 46,400,255 (+)	NCBI		Celera
Cytogenetic Map	13	q13	NCBI

KDM5B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	202,724,495 - 202,808,421 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	202,724,495 - 202,808,487 (-)	Ensembl			hg38	GRCh38
GRCh37	1	202,693,623 - 202,777,549 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	200,963,155 - 201,044,172 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	1	199,428,188 - 199,509,206	NCBI
Celera	1	175,824,418 - 175,906,769 (-)	NCBI		Celera
Cytogenetic Map	1	q32.1	NCBI
HuRef	1	173,862,355 - 173,943,136 (-)	NCBI		HuRef
CHM1_1	1	204,118,752 - 204,199,788 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	201,986,695 - 202,071,080 (-)	NCBI		T2T-CHM13v2.0

Kdm5b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	134,487,916 - 134,560,621 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	1	134,487,909 - 134,563,023 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	1	134,560,178 - 134,632,878 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	134,560,171 - 134,635,285 (+)	Ensembl			mm10	GRCm38
MGSCv37	1	136,456,755 - 136,529,455 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	1	136,376,606 - 136,449,288 (+)	NCBI		MGSCv36	mm8
Celera	1	137,167,324 - 137,243,758 (+)	NCBI		Celera
Cytogenetic Map	1	E4	NCBI
cM Map	1	58.24	NCBI

Kdm5b
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955406	38,755,220 - 38,823,088 (-)	Ensembl
ChiLan1.0	NW_004955406	38,755,220 - 38,823,094 (-)	NCBI	ChiLan1.0	ChiLan1.0

KDM5B
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	1	46,574,059 - 46,654,480 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	46,540,718 - 46,623,372 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	178,323,073 - 178,406,608 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	182,620,358 - 182,702,994 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	182,622,425 - 182,702,994 (-)	Ensembl			panPan2	panpan1.1

KDM5B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	7	336,452 - 415,568 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	7	330,705 - 412,386 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	7	389,052 - 475,184 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	7	343,885 - 430,080 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	7	339,836 - 422,462 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	7	332,707 - 418,792 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	7	441,516 - 527,633 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	7	464,790 - 550,918 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Kdm5b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409344	72,547,343 - 72,626,164 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936567	1,781,995 - 1,863,461 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936567	1,782,056 - 1,860,861 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

KDM5B
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	10	24,736,838 - 24,831,447 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	10	24,739,115 - 24,831,537 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	10	29,186,615 - 29,191,730 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

KDM5B
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	25	26,599,740 - 26,685,256 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	25	26,600,736 - 26,683,632 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666055	27,379,047 - 27,463,383 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Kdm5b
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624807	8,011,878 - 8,093,758 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624807	8,011,731 - 8,091,352 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Kdm5b
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	10	1,078,328 - 1,150,141 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Kdm5b
442 total Variants

miRNA Target Status (No longer updated)

