Nkx2-5 (NK2 homeobox 5) - Rat Genome Database

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Gene: Nkx2-5 (NK2 homeobox 5) Rattus norvegicus
Analyze
Symbol: Nkx2-5
Name: NK2 homeobox 5
RGD ID: 620520
Description: Enables several functions, including DNA-binding transcription factor activity; histone deacetylase binding activity; and identical protein binding activity. Involved in several processes, including cellular response to hydrogen peroxide; negative regulation of transcription by RNA polymerase II; and response to estradiol. Located in nucleus. Biomarker of pulmonary fibrosis. Human ortholog(s) of this gene implicated in aortic valve disease 2; atrioventricular block; congenital heart disease (multiple); and congenital nongoitrous hypothyroidism 5. Orthologous to human NKX2-5 (NK2 homeobox 5); INTERACTS WITH acrylamide; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Csx; homeobox protein NK-2 homolog E; homeobox protein Nkx-2.5; NK2 transcription factor related, locus 5; NK2 transcription factor related, locus 5 (Drosophila); Nkx2.5; rNKx-2.5
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
mRatBN7.21016,340,428 - 16,347,004 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1016,344,159 - 16,346,934 (+)Ensembl
Rnor_6.01016,635,989 - 16,638,758 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1016,635,989 - 16,638,764 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01016,520,570 - 16,527,836 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41016,606,183 - 16,608,952 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11016,607,231 - 16,610,001 (+)NCBI
Celera1016,004,548 - 16,007,317 (+)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult heart development  (IEA,ISO)
apoptotic process involved in heart morphogenesis  (IEA,ISO)
atrial cardiac muscle tissue development  (IEA,ISO)
atrial septum morphogenesis  (IEA,ISO)
atrioventricular node cell development  (IEA,ISO)
atrioventricular node cell fate commitment  (IEA,ISO)
atrioventricular node development  (ISO)
bundle of His development  (IEA,ISO)
cardiac conduction system development  (ISO)
cardiac muscle cell development  (ISO)
cardiac muscle cell differentiation  (IEP,ISO)
cardiac muscle cell proliferation  (IEA,ISO)
cardiac muscle contraction  (IEA,ISO)
cardiac muscle tissue development  (ISO)
cardiac muscle tissue morphogenesis  (ISO)
cardiac ventricle formation  (IEA,ISO)
cardiac ventricle morphogenesis  (ISO)
cell differentiation  (IBA,ISO)
cellular response to growth factor stimulus  (IEP)
cellular response to hydrogen peroxide  (IEP)
circulatory system development  (ISO)
embryonic heart tube development  (ISO)
embryonic heart tube left/right pattern formation  (IEA,ISO)
heart contraction  (ISO)
heart development  (ISO)
heart looping  (IEA,ISO)
heart morphogenesis  (ISO)
heart trabecula formation  (IEA,ISO)
hemopoiesis  (IEA,ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of canonical Wnt signaling pathway  (IEA,ISO)
negative regulation of cardiac muscle cell apoptotic process  (IEA,ISO)
negative regulation of myotube differentiation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IDA,IEA,ISO)
outflow tract morphogenesis  (ISO)
outflow tract septum morphogenesis  (IEA,ISO)
pharyngeal system development  (IEA,ISO)
positive regulation of cardioblast differentiation  (IEA,ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of gene expression  (IEA,ISO)
positive regulation of heart contraction  (IEA,ISO)
positive regulation of neuron differentiation  (IEA,ISO)
positive regulation of sodium ion transport  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription initiation from RNA polymerase II promoter  (IEA,ISO)
positive regulation of transcription via serum response element binding  (IEA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
proepicardium development  (IEA,ISO)
pulmonary myocardium development  (IEA,ISO)
Purkinje myocyte differentiation  (IEA,ISO)
regulation of cardiac conduction  (IEA,ISO)
regulation of cardiac muscle cell proliferation  (IEA,ISO)
regulation of cardiac muscle contraction  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
response to estradiol  (IEP)
right ventricular cardiac muscle tissue morphogenesis  (IEA,ISO)
sarcomere organization  (IEA,ISO)
septum secundum development  (IEA,ISO)
spleen development  (IEA,ISO,ISS)
thyroid gland development  (IEA,ISO)
vasculogenesis  (IEA,ISO)
ventricular cardiac myofibril assembly  (IEA,ISO)
ventricular septum morphogenesis  (IEA,ISO)
ventricular trabecula myocardium morphogenesis  (IEA,ISO)

