Nkx3-1 (NK3 homeobox 1) - Rat Genome Database

Name: Nkx3-1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Nkx3-1 (NK3 homeobox 1) Rattus norvegicus

Analyze

Symbol:

Nkx3-1

Name:

NK3 homeobox 1

RGD ID:

1305369

Description:

Predicted to enable several functions, including MADS box domain binding activity; cysteine-type endopeptidase activator activity involved in apoptotic process; and histone deacetylase binding activity. Predicted to be involved in several processes, including morphogenesis of a branching epithelium; positive regulation of cell communication; and regulation of gene expression. Predicted to be located in cytosol; nucleoplasm; and site of DNA damage. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in hepatocellular carcinoma. Orthologous to human NKX3-1 (NK3 homeobox 1); PARTICIPATES IN forkhead class A signaling pathway; prostate cancer pathway; INTERACTS WITH acrylamide; bisphenol A; C60 fullerene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

homeobox protein Nkx-3.1; LOC305999; MGC124859; NK-3 transcription factor, locus 1; NK-3 transcription factor, locus 1 (Drosophila); Nkx3.1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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):	NKX3-1 (NK3 homeobox 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Nkx3-1 (NK3 homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Nkx3-1 (NK3 homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NKX3-1 (NK3 homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NKX3-1 (NK3 homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nkx3-1 (NK3 homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NKX3-1 (NK3 homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NKX3-1 (NK3 homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nkx3-1 (NK3 homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	NKX2-8 (NK2 homeobox 8)	HGNC	PhylomeDB
Alliance orthologs ³
Homo sapiens (human):	NKX3-1 (NK3 homeobox 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Nkx3-1 (NK3 homeobox 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	nkx3-1 (NK3 homeobox 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	nkx3-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoInspector\|PANTHER\|PhylomeDB)

Allele / Splice:

Nkx3-1^em1Pjhak

Genetic Models:

SD-Nkx3-1^em1Pjhak-/- SD-Nkx3-1^em1Pjhak+/-

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	15	44,473,851 - 44,476,443 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	44,473,851 - 44,476,441 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	15	48,591,788 - 48,594,380 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	15	49,703,277 - 49,705,869 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	15	46,562,612 - 46,565,204 (+)	NCBI	Rnor_WKY
Rnor_6.0	15	51,065,316 - 51,067,908 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	51,065,316 - 51,068,421 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	54,796,102 - 54,798,694 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	49,743,313 - 49,745,905 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	15	49,752,541 - 49,761,067 (+)	NCBI
Celera	15	44,157,589 - 44,160,181 (+)	NCBI		Celera
Cytogenetic Map	15	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

amenorrhea (ISO)

Conotruncal Cardiac Defects (ISO)

genetic disease (ISO)

hepatocellular carcinoma (ISO)

prostate cancer (ISS)

Prostatic Neoplasms (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-Arctigenin (ISO)

17beta-estradiol (ISO)

17beta-hydroxy-17-methylestra-4,9,11-trien-3-one (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4-Dihydroxybenzophenone (ISO)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

9-cis-retinoic acid (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bicalutamide (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

C60 fullerene (EXP)

cadmium dichloride (ISO)

celastrol (ISO)

chlordecone (ISO)

cisplatin (ISO)

clofibrate (ISO)

copper atom (ISO)

copper(0) (ISO)

crocidolite asbestos (ISO)

curcumin (ISO)

daidzein (ISO)

dapsone (ISO)

difenoconazole (ISO)

dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate (ISO)

doxorubicin (ISO)

enzalutamide (ISO)

equol (ISO)

fentin acetate (ISO)

flufenamic acid (ISO)

flutamide (ISO)

fulvestrant (ISO)

gedunin (ISO)

genistein (ISO)

indometacin (ISO)

isoflavones (ISO)

