Nkx2-1 (NK2 homeobox 1) - Rat Genome Database

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Gene: Nkx2-1 (NK2 homeobox 1) Rattus norvegicus
Analyze
Symbol: Nkx2-1
Name: NK2 homeobox 1
RGD ID: 3866
Description: Enables several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; TBP-class protein binding activity; and transcription cis-regulatory region binding activity. Involved in several processes, including cellular response to leptin stimulus; embryonic lung development; and hyperosmotic salinity response. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. Human ortholog(s) of this gene implicated in choreatic disease and thyroid gland papillary carcinoma. Orthologous to human NKX2-1 (NK2 homeobox 1); PARTICIPATES IN forkhead class A signaling pathway; INTERACTS WITH acetylsalicylic acid; all-trans-retinoic acid; all-trans-retinol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: homeobox protein Nkx-2.1; thyroid nuclear factor 1; thyroid transcription factor 1; thyroid transcription factor 1 TTF-1 NK-2; Thyroid transcription factor 1 TTF-1 NK-2 (Drosophila) homolog A (thyroid nuclear factor); thyroid-specific transcription factor 1; Titf1; TTF-1; TTF1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2673,996,601 - 74,001,483 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl673,996,601 - 73,999,791 (-)Ensembl
Rnor_6.0677,418,096 - 77,423,383 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl677,418,096 - 77,421,286 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0686,945,224 - 86,950,040 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4676,916,943 - 76,920,133 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1676,920,108 - 76,923,259 (-)NCBI
Celera672,803,847 - 72,807,046 (-)NCBICelera
RH 3.4 Map6523.61RGD
Cytogenetic Map6q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure formation involved in morphogenesis  (IEA,ISO)
animal organ morphogenesis  (ISO)
axon guidance  (IEA,ISO)
brain development  (ISO)
cell differentiation  (IBA)
cellular response to leptin stimulus  (IEP)
cerebral cortex cell migration  (IEA,ISO)
cerebral cortex GABAergic interneuron differentiation  (IEA,ISO)
cerebral cortex neuron differentiation  (ISO)
circadian rhythm  (IEP)
club cell differentiation  (IEA,ISO)
development of primary female sexual characteristics  (IEP)
developmental induction  (IEA,ISO)
embryonic lung development  (IEP)
endoderm development  (IEA,ISO)
epithelial tube branching involved in lung morphogenesis  (IEA,ISO)
feeding behavior  (IMP)
forebrain development  (ISO)
forebrain dorsal/ventral pattern formation  (IEA,ISO)
forebrain neuron differentiation  (ISO)
forebrain neuron fate commitment  (IEA,ISO)
globus pallidus development  (IEA,ISO)
hippocampus development  (IEA,ISO)
hyperosmotic salinity response  (IDA)
Leydig cell differentiation  (IEA,ISO)
locomotory behavior  (IEA,ISO)
lung development  (ISO)
lung saccule development  (IEA,ISO)
negative regulation of cell migration  (IEA,ISO)
negative regulation of epithelial to mesenchymal transition  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transcription, DNA-templated  (ISO,ISS)
negative regulation of transforming growth factor beta receptor signaling pathway  (IEA,ISO)
neuron fate commitment  (ISO)
neuron migration  (IEA,ISO)
oligodendrocyte differentiation  (IEA,ISO)
pattern specification process  (ISO)
phospholipid metabolic process  (IEA,ISO)
pituitary gland development  (IEA,ISO)
positive regulation of circadian rhythm  (IEA,ISO,ISS)
positive regulation of gene expression  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IDA,IEA,IMP,ISO)
positive regulation of transcription, DNA-templated  (IDA,IMP,ISO)
regulation of blood volume by renin-angiotensin  (IDA)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of transcription, DNA-templated  (IDA,ISO)
response to ethanol  (IEP)
response to hormone  (IEA,ISO)
response to lipopolysaccharide  (IDA)
telencephalon cell migration  (ISO)
telencephalon development  (ISO)
thyroid gland development  (IEA,ISO)
type II pneumocyte differentiation  (IEA,ISO)

Cellular Component
nucleoplasm  (IDA)
nucleus  (IBA,IEA,IMP,ISO,TAS)
transcription regulator complex  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Breedveld GJ, etal., Hum Mol Genet. 2002 Apr 15;11(8):971-9.