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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
10755495	Bp387	Blood pressure QTL 387	3.78		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	37216241	90057603	Rat
9589141	Insul28	Insulin level QTL 28	10.82	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	13	11866254	56866254	Rat
6893344	Cm79	Cardiac mass QTL 79	1.5	0.04	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	13	46272922	51216694	Rat
1354655	Bp241	Blood pressure QTL 241	3.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	38975045	103588154	Rat
70220	Bp55	Blood pressure QTL 55	5.75		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	13	39924693	84924693	Rat
61391	Bp5	Blood pressure QTL 5	5.6		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	24853925	69853925	Rat
4889861	Pur29	Proteinuria QTL 29	13.8	0.005	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	13	39968211	83286298	Rat
2317040	Aia21	Adjuvant induced arthritis QTL 21	2.75		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	13	12384320	57384320	Rat
631645	Bp121	Blood pressure QTL 121	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	17468282	62468282	Rat
2317046	Aia8	Adjuvant induced arthritis QTL 8	3.9700000286102295		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	13	12384320	57384320	Rat
619615	Bp80	Blood pressure QTL 80		0.0354	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	7421791	87286911	Rat
1331784	Bp222	Blood pressure QTL 222	2.944		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	24335432	55601132	Rat
61340	Bp25	Blood pressure QTL 25	4.2	0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	37087983	82087983	Rat
1581573	Uae36	Urinary albumin excretion QTL 36			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	6002008	88706694	Rat
1549897	Stresp12	Stress response QTL 12	3.35		stress-related behavior trait (VT:0010451)	number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)	13	40983585	85983585	Rat
724564	Uae11	Urinary albumin excretion QTL 11	5.7		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	13	47354258	94285672	Rat
2302275	Gluco37	Glucose level QTL 37	3.8		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	13	12448421	48744906	Rat
7207885	Glom27	Glomerulus QTL 27	3.9		kidney glomerulus integrity trait (VT:0010546)	kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)	13	21120177	109350286	Rat
4145117	Mcs27	Mammary carcinoma susceptibility QTL 27		0.0001	mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	13	45990077	50392939	Rat
1558644	Cm45	Cardiac mass QTL 45	3.6	0.002	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	13	26244808	71244808	Rat
70181	BpQTLcluster11	Blood pressure QTL cluster 11	6.922		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	13	33794096	78794096	Rat
61349	Bp31	Blood pressure QTL 31	5.75		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	13	39924693	84924693	Rat
2303563	Bw89	Body weight QTL 89	6		body mass (VT:0001259)	body weight (CMO:0000012)	13	34834947	79834947	Rat
1354621	Rf47	Renal function QTL 47	3.7		kidney renin amount (VT:0010559)	kidney renin level (CMO:0002166)	13	11081740	103588154	Rat
2301962	Cm72	Cardiac mass QTL 72	4.12		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	13	33794096	60914504	Rat
1581554	Pur11	Proteinuria QTL 11			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	6002008	88706694	Rat
12879477	Bp401	Blood pressure QTL 401			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	39814726	84814726	Rat
1331750	Bp220	Blood pressure QTL 220	2.98		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	13	39968211	84968211	Rat
6893338	Cm76	Cardiac mass QTL 76	0	0.99	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	13	26244808	71244808	Rat
12879472	Bp399	Blood pressure QTL 399			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	47780418	50392939	Rat
11530006	Niddm72	Non-insulin dependent diabetes mellitus QTL 72		0.001	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	13	38286298	83286298	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	1	103588154	Rat
9589164	Gluco66	Glucose level QTL 66	6.67	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	13	17711336	62711336	Rat
7411662	Foco29	Food consumption QTL 29	20.8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	13	11866254	56866254	Rat

Markers in Region

D13Mco9

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	13	46,025,527 - 46,025,790 (+)	MAPPER	mRatBN7.2
Rnor_6.0	13	51,407,374 - 51,407,636	NCBI	Rnor6.0
Rnor_5.0	13	56,461,941 - 56,462,203	UniSTS	Rnor5.0
RGSC_v3.4	13	47,525,587 - 47,525,849	UniSTS	RGSC3.4
RGSC_v3.4	13	47,525,586 - 47,525,849	RGD	RGSC3.4
Celera	13	46,351,767 - 46,352,029	UniSTS
RGSC_v3.1	13	47,539,629 - 47,539,892	RGD
Cytogenetic Map	13	q13	UniSTS

RH132812

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	13	46,073,515 - 46,073,720 (+)	MAPPER	mRatBN7.2
Rnor_6.0	13	51,455,032 - 51,455,236	NCBI	Rnor6.0
Rnor_5.0	13	56,509,241 - 56,509,445	UniSTS	Rnor5.0
RGSC_v3.4	13	47,576,594 - 47,576,798	UniSTS	RGSC3.4
Celera	13	46,399,903 - 46,400,107	UniSTS
RH 3.4 Map	13	171.0	UniSTS
Cytogenetic Map	13	q13	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