Licochalcone B (ISO)

lipopolysaccharide (ISO)

methylisothiazolinone (ISO)

methylmercury chloride (ISO)

methylseleninic acid (ISO)

mibolerone (ISO)

niclosamide (ISO)

paracetamol (ISO)

pioglitazone (ISO)

piroxicam (ISO)

quercetin (ISO)

resveratrol (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

serpentine asbestos (ISO)

silicon dioxide (ISO)

sirtinol (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

tert-butyl hydroperoxide (ISO)

testosterone (ISO)

tetramethrin (ISO)

triclosan (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

XL147 (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of cysteine-type endopeptidase activity involved in apoptotic process (ISO,ISS)

androgen receptor signaling pathway (ISO,ISS)

apoptotic process (IEA)

branching involved in prostate gland morphogenesis (ISO,ISS)

branching morphogenesis of an epithelial tube (ISO,ISS)

cell differentiation (IBA)

cellular response to hypoxia (ISO)

cellular response to interleukin-1 (ISO)

cellular response to steroid hormone stimulus (ISO,ISS)

cellular response to tumor necrosis factor (ISO)

cellular response to xenobiotic stimulus (ISO)

DNA damage response (ISO,ISS)

dorsal aorta development (ISO)

epithelial cell proliferation (ISO)

epithelial cell proliferation involved in prostate gland development (ISO)

epithelial cell proliferation involved in salivary gland morphogenesis (ISO,ISS)

heart development (ISO)

male gonad development (ISO)

metanephros development (ISO)

negative regulation of cell population proliferation (ISO,ISS)

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

negative regulation of epithelial cell proliferation (ISO,ISS)

negative regulation of epithelial cell proliferation involved in prostate gland development (ISO,ISS)

negative regulation of gene expression (ISO)

negative regulation of insulin-like growth factor receptor signaling pathway (ISO,ISS)

pharyngeal system development (ISO)

positive regulation of androgen secretion (ISO,ISS)

positive regulation of apoptotic signaling pathway (ISO)

positive regulation of cell division (ISO,ISS)

positive regulation of cell population proliferation (ISO,ISS)

positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (ISO,ISS)

positive regulation of DNA-binding transcription factor activity (ISO)

positive regulation of DNA-templated transcription (ISO,ISS)

positive regulation of gene expression (ISO,ISS)

positive regulation of intrinsic apoptotic signaling pathway (ISO,ISS)

positive regulation of mitotic cell cycle (ISO,ISS)

positive regulation of phosphatidylinositol 3-kinase signaling (ISO,ISS)

positive regulation of protein phosphorylation (ISO,ISS)

positive regulation of transcription by RNA polymerase II (ISO,ISS)

prostate gland development (ISO)

protein kinase B signaling (ISO,ISS)

regulation of protein localization (ISO)

regulation of transcription by RNA polymerase II (IBA)

response to testosterone (ISO,ISS)

salivary gland development (ISO,ISS)

somitogenesis (ISO)

urogenital system development (ISO)

Cellular Component

cytosol (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA,ISO,ISS)

site of DNA damage (ISO)

Molecular Function

cysteine-type endopeptidase activator activity involved in apoptotic process (ISO)

DNA binding (ISO)

DNA-binding transcription factor activity (ISO,ISS)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA,ISO,ISS)

DNA-binding transcription factor binding (ISO)

histone deacetylase binding (ISO)

MADS box domain binding (ISO)

nuclear estrogen receptor binding (ISO,ISS)

nuclear receptor activity (ISO,ISS)

protein binding (ISO)

protein self-association (ISO,ISS)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,ISO,ISS)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

transcription cis-regulatory region binding (ISO,ISS)

transcription regulator inhibitor activity (ISO,ISS)