Cellular Component

References

References - curated
1. Abou Hassan OK, etal., Sci Rep. 2015 Mar 6;5:8848. doi: 10.1038/srep08848.
2. Ashraf H, etal., Circ Cardiovasc Genet. 2014 Aug;7(4):423-33. doi: 10.1161/CIRCGENETICS.113.000281. Epub 2014 Jul 15.
3. Biben C, etal., Circ Res. 2000 Nov 10;87(10):888-95.
4. Chandrasekaran S, etal., FASEB J. 2009 Nov;23(11):3851-64. doi: 10.1096/fj.09-132415. Epub 2009 Jul 28.
5. Dentice M, etal., Mol Endocrinol. 2003 Aug;17(8):1508-21. Epub 2003 May 29.
6. Elles√łe SG, etal., Congenit Heart Dis. 2016 May;11(3):283-90. doi: 10.1111/chd.12317. Epub 2015 Dec 18.
7. Funke-Kaiser H, etal., FASEB J 2003 Aug;17(11):1487-9.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Goldmuntz E, etal., Circulation. 2001 Nov 20;104(21):2565-8.
10. Gutierrez-Roelens I, etal., Eur J Hum Genet. 2006 Dec;14(12):1313-6. Epub 2006 Aug 9.
11. Gutierrez-Roelens I, etal., Hum Mutat. 2002 Jul;20(1):75-6.
12. Hu B, etal., Am J Respir Cell Mol Biol. 2010 Feb;42(2):218-26. Epub 2009 Apr 24.
13. Inga A, etal., Hum Mol Genet. 2005 Jul 15;14(14):1965-75. Epub 2005 May 25.
14. Kasahara H, etal., J Biol Chem. 2001 Feb 16;276(7):4570-80. Epub 2000 Oct 20.
15. Kasahara H, etal., J Clin Invest. 2001 Jul;108(2):189-201.
16. Li T, etal., J Mol Biol. 2007 Jul 27;370(5):976-92. Epub 2007 May 18.
17. Liu XY, etal., Pediatr Cardiol. 2011 Feb;32(2):193-201. doi: 10.1007/s00246-010-9859-6. Epub 2010 Dec 25.
18. Lu T, etal., Tissue Eng Part A. 2010 Oct;16(10):3111-7.
19. Marni F, etal., Endocrinology. 2009 Feb;150(2):879-88. Epub 2008 Oct 1.
20. MGD data from the GO Consortium
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. OMIM Disease Annotation Pipeline
23. Pabst S, etal., Clin Res Cardiol. 2008 Jan;97(1):39-42. Epub 2007 Sep 25.
24. Pauli RM, etal., Am J Med Genet 1999 Aug 6;85(4):419-23.
25. Perera JL, etal., Pediatr Cardiol. 2014 Oct;35(7):1206-12. doi: 10.1007/s00246-014-0917-3. Epub 2014 Jun 1.
26. Qu XK, etal., Am J Cardiol. 2014 Dec 15;114(12):1891-5. doi: 10.1016/j.amjcard.2014.09.028. Epub 2014 Sep 28.
27. Reamon-Buettner SM and Borlak J, J Med Genet. 2004 Sep;41(9):684-90.
28. RGD automated data pipeline
29. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. RGD automated import pipeline for gene-chemical interactions
31. Risebro CA, etal., Circ Res. 2012 Jul 6;111(2):e19-31. doi: 10.1161/CIRCRESAHA.111.260695. Epub 2012 May 29.
32. Schott JJ, etal., Science. 1998 Jul 3;281(5373):108-11.
33. van Engelen K, etal., PLoS One. 2012;7(12):e52685. doi: 10.1371/journal.pone.0052685. Epub 2012 Dec 28.
34. Wang J, etal., Genet Mol Res. 2011 Nov 29;10(4):2905-15. doi: 10.4238/2011.November.29.1.
35. Wang J, etal., Int J Mol Med. 2011 Mar;27(3):369-75. doi: 10.3892/ijmm.2010.585. Epub 2010 Dec 16.
36. Zheng W, etal., Basic Res Cardiol. 2013 Jul;108(4):364. doi: 10.1007/s00395-013-0364-y. Epub 2013 Jun 7.
37. Zhu W, etal., J Biol Chem. 2000 Nov 10;275(45):35291-6.
Additional References at PubMed
PMID:7628699   PMID:8887666   PMID:8900044   PMID:9192865   PMID:9312027   PMID:9857019   PMID:9858576   PMID:10021345   PMID:10206974   PMID:10587520   PMID:11390666   PMID:11431700  
PMID:11572777   PMID:11784028   PMID:11889119   PMID:12023302   PMID:12297045   PMID:12392994   PMID:12754203   PMID:14550786   PMID:14645532   PMID:14978031   PMID:15085192   PMID:15109497  
PMID:15363409   PMID:15649947   PMID:15653675   PMID:15843414   PMID:16380715   PMID:16418214   PMID:16510504   PMID:16556915   PMID:16678093   PMID:17234970   PMID:17250822   PMID:17350578  
PMID:17360443   PMID:17498735   PMID:17604724   PMID:17823370   PMID:18079734   PMID:18285513   PMID:18689573   PMID:18722343   PMID:19035347   PMID:19253817   PMID:19479054   PMID:19483677  
PMID:19546853   PMID:19578358   PMID:20457810   PMID:20713518   PMID:20807224   PMID:21379568   PMID:21690310   PMID:21931855   PMID:22527936   PMID:22560297   PMID:22849347   PMID:23892084  
PMID:24866243   PMID:26926761   PMID:27207958   PMID:27747432   PMID:31104268   PMID:32780729   PMID:33035436  