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	164	91	90	59	92	59	6	356	192	11	143	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107177	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008769555	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063272298	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473958	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234244	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000013	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000077928 ⟹ ENSRNOP00000073808

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	13	46,002,542 - 46,073,872 (+)	Ensembl
Rnor_6.0 Ensembl	13	51,384,562 - 51,453,906 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000087025 ⟹ ENSRNOP00000072712

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	13	48,554,420 - 48,626,423 (+)	Ensembl
mRatBN7.2 Ensembl	13	46,002,542 - 46,073,868 (+)	Ensembl
Rnor_6.0 Ensembl	13	51,384,389 - 51,455,357 (+)	Ensembl

RefSeq Acc Id:

NM_001107177 ⟹ NP_001100647

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	13	48,554,397 - 48,625,713 (+)	NCBI
mRatBN7.2	13	46,002,542 - 46,073,868 (+)	NCBI
Rnor_6.0	13	51,384,396 - 51,455,384 (+)	NCBI
Rnor_5.0	13	56,438,019 - 56,509,593 (+)	NCBI
RGSC_v3.4	13	47,502,602 - 47,576,946 (+)	RGD
Celera	13	46,328,788 - 46,400,255 (+)	RGD

Sequence:

show sequence

CAAGACGTCGTCGGAGGAAGGCTGAAAAAGCCCTAGGTGTTGCCGTTGCTAGTAGAAGTCGGAC
TTGTCGCCCGAGCTGTGCGTGTGCACAGGTTTCGGACGGAGCGGAGCTCGCTGCCGCGGTTGCG
GAGCTTGCCCTGTGCTCGCCCCTGCCCACGTCGCGGTGATGGAGCCGGCCACCGCGCTGCCCCC
AGGCCCGCGCCCGGCGCTGCCCCTTGGGGGCCCCGGCCCGCTGGGAGAGTTCCTGCCTCCCCCC
GAGTGTCCGGTCTTCGAGCCCAGCTGGGAAGAGTTCGCGGACCCCTTCGCTTTCATCCACAAGA
TCCGGCCCATAGCCGAGCAGACTGGGATCTGTAAGGTGCGGCCGCCGCCGGATTGGCAGCCACC
ATTCGCTTGTGATGTTGATAAACTTCATTTTACCCCGCGTATCCAGAGGCTTAATGAGCTGGAG
GCCCAAACACGTGTAAAATTGAACTTCCTGGACCAGATTGCCAAGTATTGGGAGCTACAGGGAA
GTACTCTGAAGATTCCTCATGTGGAGAGAAAGATCTTAGACTTGTTCCAGCTAAATAAGTTAGT
