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 response to lipopolysaccharide. 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 4,4'-sulfonyldiphenol; acetylsalicylic acid; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8679,731,677 - 79,735,952 (-)NCBIGRCr8
mRatBN7.2673,996,601 - 74,001,483 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl673,996,601 - 73,999,791 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx674,392,972 - 74,396,162 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0674,699,372 - 74,702,565 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0674,126,847 - 74,130,040 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)
GABAergic neuron differentiation  (ISO)
gene expression  (IEA,ISO)
globus pallidus development  (IEA,ISO)
hippocampus development  (IEA,ISO)
hypothalamus development  (IEA,ISO)
interneuron migration  (IEA,ISO)
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 DNA-templated transcription  (ISO,ISS)
negative regulation of epithelial to mesenchymal transition  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of transforming growth factor beta receptor signaling pathway  (IEA,ISO)
neuron fate commitment  (ISO)
neuron migration  (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 DNA-templated transcription  (IDA,IMP,ISO)
positive regulation of gene expression  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IDA,IEA,IMP,ISO)
regulation of blood volume by renin-angiotensin  (IDA)
regulation of DNA-templated transcription  (IDA,ISO)
regulation of transcription by RNA polymerase II  (IBA,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)
transcription regulator complex  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mutations in TITF-1 are associated with benign hereditary chorea. Breedveld GJ, etal., Hum Mol Genet. 2002 Apr 15;11(8):971-9.
2. Leptin promotes fetal lung maturity and upregulates SP-A expression in pulmonary alveoli type-II epithelial cells involving TTF-1 activation. Chen H, etal., PLoS One. 2013 Jul 22;8(7):e69297. doi: 10.1371/journal.pone.0069297. Print 2013.
3. Nuclear factor of activated T cells regulates transcription of the surfactant protein D gene (Sftpd) via direct interaction with thyroid transcription factor-1 in lung epithelial cells. Dave V, etal., J Biol Chem. 2004 Aug 13;279(33):34578-88. Epub 2004 Jun 1.
4. Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain. Del Vecchio P, etal., Proteins. 2008 Feb 15;70(3):748-60.
5. The paired domain-containing factor Pax8 and the homeodomain-containing factor TTF-1 directly interact and synergistically activate transcription. Di Palma T, etal., J Biol Chem. 2003 Jan 31;278(5):3395-402. Epub 2002 Nov 18.
6. Nonsense mutation in TITF1 in a Portuguese family with benign hereditary chorea. do Carmo Costa M, etal., Neurogenetics. 2005 Dec;6(4):209-15. Epub 2005 Oct 12.
7. Trefoil peptide expression and goblet cell number in rat intestine: effects of KGF and fasting-refeeding. Fernandez-Estivariz C, etal., Am J Physiol Regul Integr Comp Physiol 2003 Feb;284(2):R564-73.
8. A novel NKX2.1 mutation in a family with hypothyroidism and benign hereditary chorea. Ferrara AM, etal., Thyroid. 2008 Sep;18(9):1005-9. doi: 10.1089/thy.2008.0085.
9. 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.
10. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
11. Thyroid nuclear factor 1 (TTF-1) contains a homeodomain and displays a novel DNA binding specificity. Guazzi S, etal., EMBO J 1990 Nov;9(11):3631-9.
12. Prepubertal chronic ethanol administration alters TTF-1 and Oct-2 expression in the hypothalamus of female rats. Kim HJ, etal., Brain Res Mol Brain Res. 2005 May 20;136(1-2):262-6.
13. TTF-1, a homeodomain-containing transcription factor, regulates feeding behavior in the rat hypothalamus. Kim JG, etal., Biochem Biophys Res Commun. 2006 Oct 27;349(3):969-75. Epub 2006 Sep 1.
14. Thyroid transcription factor-1 exhibits osmosensitive transcription in brain-derived cell lines. Kim JG, etal., Biochem Biophys Res Commun. 2008 Jun 6;370(3):468-72. Epub 2008 Apr 3.