2. Chen H, etal., PLoS One. 2013 Jul 22;8(7):e69297. doi: 10.1371/journal.pone.0069297. Print 2013.
3. Dave V, etal., J Biol Chem. 2004 Aug 13;279(33):34578-88. Epub 2004 Jun 1.
4. Del Vecchio P, etal., Proteins. 2008 Feb 15;70(3):748-60.
5. Di Palma T, etal., J Biol Chem. 2003 Jan 31;278(5):3395-402. Epub 2002 Nov 18.
6. do Carmo Costa M, etal., Neurogenetics. 2005 Dec;6(4):209-15. Epub 2005 Oct 12.
7. Fernandez-Estivariz C, etal., Am J Physiol Regul Integr Comp Physiol 2003 Feb;284(2):R564-73.
8. Ferrara AM, etal., Thyroid. 2008 Sep;18(9):1005-9. doi: 10.1089/thy.2008.0085.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Guazzi S, etal., EMBO J 1990 Nov;9(11):3631-9.
12. Kim HJ, etal., Brain Res Mol Brain Res. 2005 May 20;136(1-2):262-6.
13. Kim JG, etal., Biochem Biophys Res Commun. 2006 Oct 27;349(3):969-75. Epub 2006 Sep 1.
14. Kim JG, etal., Biochem Biophys Res Commun. 2008 Jun 6;370(3):468-72. Epub 2008 Apr 3.
15. Kim MS, etal., J Biol Chem 2002 Sep 27;277(39):36863-71.
16. Koht J, etal., Cerebellum Ataxias. 2016 Feb 2;3:3. doi: 10.1186/s40673-016-0041-7. eCollection 2016.
17. Konishi T, etal., J Neurol. 2013 Jan;260(1):207-13. doi: 10.1007/s00415-012-6618-z. Epub 2012 Jul 24.
18. Krude H, etal., J Clin Invest. 2002 Feb;109(4):475-80.
19. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
20. Lee BJ, etal., Mol Cell Neurosci. 2001 Jan;17(1):107-26.
21. Matagne V, etal., J Neuroendocrinol. 2012 Jun;24(6):916-29. doi: 10.1111/j.1365-2826.2012.02302.x.
22. McMichael G, etal., Eur J Med Genet. 2013 Sep;56(9):506-9. doi: 10.1016/j.ejmg.2013.07.003. Epub 2013 Jul 30.
23. MGD data from the GO Consortium
24. Missero C, etal., J Biol Chem 2001 Sep 7;276(36):33569-75.
25. Missero C, etal., Mol Cell Biol. 2000 Apr;20(8):2783-93.
26. NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Nettore IC, etal., Thyroid. 2013 Jun;23(6):675-82. doi: 10.1089/thy.2012.0267.
28. OMIM Disease Annotation Pipeline
29. Park KS, etal., J Biol Chem. 2004 Apr 23;279(17):17384-90. Epub 2004 Feb 17.
30. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
31. Reiser H and Schneeberger EE, Eur J Immunol. 1996 Apr;26(4):880-5.
32. RGD automated data pipeline
33. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
34. RGD automated import pipeline for gene-chemical interactions
35. Son YJ, etal., J Biol Chem. 2003 Jul 18;278(29):27043-52. Epub 2003 May 2.
36. Takayasu H, etal., Pediatr Surg Int. 2007 Jan 24;.
37. Tell G, etal., Biochem J. 1998 Jan 15;329 ( Pt 2):395-403.
38. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
39. Velez ML, etal., Endocrinology. 2006 Jul;147(7):3260-75. Epub 2006 Apr 20.
40. Zannini M, etal., EMBO J 1997 Jun 2;16(11):3185-97.
41. Zighelboim I, etal., Clin Cancer Res. 2007 May 15;13(10):2882-9.
Additional References at PubMed
PMID:1735431   PMID:7559607   PMID:7635972   PMID:7713914   PMID:7896788   PMID:7980615   PMID:8282100   PMID:8557195   PMID:8675988   PMID:8813084   PMID:8898894   PMID:9430685  
PMID:9806931   PMID:10208743   PMID:10393115   PMID:10706142   PMID:11163262   PMID:11171336   PMID:11493571   PMID:11724907   PMID:11733512   PMID:11830575   PMID:11854318   PMID:11914369  
PMID:12399445   PMID:12829717   PMID:12902388   PMID:12930780   PMID:14960358   PMID:15028753   PMID:15181011   PMID:15356023   PMID:15494458   PMID:15576401   PMID:15581879   PMID:16033766  
PMID:16150900   PMID:16260629   PMID:16510470   PMID:16601074   PMID:16960125   PMID:16998587   PMID:17079460   PMID:17164424   PMID:17182767   PMID:17347682   PMID:17371871   PMID:17409236  
PMID:17412341   PMID:17464199   PMID:17522155   PMID:17706597   PMID:18033672   PMID:18167145   PMID:18239190   PMID:18339674   PMID:18632661   PMID:18786356   PMID:18786357   PMID:19010321  
PMID:19176457   PMID:19293183   PMID:19906647   PMID:20160132   PMID:20181579   PMID:21046115   PMID:21055024   PMID:21282365   PMID:21350014   PMID:21402781   PMID:22955271   PMID:23143308  
PMID:23382074   PMID:24380675   PMID:25051213   PMID:27435678  


Genomics

Comparative Map Data
Nkx2-1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2673,996,601 - 74,001,483 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl673,996,601 - 73,999,791 (-)Ensembl
Rnor_6.0677,418,096 - 77,423,383 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl677,418,096 - 77,421,286 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0686,945,224 - 86,950,040 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4676,916,943 - 76,920,133 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1676,920,108 - 76,923,259 (-)NCBI
Celera672,803,847 - 72,807,046 (-)NCBICelera
RH 3.4 Map6523.61RGD
Cytogenetic Map6q23NCBI
NKX2-1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1436,516,392 - 36,521,149 (-)EnsemblGRCh38hg38GRCh38
GRCh381436,516,397 - 36,520,232 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371436,985,602 - 36,989,437 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361436,055,353 - 36,059,167 (-)NCBINCBI36hg18NCBI36
Build 341436,055,352 - 36,058,654NCBI
Celera1416,849,149 - 16,852,977 (-)NCBI
Cytogenetic Map14q13.3NCBI
HuRef1417,100,276 - 17,104,039 (-)NCBIHuRef
CHM1_11436,984,732 - 36,988,564 (-)NCBICHM1_1
