Nkx2-6 (NK2 homeobox 6) - Rat Genome Database

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Gene: Nkx2-6 (NK2 homeobox 6) Rattus norvegicus
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Symbol: Nkx2-6
Name: NK2 homeobox 6
RGD ID: 1306149
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including heart development; hypothalamus development; and tongue development. Predicted to act upstream of or within several processes, including negative regulation of epithelial cell apoptotic process; pharyngeal system development; and positive regulation of epithelial cell proliferation. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in familial atrial fibrillation and ventricular septal defect. Orthologous to human NKX2-6 (NK2 homeobox 6); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: homeobox protein Nkx-2.6; LOC364418; MGC188338; NK2 transcription factor related, locus 6; NK2 transcription factor related, locus 6 (Drosophila)
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
GRCr81550,852,965 - 50,857,060 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1550,852,646 - 50,857,059 (+)EnsemblGRCr8
mRatBN7.21544,443,151 - 44,447,248 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1544,443,101 - 44,447,247 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1548,561,087 - 48,565,185 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01549,672,576 - 49,676,672 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01546,531,915 - 46,536,011 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01551,034,620 - 51,038,715 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1551,034,620 - 51,038,704 (+)Ensemblrn6Rnor6.0
Rnor_5.01554,764,663 - 54,768,758 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41549,712,260 - 49,716,355 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1544,129,112 - 44,133,203 (+)NCBICelera
RGSC_v3.11549,727,628 - 49,731,457 (+)NCBI
Cytogenetic Map15p11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,IEA)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Common arterial trunk associated with a homeodomain mutation of NKX2.6. Heathcote K, etal., Hum Mol Genet. 2005 Mar 1;14(5):585-93. doi: 10.1093/hmg/ddi055. Epub 2005 Jan 13.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. NKX2-6 mutation predisposes to familial atrial fibrillation. Wang J, etal., Int J Mol Med. 2014 Dec;34(6):1581-90. doi: 10.3892/ijmm.2014.1971. Epub 2014 Oct 16.
8. A novel NKX2.6 mutation associated with congenital ventricular septal defect. Wang J, etal., Pediatr Cardiol. 2015 Mar;36(3):646-56. doi: 10.1007/s00246-014-1060-x. Epub 2014 Nov 8.
Additional References at PubMed
PMID:9486544   PMID:9545560   PMID:9621431   PMID:11390666   PMID:12477932  