15. Regulation of pituitary adenylate cyclase-activating polypeptide gene transcription by TTF-1, a homeodomain-containing transcription factor. Kim MS, etal., J Biol Chem 2002 Sep 27;277(39):36863-71.
16. Benign hereditary chorea, not only chorea: a family case presentation. Koht J, etal., Cerebellum Ataxias. 2016 Feb 2;3:3. doi: 10.1186/s40673-016-0041-7. eCollection 2016.
17. Benign hereditary chorea: dopaminergic brain imaging in patients with a novel intronic NKX2.1 gene mutation. Konishi T, etal., J Neurol. 2013 Jan;260(1):207-13. doi: 10.1007/s00415-012-6618-z. Epub 2012 Jul 24.
18. Choreoathetosis, hypothyroidism, and pulmonary alterations due to human NKX2-1 haploinsufficiency. Krude H, etal., J Clin Invest. 2002 Feb;109(4):475-80.
19. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
20. TTF-1, a homeodomain gene required for diencephalic morphogenesis, is postnatally expressed in the neuroendocrine brain in a developmentally regulated and cell-specific fashion. Lee BJ, etal., Mol Cell Neurosci. 2001 Jan;17(1):107-26.
21. Thyroid transcription factor 1, a homeodomain containing transcription factor, contributes to regulating periodic oscillations in GnRH gene expression. Matagne V, etal., J Neuroendocrinol. 2012 Jun;24(6):916-29. doi: 10.1111/j.1365-2826.2012.02302.x.
22. NKX2-1 mutation in a family diagnosed with ataxic dyskinetic cerebral palsy. 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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
24. The DNA glycosylase T:G mismatch-specific thymine DNA glycosylase represses thyroid transcription factor-1-activated transcription. Missero C, etal., J Biol Chem 2001 Sep 7;276(36):33569-75.
25. Multiple ras downstream pathways mediate functional repression of the homeobox gene product TTF-1. Missero C, etal., Mol Cell Biol. 2000 Apr;20(8):2783-93.
26. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Identification and functional characterization of a novel mutation in the NKX2-1 gene: comparison with the data in the literature. Nettore IC, etal., Thyroid. 2013 Jun;23(6):675-82. doi: 10.1089/thy.2012.0267.
28. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
29. TAZ interacts with TTF-1 and regulates expression of surfactant protein-C. Park KS, etal., J Biol Chem. 2004 Apr 23;279(17):17384-90. Epub 2004 Feb 17.
30. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
31. Expression and function of B7-1 and B7-2 in hapten-induced contact sensitivity. Reiser H and Schneeberger EE, Eur J Immunol. 1996 Apr;26(4):880-5.
32. GOA pipeline RGD automated data pipeline
33. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
34. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
35. TTF-1, a homeodomain-containing transcription factor, participates in the control of body fluid homeostasis by regulating angiotensinogen gene transcription in the rat subfornical organ. Son YJ, etal., J Biol Chem. 2003 Jul 18;278(29):27043-52. Epub 2003 May 2.
36. Impaired alveolar epithelial cell differentiation in the hypoplastic lung in nitrofen-induced congenital diaphragmatic hernia. Takayasu H, etal., Pediatr Surg Int. 2007 Jan 24;.
37. Structural and functional properties of the N transcriptional activation domain of thyroid transcription factor-1: similarities with the acidic activation domains. Tell G, etal., Biochem J. 1998 Jan 15;329 ( Pt 2):395-403.
38. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
39. Bacterial lipopolysaccharide stimulates the thyrotropin-dependent thyroglobulin gene expression at the transcriptional level by involving the transcription factors thyroid transcription factor-1 and paired box domain transcription factor 8. Velez ML, etal., Endocrinology. 2006 Jul;147(7):3260-75. Epub 2006 Apr 20.
40. TTF-2, a new forkhead protein, shows a temporal expression in the developing thyroid which is consistent with a role in controlling the onset of differentiation. Zannini M, etal., EMBO J 1997 Jun 2;16(11):3185-97.
41. Differential methylation hybridization array of endometrial cancers reveals two novel cancer-specific methylation markers. 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   PMID:33622350  