Genomics

Comparative Map Data
Nkx2-5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21016,340,428 - 16,347,004 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1016,344,159 - 16,346,934 (+)Ensembl
Rnor_6.01016,635,989 - 16,638,758 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1016,635,989 - 16,638,764 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01016,520,570 - 16,527,836 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41016,606,183 - 16,608,952 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11016,607,231 - 16,610,001 (+)NCBI
Celera1016,004,548 - 16,007,317 (+)NCBICelera
Cytogenetic Map10q12NCBI
NKX2-5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5173,232,109 - 173,235,311 (-)EnsemblGRCh38hg38GRCh38
GRCh385173,232,109 - 173,235,321 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375172,659,112 - 172,662,209 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365172,591,744 - 172,594,868 (-)NCBINCBI36hg18NCBI36
Celera5168,692,473 - 168,695,681 (-)NCBI
Cytogenetic Map5q35.1NCBI
HuRef5167,754,405 - 167,757,613 (-)NCBIHuRef
CHM1_15172,091,589 - 172,094,797 (-)NCBICHM1_1
Nkx2-5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,057,638 - 27,063,962 (-)NCBIGRCm39mm39
GRCm39 Ensembl1727,057,638 - 27,063,983 (-)Ensembl
GRCm381726,838,664 - 26,844,988 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1726,838,664 - 26,845,009 (-)EnsemblGRCm38mm10GRCm38
MGSCv371726,975,610 - 26,978,510 (-)NCBIGRCm37mm9NCBIm37
MGSCv361726,566,254 - 26,569,154 (-)NCBImm8
Celera1727,375,289 - 27,378,187 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1713.6NCBI
Nkx2-5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540825,832,683 - 25,836,840 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540825,833,649 - 25,836,673 (-)NCBIChiLan1.0ChiLan1.0
NKX2-5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15175,492,288 - 175,495,514 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5175,492,288 - 175,495,514 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05168,584,197 - 168,589,406 (-)NCBIMhudiblu_PPA_v0panPan3
NKX2-5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1439,240,755 - 39,254,585 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl439,244,286 - 39,247,592 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha439,189,667 - 39,192,973 (+)NCBI
ROS_Cfam_1.0439,612,560 - 39,618,296 (+)NCBI
UMICH_Zoey_3.1439,432,539 - 39,435,856 (+)NCBI
UNSW_CanFamBas_1.0439,621,539 - 39,624,869 (+)NCBI
UU_Cfam_GSD_1.0440,130,495 - 40,133,809 (+)NCBI
Nkx2-5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721393,683,325 - 93,686,308 (+)NCBI
SpeTri2.0NW_0049366092,406,004 - 2,408,980 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NKX2-5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1651,086,011 - 51,089,165 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11651,086,014 - 51,089,165 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21655,400,567 - 55,403,626 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NKX2-5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12375,391,833 - 75,399,003 (-)NCBI
ChlSab1.1 Ensembl2375,391,847 - 75,395,205 (-)Ensembl
Vero_WHO_p1.0NW_0236660343,212,995 - 3,216,184 (+)NCBI
Nkx2-5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473316,881,189 - 16,884,245 (+)NCBI