TGCAGAGGAAGGTGGGTTTGCAGTTGTTTGCAAGGACAGAAAATGGACCAAAATTGCCACCAAG
ATGGGTTTTGCTCCTGGTAAAGCAGTGGGCTCACATATCAGGGGACATTATGAGCGAATCCTCA
ATCCGTACAATTTGTTCCTATCTGGGGACAGCCTGAGGTGTCTTCAGAAGCCTAACCTGACCTC
GGACACAAAGGACAAGGAGTACAAACCCCATGATATTCCCCAGAGGCAGTCTGTGCAGCCCTCA
GAAACCTGCCCTCCGGCCCGCCGAGCAAAGCGCATGAGAGCAGAGGCTATGAATATTAAAATTG
AGCCAGAAGAGGCAACAGAAGCCAGGACTCATAACCTGAGGCGCCGAATGGGCTGTGCCACTCC
AAAACGGGAAAACGAGAAAGAAGTGAAAAGTACCATCAAGCAAGAACCCACCGAGAAGAAAGAC
TGTGTGTTAGAAAGTGAGAAGGACAAGCCCAAGAGCCGTGCCAAGAAAACCGCCACTGCTGTGG
ACCTGTATGTGTGCCTCTTATGTGGCAGCGGCAATGACGAGGACCGGCTGCTCCTGTGTGACGG
CTGTGACGACAGTTACCACACCTTCTGCCTGCTTCCCCCTCTCCATGATGTTCCCAAGGGAGAC
TGGAGGTGTCCTAAGTGTTTGGCTCAAGAGTGTAGTAAGCCACAAGAAGCTTTCGGCTTTGAAC
AGGCTGCAAGGGACTATACACTCCGTACGTTTGGGGAAATGGCAGATGCATTCAAATCTGATTA
CTTCAACATGCCGGTCCATATGGTTCCCACAGAGCTGGTGGAGAAGGAGTTTTGGCGGCTGGTA
AGCACTATTGAAGAAGACGTCACCGTGGAGTATGGAGCTGATATTGCTTCAAAAGAGTTTGGCA
GTGGCTTTCCTGTTCGAGATGGCAAAATCAAGATTTCTCCTGAGGAAGAGGAGTATCTTGATAG
TGGCTGGAATTTGAATAACATGCCAGTGATGGAGCAGTCTGTCCTTGCTCACATTACTGCTGAT
ATATGCGGCATGAAACTGCCTTGGTTGTATGTGGGCATGTGCTTTTCTTCCTTCTGTTGGCATA
TCGAAGACCACTGGAGCTATTCAATCAACTACCTGCACTGGGGTGAGCCGAAAACCTGGTATGG
AGTTCCAGGATATGCTGCTGAGCAGCTTGAAAACGTAATGAAGAAGCTGGCTCCAGAGCTCTTT
GTGTCCCAGCCAGACCTCCTCCACCAGCTTGTGACGATCATGAACCCCAATACGCTGATGACTC
ACGAAGTGCCTGTGTATCGAACGAATCAGTGTGCTGGGGAGTTTGTCATTACGTTCCCGAGAGC
CTACCACAGTGGCTTCAATCAAGGCTTTAATTTTGCTGAGGCAGTTAACTTCTGCACTGTTGAT
TGGCTGCCGTTGGGCCGCCAGTGCGTGGAGCATTATCGCCTGCTGCACCGCTACTGCGTCTTTT
CCCATGATGAGATGATATGCAAGATGGCTTCCAAGGCTGATGTGTTAGACGTGGTAGTGGCATC
CACTGTTCAGAAGGACATGGCCATCATGATTGAGGATGAAAAGGCTTTAAGGGAAACTGTCCGT
AAACTGGGAGTGATTGATTCTGAGAGAATGGACTTTGAGCTGTTGCCCGATGATGAGCGGCAGT
GTATAAAGTGCAAAACTACGTGCTTCATGTCTGCCATCTCCTGCTCCTGTAAACCTGGCCTGCT
TGTTTGCCTGCATCATGTCAAAGAGCTGTGCTCCTGTCCCCCTTACAAGTATAACCTGCGGTAT
AGATACACTCTGGATGATCTCTATCCGATGATGAATGCGTTGAAGCTTCGAGCAGAGTCGTACA
ATGAATGGGCCTTAAATGTGAATGAAGCCTTGGAAGCAAAGATTAATAAGAAGAAAAGTCTCGT