Genomics

Comparative Map Data
Nkx2-1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8679,731,677 - 79,735,952 (-)NCBIGRCr8
mRatBN7.2673,996,601 - 74,001,483 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl673,996,601 - 73,999,791 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx674,392,972 - 74,396,162 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0674,699,372 - 74,702,565 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0674,126,847 - 74,130,040 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381436,516,397 - 36,520,232 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1436,516,392 - 36,521,149 (-)EnsemblGRCh38hg38GRCh38
GRCh371436,985,602 - 36,989,437 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361436,055,353 - 36,059,167 (-)NCBINCBI36Build 36hg18NCBI36
Build 341436,055,352 - 36,058,654NCBI
Celera1416,849,149 - 16,852,977 (-)NCBICelera
Cytogenetic Map14q13.3NCBI
HuRef1417,100,276 - 17,104,039 (-)NCBIHuRef
CHM1_11436,984,732 - 36,988,564 (-)NCBICHM1_1
T2T-CHM13v2.01430,705,671 - 30,709,516 (-)NCBIT2T-CHM13v2.0
Nkx2-1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391256,578,741 - 56,583,570 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1256,578,743 - 56,583,693 (-)EnsemblGRCm39 Ensembl
GRCm381256,531,935 - 56,536,908 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1256,531,958 - 56,536,908 (-)EnsemblGRCm38mm10GRCm38
MGSCv371257,632,922 - 57,637,895 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361257,449,970 - 57,454,920 (-)NCBIMGSCv36mm8
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
LOC100983103
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21537,786,124 - 37,826,698 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11437,002,629 - 37,043,203 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01417,224,870 - 17,273,252 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11435,403,557 - 35,627,438 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1435,404,127 - 35,626,722 (-)Ensemblpanpan1.1panPan2
NKX2-1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha814,886,591 - 14,888,646 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0815,197,690 - 15,202,516 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl815,197,699 - 15,201,982 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1814,896,830 - 14,898,885 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0814,963,572 - 14,965,627 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0815,253,618 - 15,255,673 (-)NCBIUU_Cfam_GSD_1.0
Nkx2-1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864047,011,599 - 47,015,298 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649410,517,488 - 10,520,566 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2413,310,846 - 13,317,056 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660532,266,777 - 2,311,899 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nkx2-1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624838300,458 - 305,517 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624838300,902 - 304,944 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nkx2-1
18 total Variants
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.


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 25140.003urine total 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 8urine total 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

Markers in Region
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


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


RefSeq Acc Id: ENSRNOT00000011453   ⟹   ENSRNOP00000011453
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
GRCr8679,731,677 - 79,734,867 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8679,731,709 - 79,735,118 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8679,731,709 - 79,735,952 (-)NCBI
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_039111813   ⟹   XP_038967741
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8679,731,709 - 79,734,488 (-)NCBI
mRatBN7.2673,997,506 - 73,999,412 (-)NCBI
RefSeq Acc Id: NP_037225   ⟸   NM_013093
- UniProtKB: G3V740 (UniProtKB/TrEMBL),   A6HBN7 (UniProtKB/TrEMBL),   A0A060PW62 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240179   ⟸   XM_006240117
- Peptide Label: isoform X2
- UniProtKB: A0A060PW62 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240178   ⟸   XM_006240116
- Peptide Label: isoform X1
- UniProtKB: A0A060PW62 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011453   ⟸   ENSRNOT00000011453
RefSeq Acc Id: XP_038967741   ⟸   XM_039111813
- Peptide Label: isoform X3
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P23441-F1-model_v2 AlphaFold P23441 1-372 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:3866 AgrOrtholog
BioCyc Gene G2FUF-37436 BioCyc
Ensembl Genes ENSRNOG00000008644 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00055013596 UniProtKB/Swiss-Prot
  ENSRNOG00060021194 UniProtKB/Swiss-Prot
  ENSRNOG00065005186 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011453 ENTREZGENE
  ENSRNOT00000011453.6 UniProtKB/TrEMBL
  ENSRNOT00055023308 UniProtKB/Swiss-Prot
  ENSRNOT00060036719 UniProtKB/Swiss-Prot
  ENSRNOT00065007618 UniProtKB/Swiss-Prot
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, 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
PANTHER HOMEOBOX PROTEIN NKX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX PROTEIN NKX-2.1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
RatGTEx ENSRNOG00000008644 RatGTEx
  ENSRNOG00055013596 RatGTEx
  ENSRNOG00060021194 RatGTEx
  ENSRNOG00065005186 RatGTEx
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC209572
UniProt A0A060PW62 ENTREZGENE, UniProtKB/TrEMBL
  A6HBN7 ENTREZGENE, 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