Position Markers
Nkx2-5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21016,346,390 - 16,347,001 (+)MAPPERmRatBN7.2
Rnor_6.01016,638,221 - 16,638,831NCBIRnor6.0
Rnor_5.01016,527,223 - 16,527,833UniSTSRnor5.0
RGSC_v3.41016,608,415 - 16,609,025UniSTSRGSC3.4
Celera1016,006,780 - 16,007,390UniSTS
Cytogenetic Map10q12UniSTS
RH133759  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21016,346,853 - 16,347,004 (+)MAPPERmRatBN7.2
Rnor_6.01016,638,684 - 16,638,834NCBIRnor6.0
Rnor_5.01016,527,686 - 16,527,836UniSTSRnor5.0
RGSC_v3.41016,608,878 - 16,609,028UniSTSRGSC3.4
Celera1016,007,243 - 16,007,393UniSTS
RH 3.4 Map10149.46UniSTS
Cytogenetic Map10q12UniSTS
UniSTS:463422  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21016,344,531 - 16,346,227 (+)MAPPERmRatBN7.2
Rnor_6.01016,636,362 - 16,638,057NCBIRnor6.0
Rnor_5.01016,525,364 - 16,527,059UniSTSRnor5.0
RGSC_v3.41016,606,556 - 16,608,251UniSTSRGSC3.4
Celera1016,004,921 - 16,006,616UniSTS
Cytogenetic Map10q12UniSTS
UniSTS:472868  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21016,346,121 - 16,346,297 (+)MAPPERmRatBN7.2
Rnor_6.01016,637,952 - 16,638,127NCBIRnor6.0
Rnor_5.01016,526,954 - 16,527,129UniSTSRnor5.0
RGSC_v3.41016,608,146 - 16,608,321UniSTSRGSC3.4
Celera1016,006,511 - 16,006,686UniSTS
Cytogenetic Map10q12UniSTS
Nkx2-5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21016,346,035 - 16,346,252 (+)MAPPERmRatBN7.2
Rnor_6.01016,637,866 - 16,638,082NCBIRnor6.0
Rnor_5.01016,526,868 - 16,527,084UniSTSRnor5.0
RGSC_v3.41016,608,060 - 16,608,276UniSTSRGSC3.4
Celera1016,006,425 - 16,006,641UniSTS
Cytogenetic Map10q12UniSTS
Nkx2-5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21016,344,042 - 16,344,577 (+)MAPPERmRatBN7.2
Rnor_6.01016,635,873 - 16,636,407NCBIRnor6.0
Rnor_5.01016,524,875 - 16,525,409UniSTSRnor5.0
RGSC_v3.41016,606,067 - 16,606,601UniSTSRGSC3.4
Celera1016,004,432 - 16,004,966UniSTS
Cytogenetic Map10q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:60
Count of miRNA genes:56
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000028155
Prediction methods: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

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 43 2 3
Low 4 4 9 4 4 6
Below cutoff 12 7 4 7 1 1 4 5 13 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028155   ⟹   ENSRNOP00000028155
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1016,344,159 - 16,346,934 (+)Ensembl
Rnor_6.0 Ensembl1016,635,989 - 16,638,764 (+)Ensembl
RefSeq Acc Id: NM_053651   ⟹   NP_446103
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21016,344,146 - 16,347,004 (+)NCBI
Rnor_6.01016,635,989 - 16,638,758 (+)NCBI
Rnor_5.01016,520,570 - 16,527,836 (+)NCBI
RGSC_v3.41016,606,183 - 16,608,952 (+)RGD
Celera1016,004,548 - 16,007,317 (+)RGD
Sequence:
RefSeq Acc Id: XM_039085022   ⟹   XP_038940950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21016,340,428 - 16,347,004 (+)NCBI
Protein Sequences
Protein RefSeqs NP_446103 (Get FASTA)   NCBI Sequence Viewer  
  XP_038940950 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB62696 (Get FASTA)   NCBI Sequence Viewer  
  EDM04040 (Get FASTA)   NCBI Sequence Viewer  
  O35767 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446103   ⟸   NM_053651
- Sequence:
RefSeq Acc Id: ENSRNOP00000028155   ⟸   ENSRNOT00000028155
RefSeq Acc Id: XP_038940950   ⟸   XM_039085022
- Peptide Label: isoform X1
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)
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
M520/NRrrcMcwi (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
MHS/Gib (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
MNS/Gib (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
MR/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
MR/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
MWF/Hsd (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
PVG/Seac (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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/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
SBN/Ygl (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: 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)
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/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SHRSP/Gcrc (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
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: 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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620520 AgrOrtholog
Ensembl Genes ENSRNOG00000020747 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000028155 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028155 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
  NKX-2.5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114109 UniProtKB/Swiss-Prot
NCBI Gene 114109 ENTREZGENE
PANTHER PTHR24340:SF28 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nkx2-5 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
UniProt G3V8T2_RAT UniProtKB/TrEMBL
  NKX25_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Nkx2-5  NK2 homeobox 5  Nkx2-5  NK2 transcription factor related, locus 5 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Nkx2-5  NK2 transcription factor related, locus 5 (Drosophila)  Csx    Symbol updated 1299863 APPROVED
2002-08-07 Csx  NK2 transcription factor related, locus 5 (Drosophila)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function binds within the ECE-1c promoter to activate expression of Endothelin-converting enzyme-1 727751