CAGCTTTAAAGCTTTGATTGAAGAATCAGAAATGAAGAAATTCCCAGACAATGATCTTTTGCGT
CACCTTCGCCTAGTTACGCAGGATGCAGAAAAGTGTGCCTCTGTTGCCCAGCAGTTGCTTAATG
GCAAAAGGCAAACGAGGTATCGATCTGGTGGAGGGAAGTCTCAGAGTCAGCTGACAGTGAATGA
GCTTCGGCAGTTCGTGACTCAGCTGTGCGCTCTTCCCTGCGTCCTTAGTCAGACACCACTGCTA
AAGGATCTCTTGAATCGTGTGGAAGATTTCCAGCAGCAAAGCCAGAGACTGCTGTCTGAGGAGA
GGCCCCGTGCTTCTGAGCTTCAGCAGTTGCTGGATGTCAGCTTCACTTTTGATGTTGAACTTCC
ACAGCTAGCTGAGATGCGTATCCGCTTAGAACAGGCCCGTTGGCTAGAAGAGGTTCAGCAGGCT
TGCCTGGACTCCAGCTCCCTTTCTTTGGATGATATGAGACGACTCATAGACTTAGGGGTGGGGC
TAGCTCCATATTCTGCCGTGGAGAAAGCTATGGCCCGCCTGCAGGAACTGCTAACAGTGTCAGA
GCACTGGGACGACAAAGCCAAGAGTCTCCTCAGAGCAAGACCTCGGCATTCCTTGAGTAGCCTT
GCTACAGCAGTAAAAGAGATGGAGGAGATCCCCGCCTATCTGCCCAATGGTACAGTCCTGAAGG
ATTCTGTGCAGAAAGCCAGAGACTGGGTTCAGGATGTAGATGCATTGCAGGCAGGAGGACGCGT
GCCAGTGTTAGAAACACTCATTGAACTTGTCGCAAGAGGCCGATCCATCCCGGTACATCTGAAT
TCTTTACCCAGATTGGAAATGCTAGTATCCGAGGTTCATGCTTGGAAAGAAAGCGCTGCTAAAA
CATTCCTGCTTGAGAATTCGCCATACTCTCTGTTAGAGGTTCTTTGTCCTCGGTGTGACATTGG
CCTTTTGGGATTGAAAAGGAAGCAGAGAAAGTTGAAGGATCCCTTGCCAAGTGGGAAGAAGAGA
AGCACCAAGTTAGAGAGTCTGAGTGATCTGGAAAGGGCTCTGACTGAGAGCAAAGAGACGGCGT
CAGCTATGGCAACTCTTGGGGAAGCTCGCCTACGAGAGATGGAAGCTTTGCAGTCTCTCAGATT
TGCCAATGAAGAGAAATTGCTGTCACCTGCCCAAGATGTGGAGACGAAGGTTTGCTTGTGTCAG
AAGACTCCAGCCACTCCCATGATTCAGTGTGAACTCTGCAGGGATGCTTTCCATACTAGTTGTG
TGGCGGTGTCCAGTATTTCACAAAGCTCCCGAATCTGGCTTTGTCCTCACTGTCGAAGGTCAGA
GAAGCCTCCATTAGAGAAAATTCTGCCTCTGCTGGCCTCCCTACAGCGTATAAGAGTTCGTCTT
CCTGAAGGGGATGCACTCCGATACATGATTGAAAGAACCGTGAACTGGCAACATAGAGCCCAGC
AACTGCTTTCTTCAGGGAATCTAAAACTTGTGCAGGACCAAGCGGGTTCTGGACTGTTGTTTAG
CAGATGGCCAGCCTCAGCAGGAACGGCGTCAGCAGCAGACAAGGTGTCTCAACCTCCTGGCACA
ACATCCTTTTCATTGCCGGAAGACTGGGACAACAGAACCTCATATTTACACTCTCCCTTCTCTA
CCGGTCAGAGTTGTATCCCCCTTCATGGTTTGAGTCCAGAGGTGAATGAATTGCTGATGGAAGC
CCAGTTGCTCCAGGTGTCCCTCCCTGAAGTCCAGGAGCTTTATCAGACTTTACTTACGAAGCCA
AGCTCTGCTCAGCAAGCCGACCGAAGCTCACCAGTCAGACCCAGCAGTGAGAAGAACGATTGTC