Genomics

Comparative Map Data
Nkx2-6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81550,852,965 - 50,857,060 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1550,852,646 - 50,857,059 (+)EnsemblGRCr8
mRatBN7.21544,443,151 - 44,447,248 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1544,443,101 - 44,447,247 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1548,561,087 - 48,565,185 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01549,672,576 - 49,676,672 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01546,531,915 - 46,536,011 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01551,034,620 - 51,038,715 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1551,034,620 - 51,038,704 (+)Ensemblrn6Rnor6.0
Rnor_5.01554,764,663 - 54,768,758 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41549,712,260 - 49,716,355 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1544,129,112 - 44,133,203 (+)NCBICelera
RGSC_v3.11549,727,628 - 49,731,457 (+)NCBI
Cytogenetic Map15p11NCBI
NKX2-6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38823,701,740 - 23,706,756 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl823,701,740 - 23,706,756 (-)Ensemblhg38GRCh38
GRCh37823,559,253 - 23,564,269 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36823,615,909 - 23,621,070 (-)NCBIBuild 36Build 36hg18NCBI36
Celera822,523,400 - 22,527,359 (-)NCBICelera
Cytogenetic Map8p21.2NCBI
HuRef822,105,267 - 22,109,415 (-)NCBIHuRef
CHM1_1823,762,157 - 23,766,304 (-)NCBICHM1_1
T2T-CHM13v2.0823,976,698 - 23,981,714 (-)NCBIT2T-CHM13v2.0
Nkx2-6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391469,409,251 - 69,412,989 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1469,409,251 - 69,412,967 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381469,171,802 - 69,175,540 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1469,171,802 - 69,175,518 (+)Ensemblmm10GRCm38
MGSCv371469,790,076 - 69,793,597 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361468,125,349 - 68,128,870 (+)NCBIMGSCv36mm8
Celera1466,952,443 - 66,955,964 (+)NCBICelera
Cytogenetic Map14D2NCBI
cM Map1436.01NCBI
Nkx2-6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540346,831,696 - 46,836,333 (-)Ensembl
ChiLan1.0NW_00495540346,831,758 - 46,836,358 (-)NCBIChiLan1.0ChiLan1.0
NKX2-6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2742,204,403 - 42,211,662 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1817,931,511 - 17,938,767 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0822,949,843 - 22,955,391 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1819,884,480 - 19,888,643 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl819,884,480 - 19,888,643 (-)EnsemblpanPan2panpan1.1
NKX2-6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12533,781,294 - 33,787,460 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2533,781,249 - 33,785,761 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2534,370,107 - 34,374,138 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02533,988,361 - 33,992,399 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2533,988,510 - 33,992,399 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12533,935,492 - 33,939,530 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02533,789,519 - 33,793,555 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02533,944,503 - 33,948,541 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nkx2-6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494311,455,615 - 11,458,881 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365557,111,678 - 7,114,944 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365557,111,678 - 7,114,944 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NKX2-6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl147,811,200 - 7,815,645 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1147,811,200 - 7,815,553 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2148,654,370 - 8,658,776 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NKX2-6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1821,820,940 - 21,827,124 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl821,821,711 - 21,825,801 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605220,394,928 - 20,400,623 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nkx2-6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475818,911,010 - 18,914,001 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475818,908,988 - 18,914,794 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Nkx2-6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11254,955,203 - 54,959,513 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nkx2-6
32 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:64
Interacting mature miRNAs:73
Transcripts:ENSRNOT00000032826
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1544806773104695021Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)154367724488677244Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)154367724488677244Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154046315285463152Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)154367724488677244Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154480677352597086Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)154367724488677244Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154446544756583797Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)154367724488677244Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
1 19 20 6 7 1 7 1 36 26 20 8 26 6 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000032826   ⟹   ENSRNOP00000034838
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1550,852,646 - 50,857,059 (+)Ensembl
mRatBN7.2 Ensembl1544,443,101 - 44,447,247 (+)Ensembl
Rnor_6.0 Ensembl1551,034,620 - 51,038,704 (+)Ensembl
RefSeq Acc Id: NM_001127653   ⟹   NP_001121125
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81550,852,965 - 50,857,060 (+)NCBI
mRatBN7.21544,443,151 - 44,447,248 (+)NCBI
Rnor_6.01551,034,620 - 51,038,715 (+)NCBI
Rnor_5.01554,764,663 - 54,768,758 (+)NCBI
RGSC_v3.41549,712,260 - 49,716,355 (+)RGD
Celera1544,129,112 - 44,133,203 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001121125 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI60896 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034838.6
RefSeq Acc Id: NP_001121125   ⟸   NM_001127653
- UniProtKB: B1H280 (UniProtKB/TrEMBL),   F7EZF0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000034838   ⟸   ENSRNOT00000032826

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1H280-F1-model_v2 AlphaFold B1H280 1-213 view protein structure

Transcriptome

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

Promoters
RGD ID:13699794
Promoter ID:EPDNEW_R10318
Type:single initiation site
Name:Nkx2-6_1
Description:NK2 homeobox 6
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01551,034,596 - 51,034,656EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306149 AgrOrtholog
BioCyc Gene G2FUF-13270 BioCyc
Ensembl Genes ENSRNOG00000021910 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032826.7 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7453070 IMAGE-MGC_LOAD
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_NK-like UniProtKB/TrEMBL
  Homeobox_region UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:364418 UniProtKB/TrEMBL
MGC_CLONE MGC:188338 IMAGE-MGC_LOAD
NCBI Gene 364418 ENTREZGENE
PANTHER HOMEOBOX PROTEIN NKX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN NKX-2.6 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Nkx2-6 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021910 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt B1H280 ENTREZGENE, UniProtKB/TrEMBL
  F7EZF0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Nkx2-6  NK2 homeobox 6  Nkx2-6  NK2 transcription factor related, locus 6 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Nkx2-6  NK2 transcription factor related, locus 6 (Drosophila)   Nkx2-6_predicted  NK2 transcription factor related, locus 6 (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nkx2-6_predicted  NK2 transcription factor related, locus 6 (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED