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. Predicted to be located in cytoplasm. Predicted to be part of Nkx-2.5 complex and protein-DNA complex. Predicted to be active 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
Previously 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81016,844,888 - 16,851,458 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1016,848,582 - 16,851,452 (+)EnsemblGRCr8
mRatBN7.21016,340,428 - 16,347,004 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1016,344,159 - 16,346,934 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1021,093,028 - 21,095,888 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01020,581,977 - 20,584,837 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01016,071,642 - 16,074,502 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01016,635,989 - 16,638,758 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1016,635,989 - 16,638,764 (+)Ensemblrn6Rnor6.0
Rnor_5.01016,520,570 - 16,527,836 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41016,606,183 - 16,608,952 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1016,004,548 - 16,007,317 (+)NCBICelera
RGSC_v3.11016,607,231 - 16,610,001 (+)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult heart development  (IEA,ISO)
apoptotic process involved in heart morphogenesis  (ISO)
atrial cardiac muscle tissue development  (IEA,ISO)
atrial septum morphogenesis  (IEA,ISO)
atrioventricular node cell development  (ISO)
atrioventricular node cell fate commitment  (ISO)
atrioventricular node development  (IEA,ISO)
bundle of His development  (ISO)
cardiac conduction system development  (ISO)
cardiac muscle cell development  (IEA,ISO)
cardiac muscle cell differentiation  (IEA,IEP,ISO)
cardiac muscle cell proliferation  (ISO)
cardiac muscle contraction  (ISO)
cardiac muscle tissue development  (ISO)
cardiac muscle tissue morphogenesis  (IEA,ISO)
cardiac septum morphogenesis  (IEA,ISO)
cardiac ventricle formation  (ISO)
cardiac ventricle morphogenesis  (ISO)
cell differentiation  (IBA,ISO)
cellular response to growth factor stimulus  (IEP)
cellular response to hydrogen peroxide  (IEP)
embryonic heart tube development  (ISO)
embryonic heart tube left/right pattern formation  (ISO)
heart contraction  (ISO)
heart development  (ISO)
heart looping  (ISO)
heart morphogenesis  (ISO)
heart trabecula formation  (ISO)
hemopoiesis  (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  (ISO)
positive regulation of cardioblast differentiation  (IEA,ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of DNA-templated transcription  (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  (IEA,ISO,ISS)
positive regulation of transcription initiation by RNA polymerase II  (IEA,ISO)
proepicardium development  (ISO)
pulmonary myocardium development  (ISO)
Purkinje myocyte differentiation  (ISO)
regulation of cardiac conduction  (IEA,ISO)
regulation of cardiac muscle cell proliferation  (ISO)
regulation of cardiac muscle contraction  (IEA,ISO)
regulation of DNA-templated transcription  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
response to estradiol  (IEP)
right ventricular cardiac muscle tissue morphogenesis  (IEA,ISO)
septum secundum development  (IEA,ISO)
spleen development  (IEA,ISO,ISS)
thyroid gland development  (IEA,ISO)
vasculogenesis  (ISO)
ventricular cardiac myofibril assembly  (ISO)
ventricular septum morphogenesis  (IEA,ISO)
ventricular trabecula myocardium morphogenesis  (ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. NKX2-5 mutations in an inbred consanguineous population: genetic and phenotypic diversity. Abou Hassan OK, etal., Sci Rep. 2015 Mar 6;5:8848. doi: 10.1038/srep08848.
2. A mouse model of human congenital heart disease: high incidence of diverse cardiac anomalies and ventricular noncompaction produced by heterozygous Nkx2-5 homeodomain missense mutation. Ashraf H, etal., Circ Cardiovasc Genet. 2014 Aug;7(4):423-33. doi: 10.1161/CIRCGENETICS.113.000281. Epub 2014 Jul 15.
3. Cardiac septal and valvular dysmorphogenesis in mice heterozygous for mutations in the homeobox gene Nkx2-5. Biben C, etal., Circ Res. 2000 Nov 10;87(10):888-95.
4. Histone deacetylases facilitate sodium/calcium exchanger up-regulation in adult cardiomyocytes. Chandrasekaran S, etal., FASEB J. 2009 Nov;23(11):3851-64. doi: 10.1096/fj.09-132415. Epub 2009 Jul 28.
5. The different cardiac expression of the type 2 iodothyronine deiodinase gene between human and rat is related to the differential response of the Dio2 genes to Nkx-2.5 and GATA-4 transcription factors. Dentice M, etal., Mol Endocrinol. 2003 Aug;17(8):1508-21. Epub 2003 May 29.
6. Familial Atrial Septal Defect and Sudden Cardiac Death: Identification of a Novel NKX2-5 Mutation and a Review of the Literature. Ellesøe SG, etal., Congenit Heart Dis. 2016 May;11(3):283-90. doi: 10.1111/chd.12317. Epub 2015 Dec 18.
7. Endothelin-converting enzyme-1 (ECE-1) is a downstream target of the homeobox transcription factor Nkx2-5. Funke-Kaiser H, etal., FASEB J 2003 Aug;17(11):1487-9.
8. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. NKX2.5 mutations in patients with tetralogy of fallot. Goldmuntz E, etal., Circulation. 2001 Nov 20;104(21):2565-8.
10. A novel CSX/NKX2-5 mutation causes autosomal-dominant AV block: are atrial fibrillation and syncopes part of the phenotype? Gutierrez-Roelens I, etal., Eur J Hum Genet. 2006 Dec;14(12):1313-6. Epub 2006 Aug 9.
11. Progressive AV-block and anomalous venous return among cardiac anomalies associated with two novel missense mutations in the CSX/NKX2-5 gene. Gutierrez-Roelens I, etal., Hum Mutat. 2002 Jul;20(1):75-6.
12. Nkx2.5/Csx represses myofibroblast differentiation. Hu B, etal., Am J Respir Cell Mol Biol. 2010 Feb;42(2):218-26. Epub 2009 Apr 24.
13. Functional dissection of sequence-specific NKX2-5 DNA binding domain mutations associated with human heart septation defects using a yeast-based system. Inga A, etal., Hum Mol Genet. 2005 Jul 15;14(14):1965-75. Epub 2005 May 25.
14. Characterization of homo- and heterodimerization of cardiac Csx/Nkx2.5 homeoprotein. Kasahara H, etal., J Biol Chem. 2001 Feb 16;276(7):4570-80. Epub 2000 Oct 20.
15. Progressive atrioventricular conduction defects and heart failure in mice expressing a mutant Csx/Nkx2.5 homeoprotein. Kasahara H, etal., J Clin Invest. 2001 Jul;108(2):189-201.
16. Carboxyl terminus of Nkx2.5 impairs its interaction with p300. Li T, etal., J Mol Biol. 2007 Jul 27;370(5):976-92. Epub 2007 May 18.
17. Novel NKX2-5 mutations in patients with familial atrial septal defects. Liu XY, etal., Pediatr Cardiol. 2011 Feb;32(2):193-201. doi: 10.1007/s00246-010-9859-6. Epub 2010 Dec 25.
18. Cardiomyocyte differentiation of rat bone marrow multipotent progenitor cells is associated with downregulation of Oct-4 expression. Lu T, etal., Tissue Eng Part A. 2010 Oct;16(10):3111-7.
19. 17 beta-estradiol modulates expression of low-voltage-activated Ca(V)3.2 T-type calcium channel via extracellularly regulated kinase pathway in cardiomyocytes. Marni F, etal., Endocrinology. 2009 Feb;150(2):879-88. Epub 2008 Oct 1.
20. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
21. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
23. A novel stop mutation truncating critical regions of the cardiac transcription factor NKX2-5 in a large family with autosomal-dominant inherited congenital heart disease. Pabst S, etal., Clin Res Cardiol. 2008 Jan;97(1):39-42. Epub 2007 Sep 25.
24. Ventricular noncompaction and distal chromosome 5q deletion. Pauli RM, etal., Am J Med Genet 1999 Aug 6;85(4):419-23.
25. Novel and highly lethal NKX2.5 missense mutation in a family with sudden death and ventricular arrhythmia. Perera JL, etal., Pediatr Cardiol. 2014 Oct;35(7):1206-12. doi: 10.1007/s00246-014-0917-3. Epub 2014 Jun 1.
26. A novel NKX2.5 loss-of-function mutation associated with congenital bicuspid aortic valve. 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. Somatic NKX2-5 mutations as a novel mechanism of disease in complex congenital heart disease. Reamon-Buettner SM and Borlak J, J Med Genet. 2004 Sep;41(9):684-90.
28. GOA pipeline RGD automated data pipeline
29. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
31. Epistatic rescue of Nkx2.5 adult cardiac conduction disease phenotypes by prospero-related homeobox protein 1 and HDAC3. Risebro CA, etal., Circ Res. 2012 Jul 6;111(2):e19-31. doi: 10.1161/CIRCRESAHA.111.260695. Epub 2012 May 29.
32. Congenital heart disease caused by mutations in the transcription factor NKX2-5. Schott JJ, etal., Science. 1998 Jul 3;281(5373):108-11.
33. The ambiguous role of NKX2-5 mutations in thyroid dysgenesis. van Engelen K, etal., PLoS One. 2012;7(12):e52685. doi: 10.1371/journal.pone.0052685. Epub 2012 Dec 28.
34. Novel NKX2-5 mutations responsible for congenital heart disease. Wang J, etal., Genet Mol Res. 2011 Nov 29;10(4):2905-15. doi: 10.4238/2011.November.29.1.
35. A novel NKX2-5 mutation in familial ventricular septal defect. Wang J, etal., Int J Mol Med. 2011 Mar;27(3):369-75. doi: 10.3892/ijmm.2010.585. Epub 2010 Dec 16.
36. SIRT1 mediates the protective function of Nkx2.5 during stress in cardiomyocytes. Zheng W, etal., Basic Res Cardiol. 2013 Jul;108(4):364. doi: 10.1007/s00395-013-0364-y. Epub 2013 Jun 7.
37. Functional analyses of three Csx/Nkx-2.5 mutations that cause human congenital heart disease. 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
GRCr81016,844,888 - 16,851,458 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1016,848,582 - 16,851,452 (+)EnsemblGRCr8
mRatBN7.21016,340,428 - 16,347,004 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1016,344,159 - 16,346,934 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1021,093,028 - 21,095,888 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01020,581,977 - 20,584,837 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01016,071,642 - 16,074,502 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01016,635,989 - 16,638,758 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1016,635,989 - 16,638,764 (+)Ensemblrn6Rnor6.0
Rnor_5.01016,520,570 - 16,527,836 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41016,606,183 - 16,608,952 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1016,004,548 - 16,007,317 (+)NCBICelera
RGSC_v3.11016,607,231 - 16,610,001 (+)NCBI
Cytogenetic Map10q12NCBI
NKX2-5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385173,232,109 - 173,235,206 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5173,232,109 - 173,235,311 (-)Ensemblhg38GRCh38
GRCh375172,659,112 - 172,662,209 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365172,591,744 - 172,594,868 (-)NCBIBuild 36Build 36hg18NCBI36
Celera5168,692,473 - 168,695,681 (-)NCBICelera
Cytogenetic Map5q35.1NCBI
HuRef5167,754,405 - 167,757,613 (-)NCBIHuRef
CHM1_15172,091,589 - 172,094,797 (-)NCBICHM1_1
T2T-CHM13v2.05173,772,181 - 173,775,278 (-)NCBIT2T-CHM13v2.0
Nkx2-5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,057,638 - 27,063,962 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1727,057,638 - 27,063,983 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381726,838,664 - 26,844,988 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1726,838,664 - 26,845,009 (-)Ensemblmm10GRCm38
MGSCv371726,975,610 - 26,978,510 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361726,566,254 - 26,569,154 (-)NCBIMGSCv36mm8
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 (-)Ensembl
ChiLan1.0NW_00495540825,833,649 - 25,836,673 (-)NCBIChiLan1.0ChiLan1.0
NKX2-5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24168,367,607 - 168,372,490 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15166,507,149 - 166,512,032 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05168,584,197 - 168,589,406 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15175,492,288 - 175,495,514 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5175,492,288 - 175,495,514 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha439,189,667 - 39,192,973 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0439,612,560 - 39,618,296 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl439,614,913 - 39,618,296 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1439,432,539 - 39,435,856 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0439,621,539 - 39,624,869 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0440,130,495 - 40,133,809 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nkx2-5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721393,683,325 - 93,686,308 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366092,406,004 - 2,409,046 (+)EnsemblSpeTri2.0 Ensembl
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 - 51,089,162 (+)EnsemblsusScr11Sscrofa11.1
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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2375,391,847 - 75,395,205 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660343,212,995 - 3,216,184 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nkx2-5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473316,881,191 - 16,884,210 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473316,881,189 - 16,884,245 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Nkx2-5
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v194,615,250 - 4,618,109 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nkx2-5
21 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
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)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101576223019737486Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)101617552561175525Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat

Markers in Region
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
GRCr81016,851,307 - 16,851,458 (+)Marker Load Pipeline
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


Expression

RNA-SEQ Expression

appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
1 61 14 26 33 12 24 12 109 90 2 9 6 38 21

Sequence


Ensembl Acc Id: ENSRNOT00000028155   ⟹   ENSRNOP00000028155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1016,848,582 - 16,851,452 (+)Ensembl
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
GRCr81016,848,600 - 16,851,458 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81016,844,888 - 16,851,454 (+)NCBI
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  
Ensembl Protein ENSRNOP00000028155
GenBank Protein O35767 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_446103   ⟸   NM_053651
- UniProtKB: O35767 (UniProtKB/Swiss-Prot),   G3V8T2 (UniProtKB/TrEMBL),   A6HDD5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000028155   ⟸   ENSRNOT00000028155
RefSeq Acc Id: XP_038940950   ⟸   XM_039085022
- Peptide Label: isoform X1
- UniProtKB: O35767 (UniProtKB/Swiss-Prot),   G3V8T2 (UniProtKB/TrEMBL),   A6HDD5 (UniProtKB/TrEMBL)
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O35767-F1-model_v2 AlphaFold O35767 1-318 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620520 AgrOrtholog
BioCyc Gene G2FUF-25651 BioCyc
Ensembl Genes ENSRNOG00000020747 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000028155 ENTREZGENE
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Homeobox_metazoa UniProtKB/Swiss-Prot
  Homeobox_NK-like UniProtKB/Swiss-Prot
KEGG Report rno:114109 UniProtKB/Swiss-Prot
NCBI Gene 114109 ENTREZGENE
PANTHER HOMEOBOX PROTEIN NKX UniProtKB/Swiss-Prot
  PTHR24340:SF28 UniProtKB/Swiss-Prot
Pfam Homeodomain UniProtKB/Swiss-Prot
PhenoGen Nkx2-5 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000020747 RatGTEx
SMART HOX UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot
UniProt A6HDD5 ENTREZGENE, UniProtKB/TrEMBL
  G3V8T2 ENTREZGENE, 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