TTCGAGGGAAACGAGATGCAATCAACAGTCTTGAGAGAAAACTGAAAAGACGCCCAGAAAGAGA
AGGCCTTCCCAGTGAACGGTGGGATCGAGTTAAAAAAATGCGGACCCCTCAAAAGAAGAAAATC
AAACTGAGTCACCCCAAGGACATGAACAATTTCAAATTAGAAAGAGAGCGTAGCTATGACTTAG
TCCGGAATGCTGAAACTCATTCCCTGCCCTCAGACACATCCTACTCCGAGCAGGAGGACTCTGA
GGATGAAGATGCCATCTGTCCAGCTGTGAGCTGCCTGCAGCCAGAAGGAGATGAGGTGGACTGG
GTCCAGTGTGATGGCAGCTGCAATCAGTGGTTTCATCAGGTCTGTGTTGGTGTCTCTCCAGAGA
TGGCAGAGAAAGAAGACTACATCTGTGTGCGCTGTACTGGAAAGGACGCACCAAGCCGAAAGTA
AAAACAAAACACACACTCACTTCATGTAATTCAGGACTCCAATAAAGAAGATTTCCTCAATCTC
AGCAAAGCTACAGGACTGGGATCGAGCCAGCCTGTACACGGTGCTATTTCTATTCCTTATGGGA
TCATTTTTCCAGAACTCTTTGAAAAAAAGAAAAAACAACTAAAAAATTTTTGACACTTTTTTGT
AATTTTTTCCTTAAAAGCTGTTTGTGGTTGTTGAAGTTTAAAATGCTGACTGTTTTTTGCAGGG
GTCTCTACTGATTTCGAAGGTCTTGGAGTTTGCACCTTTTTGTGTACAGCATTAACATTGTACT
TGTGCCTGGGATACACCGGCCTAAGAGTCTAACTCAGTGTCAGGGCCCAGGACGGGCACCAGAA
TTCCAGTAGCCCTCGCTGAGCAGCCGCTCTCCTTTCTCTGTCACCACATTGGGGGACTTTTAAG
TTTTCACTTTGGGGTTTTTGTTCCTTTCTTTCTCTCCTTTTCCTTTCTGGTAGGCTAGGTTTAT
TTATCTGAGCAATAACTTCTATGTTGGTTTCAGTGGCTGGAATTAAAACAAAACAAACTTCTAA
ACAGTGTGTTGGTTTAGCATTTGGTTAATGTACAGAAAGCAAACGTCTAGTTTCTGGTGTCACT
GAACTAGTGATGTAGGAAGAGACTTCGCTGTAAGTAATCGCCACGGCTGTATTTTGGCTTTCTC
CCTACTCAGTTCTTCCCCACCCCCATCTCACACCCCACCTTTTTTTTTTTTTTTGGTAGAATGT
ATCAAATGTTGCAGTTTTTATTGTGGAATAATAAATCCTTGGTCCTCTTATAACACTAGACTAC
AGAGCTTCTTCTGCCCTCCCCCCTGTGGGCCTGCACAACCAGAGGGGTTGTTTGCATTTGCTCC
TTCCCAGGCAGCCTGCAGCAGGAGTGTGTGTGCTGGAGGAGTCTCTGTAGCCTGATTCTTTGTG
GGTCTGGGCCCTCTTGTCCCACTAATAGAGAGTCCCTGTCTTCAAAGACCACAGCCAGTTCTTC
AAGCCGTGTTCTTTTTCCATAATCTCTCAGAATGTTGGAGCTGTCCCTCCATCACTCCAGACTG
TAAGACAGCACTCCCGTGGAATGCTTGACAGGGAAGTTTGGCCGAGAGTTAAGTTGCTGTGGCC
CATCATCTTAGAGGGTTGGTTCTCTTGTATCATTTTTGGAGAACCTTGGGCCTGCCTGGGATTC
CTCTGCCTTCTATGTAATTCCATCAGTCTTTCTGGTTGTGGACGGCCCATACCTGTTTGCCCCT
GTTCTGTAGAGAGGAGGACTTCCTGGTGAACAGAAGGACAAGCTCTCGCTCACTCGTCTTCCTC
ACTGTCTATAGCCATACGCCTGATGGTGGGCAGAGCTAGCAGACCTTTACTAAAACATCAAAAA
GCGGTTTGTAAAGTAGCGAGAATTTAAATGTACTGTCCCCTATGCAATCCAGATAATTAAATCT
GTTT