Molecular Pathway Annotations Click to see Annotation Detail View

forkhead class A signaling pathway (ISO)

prostate cancer pathway (IEA)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

abnormal copulatory plug deposition (IMP)

decreased litter size (IMP)

decreased prostate gland weight (IMP)

prostate gland epithelial hyperplasia (IMP)

reduced male fertility (IMP)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	NK3 homeobox 1 (NKX3.1) up-regulates forkhead box O1 expression in hepatocellular carcinoma and thereby suppresses tumor proliferation and invasion.	Jiang J, etal., J Biol Chem. 2017 Nov 24;292(47):19146-19159. doi: 10.1074/jbc.M117.793760. Epub 2017 Sep 27.
4.	TALEN-mediated generation of Nkx3.1 knockout rat model.	Lee JM, etal., Prostate. 2021 Feb;81(3):182-193. doi: 10.1002/pros.24095. Epub 2020 Dec 28.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
7.	PID Annotation Import Pipeline	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
8.	GOA pipeline	RGD automated data pipeline
9.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:9142502	PMID:9621431	PMID:10215624	PMID:10906459	PMID:10993896	PMID:11002344	PMID:11839815	PMID:12477932	PMID:15987773	PMID:16782701	PMID:17486276	PMID:18296735
PMID:18360715	PMID:18757402	PMID:18794125	PMID:18974119	PMID:19258508	PMID:19263243	PMID:19266349	PMID:19597465	PMID:19780584	PMID:19797053	PMID:19886863	PMID:20395202
PMID:20599703	PMID:20716579	PMID:20855495	PMID:21056661

Genomics

Comparative Map Data

Nkx3-1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	15	44,473,851 - 44,476,443 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	44,473,851 - 44,476,441 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	15	48,591,788 - 48,594,380 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	15	49,703,277 - 49,705,869 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	15	46,562,612 - 46,565,204 (+)	NCBI	Rnor_WKY
Rnor_6.0	15	51,065,316 - 51,067,908 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	51,065,316 - 51,068,421 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	54,796,102 - 54,798,694 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	49,743,313 - 49,745,905 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	15	49,752,541 - 49,761,067 (+)	NCBI
Celera	15	44,157,589 - 44,160,181 (+)	NCBI		Celera
Cytogenetic Map	15	p11	NCBI

NKX3-1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	8	23,678,693 - 23,682,938 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	8	23,678,697 - 23,682,938 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	8	23,536,206 - 23,540,451 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	8	23,592,173 - 23,596,395 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	8	23,592,172 - 23,596,395	NCBI
Celera	8	22,499,634 - 22,503,878 (-)	NCBI		Celera
Cytogenetic Map	8	p21.2	NCBI
HuRef	8	22,081,521 - 22,085,754 (-)	NCBI		HuRef
CHM1_1	8	23,738,407 - 23,742,639 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	8	23,953,650 - 23,957,884 (-)	NCBI		T2T-CHM13v2.0

Nkx3-1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	69,428,141 - 69,432,107 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	14	69,428,087 - 69,432,111 (+)	Ensembl		GRCm39 Ensembl
GRCm38	14	69,190,692 - 69,194,658 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	69,190,638 - 69,194,662 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	14	69,808,749 - 69,812,715 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	14	68,144,022 - 68,147,988 (+)	NCBI		MGSCv36	mm8
Celera	14	66,971,062 - 66,975,028 (+)	NCBI		Celera
Cytogenetic Map	14	D2	NCBI
cM Map	14	36.02	NCBI

Nkx3-1
(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_004955403	46,806,178 - 46,836,310 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955403	46,807,846 - 46,809,924 (-)	NCBI	ChiLan1.0	ChiLan1.0

NKX3-1
(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	8	17,908,457 - 17,912,733 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	8	22,926,145 - 22,930,396 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	8	19,860,748 - 19,864,968 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	8	19,863,275 - 19,864,942 (-)	Ensembl	panpan1.1		panPan2

NKX3-1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	25	33,815,343 - 33,817,465 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	25	33,815,095 - 33,817,474 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	25	34,403,094 - 34,405,850 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	25	34,021,324 - 34,024,080 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	25	34,021,202 - 34,024,073 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	25	33,968,569 - 33,971,325 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	25	33,822,490 - 33,825,246 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	25	33,977,508 - 33,980,265 (+)	NCBI		UU_Cfam_GSD_1.0