Nkx2-1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391256,578,720 - 56,583,693 (-)NCBIGRCm39mm39
GRCm39 Ensembl1256,578,743 - 56,583,693 (-)Ensembl
GRCm381256,531,935 - 56,536,908 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1256,531,958 - 56,536,908 (-)EnsemblGRCm38mm10GRCm38
MGSCv371257,632,922 - 57,637,895 (-)NCBIGRCm37mm9NCBIm37
MGSCv361257,449,970 - 57,454,920 (-)NCBImm8
Celera1257,681,286 - 57,686,296 (-)NCBICelera
Cytogenetic Map12C1NCBI
cM Map1224.42NCBI
Nkx2-1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540924,612,635 - 24,616,430 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540924,612,490 - 24,616,360 (+)NCBIChiLan1.0ChiLan1.0
NKX2-1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11435,403,557 - 35,627,438 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1435,404,127 - 35,626,722 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01417,224,870 - 17,273,252 (-)NCBIMhudiblu_PPA_v0panPan3
NKX2-1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha814,886,591 - 14,888,646 (-)NCBI
ROS_Cfam_1.0815,197,690 - 15,202,516 (-)NCBI
UMICH_Zoey_3.1814,896,830 - 14,898,885 (-)NCBI
UNSW_CanFamBas_1.0814,963,572 - 14,965,627 (-)NCBI
UU_Cfam_GSD_1.0815,253,618 - 15,255,673 (-)NCBI
Nkx2-1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864047,011,599 - 47,015,298 (-)NCBI
SpeTri2.0NW_00493649410,517,488 - 10,520,567 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NKX2-1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl763,487,807 - 63,491,575 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1763,487,200 - 63,491,580 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2768,395,821 - 68,400,133 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NKX2-1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12413,274,118 - 13,317,533 (-)NCBI
ChlSab1.1 Ensembl2413,310,846 - 13,317,056 (-)Ensembl
Vero_WHO_p1.0NW_0236660532,266,777 - 2,311,899 (-)NCBI
Nkx2-1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624838300,902 - 304,944 (+)NCBI

Position Markers
D6Arb16  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,997,347 - 73,997,655 (+)MAPPERmRatBN7.2
Rnor_6.0677,418,843 - 77,419,150NCBIRnor6.0
Rnor_5.0686,945,971 - 86,946,278UniSTSRnor5.0
RGSC_v3.4676,917,690 - 76,917,997UniSTSRGSC3.4
RGSC_v3.1676,920,815 - 76,921,123RGD
Celera672,804,594 - 72,804,910UniSTS
Cytogenetic Map6q23UniSTS
D6Wox26  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,997,408 - 73,997,656 (+)MAPPERmRatBN7.2
Rnor_6.0677,418,904 - 77,419,151NCBIRnor6.0
Rnor_5.0686,946,032 - 86,946,279UniSTSRnor5.0
RGSC_v3.4676,917,751 - 76,917,998UniSTSRGSC3.4
Celera672,804,655 - 72,804,911UniSTS
Cytogenetic Map6q23UniSTS
D6Wox28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2674,000,100 - 74,000,263 (+)MAPPERmRatBN7.2
Rnor_6.0677,421,596 - 77,421,754NCBIRnor6.0
Rnor_5.0686,948,724 - 86,948,882UniSTSRnor5.0
RGSC_v3.4676,920,443 - 76,920,601UniSTSRGSC3.4
Celera672,807,356 - 72,807,514UniSTS
Cytogenetic Map6q23UniSTS
D6Wox31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2674,000,044 - 74,000,263 (+)MAPPERmRatBN7.2
Rnor_6.0677,421,540 - 77,421,754NCBIRnor6.0
Rnor_5.0686,948,668 - 86,948,882UniSTSRnor5.0
RGSC_v3.4676,920,387 - 76,920,601UniSTSRGSC3.4
Celera672,807,300 - 72,807,514UniSTS
Cytogenetic Map6q23UniSTS
RH94604  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,996,697 - 73,996,789 (+)MAPPERmRatBN7.2
