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

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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 cellular response to cytokine stimulus; positive regulation of cell communication; and regulation of gene expression. Predicted to act upstream of or within several processes, including epithelial cell proliferation involved in salivary gland morphogenesis; morphogenesis of a branching epithelium; and negative regulation of epithelial cell proliferation involved in prostate gland development. 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 ...
Allele / Splice: Nkx3-1em1Pjhak  
Genetic Models: SD-Nkx3-1em1Pjhak-/- SD-Nkx3-1em1Pjhak+/-
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81550,883,661 - 50,886,253 (+)NCBIGRCr8
mRatBN7.21544,473,851 - 44,476,443 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1544,473,851 - 44,476,441 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1548,591,788 - 48,594,380 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01549,703,277 - 49,705,869 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01546,562,612 - 46,565,204 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01551,065,316 - 51,067,908 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1551,065,316 - 51,068,421 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01554,796,102 - 54,798,694 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41549,743,313 - 49,745,905 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11549,752,541 - 49,761,067 (+)NCBI
Celera1544,157,589 - 44,160,181 (+)NCBICelera
Cytogenetic Map15p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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)
2-palmitoylglycerol  (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)
diethylstilbestrol  (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)
iron dichloride  (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
androgen receptor signaling pathway  (ISO)
apoptotic process  (IEA)
branching involved in prostate gland morphogenesis  (ISO)
branching morphogenesis of an epithelial tube  (ISO)
cell differentiation  (IBA)
cellular response to hypoxia  (ISO)
cellular response to interleukin-1  (ISO)
cellular response to steroid hormone stimulus  (ISO)
cellular response to tumor necrosis factor  (ISO)
cellular response to xenobiotic stimulus  (ISO)
DNA damage response  (ISO)
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)
heart development  (ISO)
male gonad development  (ISO)
metanephros development  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA-templated transcription  (ISO)
negative regulation of epithelial cell proliferation  (ISO)
negative regulation of epithelial cell proliferation involved in prostate gland development  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of insulin-like growth factor receptor signaling pathway  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
pharyngeal system development  (ISO)
phosphatidylinositol 3-kinase/protein kinase B signal transduction  (ISO)
positive regulation of androgen secretion  (ISO)
positive regulation of apoptotic signaling pathway  (ISO)
positive regulation of cell division  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of intrinsic apoptotic signaling pathway  (ISO)
positive regulation of mitotic cell cycle  (ISO)
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
prostate gland development  (ISO)
regulation of protein localization  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
response to testosterone  (ISO)
salivary gland development  (ISO)
somitogenesis  (ISO)
urogenital system development  (ISO)

Cellular Component
cytosol  (ISO)
nucleoplasm  (ISO)
nucleus  (IBA,ISO)
site of DNA damage  (ISO)

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

Mammalian Phenotype
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81550,883,661 - 50,886,253 (+)NCBIGRCr8
mRatBN7.21544,473,851 - 44,476,443 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1544,473,851 - 44,476,441 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1548,591,788 - 48,594,380 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01549,703,277 - 49,705,869 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01546,562,612 - 46,565,204 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01551,065,316 - 51,067,908 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1551,065,316 - 51,068,421 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01554,796,102 - 54,798,694 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41549,743,313 - 49,745,905 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11549,752,541 - 49,761,067 (+)NCBI
Celera1544,157,589 - 44,160,181 (+)NCBICelera
Cytogenetic Map15p11NCBI
NKX3-1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38823,678,693 - 23,682,938 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl823,678,697 - 23,682,938 (-)EnsemblGRCh38hg38GRCh38
GRCh37823,536,206 - 23,540,451 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36823,592,173 - 23,596,395 (-)NCBINCBI36Build 36hg18NCBI36
Build 34823,592,172 - 23,596,395NCBI
Celera822,499,634 - 22,503,878 (-)NCBICelera
Cytogenetic Map8p21.2NCBI
HuRef822,081,521 - 22,085,754 (-)NCBIHuRef
CHM1_1823,738,407 - 23,742,639 (-)NCBICHM1_1
T2T-CHM13v2.0823,953,650 - 23,957,884 (-)NCBIT2T-CHM13v2.0
Nkx3-1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391469,428,141 - 69,432,107 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1469,428,087 - 69,432,111 (+)EnsemblGRCm39 Ensembl
GRCm381469,190,692 - 69,194,658 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1469,190,638 - 69,194,662 (+)EnsemblGRCm38mm10GRCm38
MGSCv371469,808,749 - 69,812,715 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361468,144,022 - 68,147,988 (+)NCBIMGSCv36mm8
Celera1466,971,062 - 66,975,028 (+)NCBICelera
Cytogenetic Map14D2NCBI
cM Map1436.02NCBI
Nkx3-1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540346,806,178 - 46,836,310 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540346,807,846 - 46,809,924 (-)NCBIChiLan1.0ChiLan1.0
NKX3-1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2742,181,366 - 42,185,602 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1817,908,475 - 17,912,736 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0822,926,145 - 22,930,396 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1819,860,748 - 19,864,968 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl819,863,275 - 19,864,942 (-)Ensemblpanpan1.1panPan2
NKX3-1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12533,815,343 - 33,817,465 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2533,815,095 - 33,817,474 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2534,403,094 - 34,405,850 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02534,021,324 - 34,024,080 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2534,021,202 - 34,024,073 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12533,968,569 - 33,971,325 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02533,822,490 - 33,825,246 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02533,977,508 - 33,980,265 (+)NCBIUU_Cfam_GSD_1.0
Nkx3-1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494311,461,374 - 11,484,403 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365557,088,577 - 7,091,334 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365557,087,677 - 7,091,334 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NKX3-1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl147,783,323 - 7,787,033 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1147,783,296 - 7,787,036 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2148,625,545 - 8,630,189 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NKX3-1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1821,792,069 - 21,797,258 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl821,791,422 - 21,796,319 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605220,424,660 - 20,428,943 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nkx3-1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475818,875,475 - 18,876,971 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475818,874,399 - 18,876,982 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154028990149308583Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154063126846187442Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat

Markers in Region
RH139441  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21544,475,589 - 44,475,730 (+)MAPPERmRatBN7.2
Rnor_6.01551,067,055 - 51,067,195NCBIRnor6.0
Rnor_5.01554,797,841 - 54,797,981UniSTSRnor5.0
RGSC_v3.41549,745,052 - 49,745,192UniSTSRGSC3.4
Celera1544,159,328 - 44,159,468UniSTS
Cytogenetic Map15p11UniSTS


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


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

Sequence


RefSeq Acc Id: ENSRNOT00000020753   ⟹   ENSRNOP00000020753
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1544,473,851 - 44,476,441 (+)Ensembl
Rnor_6.0 Ensembl1551,065,316 - 51,068,421 (+)Ensembl
RefSeq Acc Id: NM_001034144   ⟹   NP_001029316
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81550,883,661 - 50,886,253 (+)NCBI
mRatBN7.21544,473,851 - 44,476,443 (+)NCBI
Rnor_6.01551,065,316 - 51,067,908 (+)NCBI
Rnor_5.01554,796,102 - 54,798,694 (+)NCBI
RGSC_v3.41549,743,313 - 49,745,905 (+)RGD
Celera1544,157,589 - 44,160,181 (+)RGD
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  
Ensembl Protein ENSRNOP00000020753
  ENSRNOP00000020753.4
RefSeq Acc Id: NP_001029316   ⟸   NM_001034144
- UniProtKB: Q497B7 (UniProtKB/TrEMBL),   A6HTG9 (UniProtKB/TrEMBL),   F7F548 (UniProtKB/TrEMBL)
- 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 AssemblyChrPosition (strand)Source
Rnor_6.01551,065,298 - 51,065,358EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305369 AgrOrtholog
BioCyc Gene G2FUF-13269 BioCyc
Ensembl Genes ENSRNOG00000015477 Ensembl, ENTREZGENE, 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
RatGTEx ENSRNOG00000015477 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6HTG9 ENTREZGENE, UniProtKB/TrEMBL
  F7F548 ENTREZGENE, UniProtKB/TrEMBL
  Q497B7 ENTREZGENE
UniProt Secondary Q497B7 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