Nkx3-1
(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_024404943	11,461,374 - 11,484,403 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936555	7,088,577 - 7,091,334 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936555	7,087,677 - 7,091,334 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NKX3-1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	7,783,323 - 7,787,033 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	7,783,296 - 7,787,036 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	8,625,545 - 8,630,189 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NKX3-1
(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	8	21,792,069 - 21,797,258 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	8	21,791,422 - 21,796,319 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666052	20,424,660 - 20,428,943 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Nkx3-1
(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_004624758	18,875,475 - 18,876,971 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624758	18,874,399 - 18,876,982 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Nkx3-1
8 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	153
Count of miRNA genes:	115
Interacting mature miRNAs:	135
Transcripts:	ENSRNOT00000020753
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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
2298549	Neuinf12	Neuroinflammation QTL 12	3.5		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	15	1	55302115	Rat
10401805	Kidm51	Kidney mass QTL 51			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	15	306329	45306329	Rat
738017	Hcas7	Hepatocarcinoma susceptibility QTL 7	2.91		liver integrity trait (VT:0010547)	liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)	15	2266368	46921453	Rat
1582251	Gluco24	Glucose level QTL 24	3.2	0.0008	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	15	5530756	50530756	Rat
631273	Lecl2	Lens clarity QTL 2		0.001	lens clarity trait (VT:0001304)	age of onset/diagnosis of cataract (CMO:0001584)	15	10596089	55596089	Rat
2300167	Bmd63	Bone mineral density QTL 63	5.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	15	11111142	56111142	Rat
2300173	Bmd62	Bone mineral density QTL 62	12.8	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	15	11111142	56111142	Rat
2293688	Bss29	Bone structure and strength QTL 29	5.31	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	15	11111142	56111142	Rat
2317750	Glom26	Glomerulus QTL 26	4.3		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	15	12496141	65205939	Rat
61424	Scl1	Serum cholesterol level QTL 1	7.7	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	15	16725528	80672115	Rat
1331729	Rf42	Renal function QTL 42	3.071		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	15	17362897	73690657	Rat
2324620	Coatc3	Coat color QTL 3			coat/hair pigmentation trait (VT:0010463)	pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)	15	19856566	46187442	Rat
10054130	Srcrt8	Stress Responsive Cort QTL 8	2.18	0.0085	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	15	22117933	67117933	Rat
1578646	Bmd18	Bone mineral density QTL 18	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	15	22806240	98288169	Rat
1578647	Bmd17	Bone mineral density QTL 17	4		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	15	22806240	98288169	Rat
1578660	Bss19	Bone structure and strength QTL 19	4.3		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	15	22806240	98288169	Rat
1582214	Stl21	Serum triglyceride level QTL 21	3.1	0.022	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	15	28030665	82262678	Rat
1582227	Gluco30	Glucose level QTL 30	3.6	0.0003	blood glucose amount (VT:0000188)	absolute change in blood glucose level area under curve (CMO:0002034)	15	28030665	82262678	Rat
1582228	Epfw3	Epididymal fat weight QTL 3	4.1	0.0002	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	15	28030665	82262678	Rat
1582242	Gluco28	Glucose level QTL 28	3.3	0.0008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	15	28030665	82262678	Rat
1582244	Bw79	Body weight QTL 79	4	0.0002	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	15	28030665	82262678	Rat
2293691	Bmd37	Bone mineral density QTL 37	6.6	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	15	33611058	71477291	Rat
2293686	Bmd36	Bone mineral density QTL 36	7.4	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	15	33611058	71477291	Rat
1598828	Glom14	Glomerulus QTL 14	2.5		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	15	34054139	79054139	Rat
7411725	Strs7	Sensitivity to stroke QTL 7	3.8		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	15	40289901	49308583	Rat
2306968	Anxrr23	Anxiety related response QTL 23	4.83		reflex trait (VT:0001961)	amplitude of the acoustic startle response (CMO:0001520)	15	40631268	46187442	Rat
1300144	Rf23	Renal function QTL 23	3.61		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	15	40631268	98288169	Rat

Markers in Region

RH139441

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	44,475,589 - 44,475,730 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	51,067,055 - 51,067,195	NCBI	Rnor6.0
Rnor_5.0	15	54,797,841 - 54,797,981	UniSTS	Rnor5.0
RGSC_v3.4	15	49,745,052 - 49,745,192	UniSTS	RGSC3.4
Celera	15	44,159,328 - 44,159,468	UniSTS
Cytogenetic Map	15	p11	UniSTS

Genetic Models

This gene Nkx3-1 is modified in the following models/strains

SD-Nkx3-1^em1Pjhak-/-

SD-Nkx3-1^em1Pjhak+/-

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		1								2
Low	2	7						21	33	28
Below cutoff	14	9	4	10	4	1	1	33	2	10	1	1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001034144	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC141168	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC100628	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473951	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000272	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000020753 ⟹ ENSRNOP00000020753

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	44,473,851 - 44,476,441 (+)	Ensembl
Rnor_6.0 Ensembl	15	51,065,316 - 51,068,421 (+)	Ensembl

RefSeq Acc Id:

NM_001034144 ⟹ NP_001029316

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	15	44,473,851 - 44,476,443 (+)	NCBI
Rnor_6.0	15	51,065,316 - 51,067,908 (+)	NCBI
Rnor_5.0	15	54,796,102 - 54,798,694 (+)	NCBI
RGSC_v3.4	15	49,743,313 - 49,745,905 (+)	RGD
Celera	15	44,157,589 - 44,160,181 (+)	RGD

Sequence:

show sequence

CGGGATGCTTAGGGTAGCGGAGCCCCAAGAGGCACGGTTGGAGGCGGGTGGTCGCAGTCCCTGG
GCAGCGCCACCCACGCAGTCCAAGCGGCTCACGTCCTTCCTCATCCAGGACATCCTGCGGGACC
ACGCAGAGCGGCGTGGGGGACAGCCGAGCACCCCGCAGCACCAGTGCCAACCAGACCCTAAGAG
GGATTCTGCTTCAGAGCTCGACGAAGCAGAGGGTAGCAGTGTGACTCTGGAGGACCCGCCAGGT
ATCCGGTCGAGCCCCACAGAGACACGGGCTGAAACCGAGTCAGATGCACATTTTGAGACTTATC
TGTTGGACTGTGAACATACTCCAGTCTTATCAAGTGCCCCCCAGGTCACCAAGCAGCCACAGAA
GCGTTCCCGGGCTGCTTTCTCTCACACTCAGGTGATTGAGTTGGAGAGGAAGTTCAGCCATCAG
AAGTACCTGTCCGCCCCTGAAAGGGCTCACCTGGCCAAGAACCTCAAACTCACCGAAACCCAAG
TAAAAATATGGTTCCAGAACAGACGCTACAAGACTAAGCGAAGGCAGCTGTCAGAAGACCTGGG
AGTCTTGGAGAAGAACTCCACATTGTCTTTGCCAACCCTGAAAGATGACAGCCTATCCAGGGCC
TCCTTGGTCTCCGTGTATGCTAGCTACCCCTACTACCCCTACCTATACTGTCTGGGCAGCTGGC
ATCCAACTTTCTGGTAACAACAGTTCAGATGACAACTGCATAGATCAGAAACTGCCTTCCCTGG
GGGTCCCTGGGAAAAAGCCAGAGTGGCTGATGTCAAGGAGTTGAAAGCAAGAAGTGTACAGACA
CAAACTGTTGGGTGTTCCCAGGGAATACTCCGATTCTTCTCTGGTGGCCAATGAAAGATCTGGG
GCAGTGGACATTTTATTATGTAGTCACAGTTCCAAGTGTTCTGTAGGTCACGGCTGTCAGTTCC
CTGTTTAGAGAGAGCTAGACAAGTTCAAGTCTTATTTCCAGAGCTTAGAGTGGCTATGGCTGCA
ATGGCTACATCGTTCCTAAGAATTCTGTTGCTGCAATTTCATCCTCTCCCATAACTGGGTATCA
TGAAAGGGCCAAGCAAGGGGAGGGATGGCCCCTTAGATGAGGATTTCCTCTTGAATTAAACTTG
TGTTTAAAAGTCTCTTGTTGGCCTTGGACTCTGACCAGAGTTTCCCTCTGCCCTTGTAAAAGTG
AGGGTAAACGGGAGATTTGAAGAAGGGGAGAAAAAACCTTAGTGATTAAGCAGGTTGGCATAGG
ACATGAAGGGGCTGGAAGGTGGCATTTTCAACTTCTTACTCCTTTTGCAGTGATGTGCCAATCC
AAGGATTTACAGGGCAGCCTGAGTGCAGCAGGGTACATATACTGAAGGGGGTTAAGACAAGCTG
TGTAAACAGTTTGCCTGCAGGGGTGGGCTTCAGAACAGACTTCCTGTCCAAGACAAGGGCCTAT
GGGGTTTCCAAACTCCAGGTGAGCTGCTTCGGTCATGACATTTTATTACCAGTGAAGGGGGAGG
GGAGATCTTAGACTCAGGAGATCCTGCAGCTTCCCTGGTCTGAGAATTCACACCTCATTATGAC
AGAGGTGCCATCATTTTTAAACAAAGGATCTTCCTTCTATTCTTTTATTTCTTGTTCTTTCTTA
CAGGACTCCTCAGTTCATTGTTTTCATATATGCCTGTCTTATTTAGTGTAAGATTTGCTCCCAC
CACCTCCCAAGTTTTATCTTTCCCAGTTTAATAACTAACTAGCTTCAGACAGATAAAAAAAAAA
AAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001029316	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI00629	(Get FASTA)	NCBI Sequence Viewer
	EDM02182	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001029316 ⟸ NM_001034144