Rnor_6.0677,418,193 - 77,418,284NCBIRnor6.0
Rnor_5.0686,945,321 - 86,945,412UniSTSRnor5.0
RGSC_v3.4676,917,040 - 76,917,131UniSTSRGSC3.4
Celera672,803,944 - 72,804,035UniSTS
RH 3.4 Map6523.61UniSTS
Cytogenetic Map6q23UniSTS
AA858694  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,996,804 - 73,997,001 (+)MAPPERmRatBN7.2
Rnor_6.0677,418,300 - 77,418,496NCBIRnor6.0
Rnor_5.0686,945,428 - 86,945,624UniSTSRnor5.0
RGSC_v3.4676,917,147 - 76,917,343UniSTSRGSC3.4
Celera672,804,051 - 72,804,247UniSTS
RH 3.4 Map6526.4UniSTS
Cytogenetic Map6q23UniSTS
PMC102181P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,996,888 - 73,997,109 (+)MAPPERmRatBN7.2
Rnor_6.0677,418,384 - 77,418,604NCBIRnor6.0
Rnor_5.0686,945,512 - 86,945,732UniSTSRnor5.0
RGSC_v3.4676,917,231 - 76,917,451UniSTSRGSC3.4
Celera672,804,135 - 72,804,355UniSTS
Cytogenetic Map6q23UniSTS
PMC152810P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,998,336 - 73,998,545 (+)MAPPERmRatBN7.2
Rnor_6.0677,419,832 - 77,420,040NCBIRnor6.0
Rnor_5.0686,946,960 - 86,947,168UniSTSRnor5.0
RGSC_v3.4676,918,679 - 76,918,887UniSTSRGSC3.4
Celera672,805,592 - 72,805,800UniSTS
Cytogenetic Map6q23UniSTS
Nkx2-1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,997,787 - 73,998,219 (+)MAPPERmRatBN7.2
Rnor_6.0677,419,283 - 77,419,714NCBIRnor6.0
Rnor_5.0686,946,411 - 86,946,842UniSTSRnor5.0
RGSC_v3.4676,918,130 - 76,918,561UniSTSRGSC3.4
Celera672,805,043 - 72,805,474UniSTS
Cytogenetic Map6q23UniSTS
Titf1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,998,435 - 73,999,492 (+)MAPPERmRatBN7.2
Rnor_6.0677,419,931 - 77,420,987NCBIRnor6.0
Rnor_5.0686,947,059 - 86,948,115UniSTSRnor5.0
RGSC_v3.4676,918,778 - 76,919,834UniSTSRGSC3.4
Celera672,805,691 - 72,806,747UniSTS
Cytogenetic Map6q23UniSTS
UniSTS:225218  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2674,000,636 - 74,000,785 (+)MAPPERmRatBN7.2
Rnor_6.0677,422,128 - 77,422,276NCBIRnor6.0
Rnor_5.0686,949,256 - 86,949,404UniSTSRnor5.0
RGSC_v3.4676,920,975 - 76,921,123UniSTSRGSC3.4
Celera672,807,888 - 72,808,036UniSTS
Cytogenetic Map6q23UniSTS
Nkx2-1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,999,760 - 74,001,088 (+)MAPPERmRatBN7.2
Rnor_6.0677,421,256 - 77,422,579NCBIRnor6.0
Rnor_5.0686,948,384 - 86,949,707UniSTSRnor5.0
Celera672,807,016 - 72,808,339UniSTS
Cytogenetic Map6q23UniSTS
Nkx2-1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,998,479 - 73,999,495 (+)MAPPERmRatBN7.2
Rnor_6.0677,419,975 - 77,420,990NCBIRnor6.0
Rnor_5.0686,947,103 - 86,948,118UniSTSRnor5.0
Celera672,805,735 - 72,806,750UniSTS
Cytogenetic Map6q23UniSTS
Nkx2-1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2673,997,785 - 73,998,219 (+)MAPPERmRatBN7.2
Rnor_6.0677,419,281 - 77,419,714NCBIRnor6.0
Rnor_5.0686,946,409 - 86,946,842UniSTSRnor5.0
Celera672,805,041 - 72,805,474UniSTS
Cytogenetic Map6q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
4889848Pur25Proteinuria QTL 25140.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65672856290198260Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)67222764181132889Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:145
Count of miRNA genes:101
Interacting mature miRNAs:109
Transcripts:ENSRNOT00000011453
Prediction methods:Microtar, Miranda, Rnahybrid
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.