hide sequence

RefSeq Acc Id:

XM_063272298 ⟹ XP_063128368

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	13	48,554,367 - 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
	ENSRNOP00000072712.2

RefSeq Acc Id:

NP_001100647 ⟸ NM_001107177

- UniProtKB:

A6ICC6 (UniProtKB/TrEMBL), A0A0G2K6G9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MEPATALPPGPRPALPLGGPGPLGEFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKV
RPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLNFLDQIAKYWELQGSTLKIPHVERKIL
DLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILNPYNLFLSGDSLR
CLQKPNLTSDTKDKEYKPHDIPQRQSVQPSETCPPARRAKRMRAEAMNIKIEPEEATEARTHNL
RRRMGCATPKRENEKEVKSTIKQEPTEKKDCVLESEKDKPKSRAKKTATAVDLYVCLLCGSGND
EDRLLLCDGCDDSYHTFCLLPPLHDVPKGDWRCPKCLAQECSKPQEAFGFEQAARDYTLRTFGE
MADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKIS
PEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLH
WGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAG
EFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKA
DVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCIKCKTTCFMSAI
SCSCKPGLLVCLHHVKELCSCPPYKYNLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEA
KINKKKSLVSFKALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLNGKRQTRYRSGGGK
SQSQLTVNELRQFVTQLCALPCVLSQTPLLKDLLNRVEDFQQQSQRLLSEERPRASELQQLLDV
SFTFDVELPQLAEMRIRLEQARWLEEVQQACLDSSSLSLDDMRRLIDLGVGLAPYSAVEKAMAR
LQELLTVSEHWDDKAKSLLRARPRHSLSSLATAVKEMEEIPAYLPNGTVLKDSVQKARDWVQDV
DALQAGGRVPVLETLIELVARGRSIPVHLNSLPRLEMLVSEVHAWKESAAKTFLLENSPYSLLE
VLCPRCDIGLLGLKRKQRKLKDPLPSGKKRSTKLESLSDLERALTESKETASAMATLGEARLRE
MEALQSLRFANEEKLLSPAQDVETKVCLCQKTPATPMIQCELCRDAFHTSCVAVSSISQSSRIW
LCPHCRRSEKPPLEKILPLLASLQRIRVRLPEGDALRYMIERTVNWQHRAQQLLSSGNLKLVQD
QAGSGLLFSRWPASAGTASAADKVSQPPGTTSFSLPEDWDNRTSYLHSPFSTGQSCIPLHGLSP
EVNELLMEAQLLQVSLPEVQELYQTLLTKPSSAQQADRSSPVRPSSEKNDCLRGKRDAINSLER
KLKRRPEREGLPSERWDRVKKMRTPQKKKIKLSHPKDMNNFKLERERSYDLVRNAETHSLPSDT
SYSEQEDSEDEDAICPAVSCLQPEGDEVDWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCT
GKDAPSRK

hide sequence

Ensembl Acc Id:

ENSRNOP00000072712 ⟸ ENSRNOT00000087025

Ensembl Acc Id:

ENSRNOP00000073808 ⟸ ENSRNOT00000077928

RefSeq Acc Id:	XP_063128368 ⟸ XM_063272298
- Peptide Label:	isoform X1
- UniProtKB:	A0A0G2K6G9 (UniProtKB/TrEMBL), 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	13	51,384,449 - 51,384,509	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1565602	AgrOrtholog
BioCyc Gene	G2FUF-18225	BioCyc
Ensembl Genes	ENSRNOG00000060544	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000087025	ENTREZGENE
	ENSRNOT00000087025.3	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
	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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - OMIM

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