- UniProtKB:

Q497B7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLRVAEPQEARLEAGGRSPWAAPPTQSKRLTSFLIQDILRDHAERRGGQPSTPQHQCQPDPKRD
SASELDEAEGSSVTLEDPPGIRSSPTETRAETESDAHFETYLLDCEHTPVLSSAPQVTKQPQKR
SRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRRQLSEDLGV
LEKNSTLSLPTLKDDSLSRASLVSVYASYPYYPYLYCLGSWHPTFW

hide sequence

RefSeq Acc Id:

ENSRNOP00000020753 ⟸ ENSRNOT00000020753

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q497B7-F1-model_v2	AlphaFold	Q497B7	1-238	view protein structure

Transcriptome

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

Promoters

RGD ID:

13699796

Promoter ID:

EPDNEW_R10319

Type:

single initiation site

Name:

Nkx3-1_1

Description:

NK3 homeobox 1

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	15	51,065,298 - 51,065,358	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305369	AgrOrtholog
BioCyc Gene	G2FUF-13269	BioCyc
Ensembl Genes	ENSRNOG00000015477	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000020753	ENTREZGENE
	ENSRNOP00000020753.4	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000020753	ENTREZGENE
	ENSRNOT00000020753.8	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7938032	IMAGE-MGC_LOAD
InterPro	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_region	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
KEGG Report	rno:305999	UniProtKB/TrEMBL
MGC_CLONE	MGC:124859	IMAGE-MGC_LOAD
NCBI Gene	305999	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN NKX	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN NKX-3.1	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
PhenoGen	Nkx3-1	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	Q497B7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-26	Nkx3-1	NK3 homeobox 1	Nkx3-1	NK-3 transcription factor, locus 1 (Drosophila)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	Nkx3-1	NK-3 transcription factor, locus 1 (Drosophila)	Nkx3-1_predicted	NK-3 transcription factor, locus 1 (Drosophila) (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Nkx3-1_predicted	NK-3 transcription factor, locus 1 (Drosophila) (predicted)			Symbol and Name status set to approved	70820	APPROVED

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)

Mammalian Phenotype

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Annotations - KEGG (archival)

Imported Annotations - PID (archival)

Mammalian Phenotype