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

alimentary part of gastrointestinal system 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 33 11
Low 2 4 6 4 4 4 1 28 1 2
Below cutoff 1 11 29 15 15 15 7 8 13 12 31 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011453   ⟹   ENSRNOP00000011453
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl673,996,601 - 73,999,791 (-)Ensembl
Rnor_6.0 Ensembl677,418,096 - 77,421,286 (-)Ensembl
RefSeq Acc Id: NM_013093   ⟹   NP_037225
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2673,996,601 - 73,999,791 (-)NCBI
Rnor_6.0677,418,096 - 77,421,286 (-)NCBI
Rnor_5.0686,945,224 - 86,950,040 (-)NCBI
RGSC_v3.4676,916,943 - 76,920,133 (-)RGD
Celera672,803,847 - 72,807,046 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240116   ⟹   XP_006240178
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2673,996,633 - 74,000,081 (-)NCBI
Rnor_6.0677,418,096 - 77,421,665 (-)NCBI
Rnor_5.0686,945,224 - 86,950,040 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240117   ⟹   XP_006240179
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2673,996,633 - 74,000,826 (-)NCBI
Rnor_6.0677,418,096 - 77,422,378 (-)NCBI
Rnor_5.0686,945,224 - 86,950,040 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240118   ⟹   XP_006240180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2673,996,633 - 74,001,483 (-)NCBI
Rnor_6.0677,418,096 - 77,423,383 (-)NCBI
Rnor_5.0686,945,224 - 86,950,040 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039111813   ⟹   XP_038967741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2673,997,506 - 73,999,412 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037225   ⟸   NM_013093
- UniProtKB: G3V740 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240180   ⟸   XM_006240118
- Peptide Label: isoform X3
- UniProtKB: G3V740 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240179   ⟸   XM_006240117
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006240178   ⟸   XM_006240116
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000011453   ⟸   ENSRNOT00000011453
RefSeq Acc Id: XP_038967741   ⟸   XM_039111813
- Peptide Label: isoform X4
Protein Domains
Homeobox

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3866 AgrOrtholog
Ensembl Genes ENSRNOG00000008644 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011453 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011453 ENTREZGENE, UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25628 UniProtKB/TrEMBL
NCBI Gene 25628 ENTREZGENE
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nkx2-1 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC209572
UniProt A0A060PW62_RAT UniProtKB/TrEMBL
  G3V740 ENTREZGENE, UniProtKB/TrEMBL
  NKX21_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O08630 UniProtKB/Swiss-Prot
  O70121 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-18 Nkx2-1  NK2 homeobox 1  Titf1  thyroid transcription factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Titf1  Thyroid transcription factor 1 TTF-1 NK-2 (Drosophila) homolog A (thyroid nuclear factor)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease defect in human TTF-1 leads to familial Goiter 625529
gene_expression postnatal mRNA expression observed in hypothalmic neurons, pre-LHRH neurons, pre-proenkephalinergic neurons of lateroventromedial nucleus of basal hypothalamus, astrocytes of median eminence and ependymal/subependymal cells of third ventricle 625529
gene_function binds and activates the promoter of thyroid specific genes such as thyroglobulin, thyroperoxidase, and thyrotropin receptor  
gene_physical_interaction binds to erbB-2 and LHRH promoters to transactivate gene transcription and represses preproenkephalin gene transcription 625529
gene_process plays a role in control of sexual maturation and reproductive behavior by neuronal transactivation and gene repression 625529
gene_process may have an active role during morphogenesis of hypothalamus and in the activation of mammalian puberty 625529
gene_process crucial in the maintenance of the thyroid differentiation phenotype  
gene_process may play a role in lung development and surfactant homeostasis  
gene_product member of Nkx family of homeodomain genes 625529
gene_regulation hypothalamic lesions leading to sexual precocity transiently elevate gene expression adjacent to lesion sites 625529
gene_regulation transient increase in hypothalamic expression precedes puberty in intact animals 625529