Nkx1-1 (NK1 homeobox 1) - Rat Genome Database

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Gene: Nkx1-1 (NK1 homeobox 1) Rattus norvegicus
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Symbol: Nkx1-1
Name: NK1 homeobox 1
RGD ID: 1564874
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in cell differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including nervous system process; regulation of generation of precursor metabolites and energy; and regulation of glucose metabolic process. Predicted to be active in nucleus. Orthologous to human NKX1-1 (NK1 homeobox 1); INTERACTS WITH bisphenol A; 4,4'-sulfonyldiphenol (ortholog); isoflurane (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC298981; NK1 transcription factor related, locus 1; NK1 transcription factor related, locus 1 (Drosophila); NK1 transcription factor-related protein 1; RGD1564874; similar to homeodomain protein Sax2
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
GRCr81481,521,206 - 81,524,788 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1481,521,220 - 81,524,566 (+)EnsemblGRCr8
mRatBN7.21477,296,676 - 77,300,575 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1477,296,796 - 77,300,036 (+)EnsemblmRatBN7.2
Rnor_6.01482,603,538 - 82,607,031 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1482,603,671 - 82,607,031 (+)Ensemblrn6Rnor6.0
Rnor_5.01483,287,754 - 83,291,039 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41483,216,329 - 83,219,569 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1476,215,871 - 76,219,364 (+)NCBICelera
Cytogenetic Map14q21NCBI
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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17879320   PMID:21126319  


Genomics

Comparative Map Data
Nkx1-1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81481,521,206 - 81,524,788 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1481,521,220 - 81,524,566 (+)EnsemblGRCr8
mRatBN7.21477,296,676 - 77,300,575 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1477,296,796 - 77,300,036 (+)EnsemblmRatBN7.2
Rnor_6.01482,603,538 - 82,607,031 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1482,603,671 - 82,607,031 (+)Ensemblrn6Rnor6.0
Rnor_5.01483,287,754 - 83,291,039 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41483,216,329 - 83,219,569 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1476,215,871 - 76,219,364 (+)NCBICelera
Cytogenetic Map14q21NCBI
NKX1-1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3841,402,932 - 1,406,442 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl41,402,932 - 1,406,442 (-)Ensemblhg38GRCh38
GRCh3741,396,720 - 1,400,230 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3641,380,072 - 1,392,453 (-)NCBIBuild 36Build 36hg18NCBI36
Celera41,324,669 - 1,339,840 (-)NCBICelera
Cytogenetic Map4p16.3NCBI
HuRef41,366,669 - 1,377,571 (-)NCBIHuRef
CHM1_141,396,490 - 1,400,000 (-)NCBICHM1_1
T2T-CHM13v2.041,401,206 - 1,404,716 (-)NCBIT2T-CHM13v2.0
Nkx1-1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39533,588,078 - 33,591,434 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl533,588,078 - 33,591,320 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38533,430,734 - 33,434,090 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl533,430,734 - 33,433,976 (-)Ensemblmm10GRCm38
MGSCv37533,773,383 - 33,776,625 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36533,773,383 - 33,776,625 (-)NCBIMGSCv36mm8
Celera530,909,910 - 30,913,492 (-)NCBICelera
Cytogenetic Map5B1NCBI
cM Map517.65NCBI
Nkx1-1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955514763,160 - 781,635 (-)Ensembl
ChiLan1.0NW_004955514763,160 - 781,635 (-)NCBIChiLan1.0ChiLan1.0
NKX1-1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v231,736,687 - 1,740,204 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan141,703,817 - 1,707,333 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v041,547,939 - 1,551,457 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.141,423,117 - 1,430,833 (-)NCBIPanPan1.1PanPan1.1panPan2
NKX1-1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1362,634,654 - 62,638,111 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl362,634,783 - 62,638,111 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha365,150,929 - 65,154,386 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0363,109,511 - 63,112,971 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl363,109,640 - 63,112,971 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1362,601,641 - 62,605,099 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0362,805,130 - 62,808,591 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0363,164,504 - 63,167,959 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nkx1-1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528568,207,850 - 68,209,154 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493647721,909,542 - 21,910,599 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NKX1-1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8608,098 - 611,859 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.18608,327 - 611,859 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
NKX1-1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12747,358,966 - 47,362,488 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2747,359,087 - 47,362,476 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366730614,442 - 17,435 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nkx1-1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475525,897,061 - 25,899,884 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475525,896,953 - 25,900,096 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Nkx1-1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11171,415,773 - 71,419,123 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nkx1-1
28 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:167
Count of miRNA genes:94
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000057911, ENSRNOT00000073177
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143802371083023710Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147764007196755654Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1477914838104348525Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143900944484009444Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147297021087582095Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143067446985041098Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147764007196755654Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143802371083023710Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1477640071100078267Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147764007196755654Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147764007196755654Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143802371083023710Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144261625899224555Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)146592028399224555Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143941117087582095Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143802371083023710Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
4 1 11 31 3 5 5 22 18 31 31 5

Sequence


Ensembl Acc Id: ENSRNOT00000073177   ⟹   ENSRNOP00000064746
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1481,521,220 - 81,524,566 (+)Ensembl
mRatBN7.2 Ensembl1477,296,796 - 77,300,036 (+)Ensembl
Rnor_6.0 Ensembl1482,603,671 - 82,607,031 (+)Ensembl
RefSeq Acc Id: XM_234082   ⟹   XP_234082
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81481,521,206 - 81,524,788 (+)NCBI
mRatBN7.21477,296,676 - 77,300,575 (+)NCBI
Rnor_6.01482,603,538 - 82,607,031 (+)NCBI
Rnor_5.01483,287,754 - 83,291,039 (+)NCBI
RGSC_v3.41483,216,329 - 83,219,569 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_234082 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064746
  ENSRNOP00000064746.3
RefSeq Acc Id: XP_234082   ⟸   XM_234082
- UniProtKB: M0R5R8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000064746   ⟸   ENSRNOT00000073177
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R5R8-F1-model_v2 AlphaFold M0R5R8 1-443 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:1564874 AgrOrtholog
BioCyc Gene G2FUF-15257 BioCyc
Ensembl Genes ENSRNOG00000005113 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073177 ENTREZGENE
  ENSRNOT00000073177.4 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox_CS UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
  Homeobox_NK-like UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
NCBI Gene 298981 ENTREZGENE
PANTHER HOMEOBOX PROTEIN NKX UniProtKB/TrEMBL
  NK1 TRANSCRIPTION FACTOR-RELATED PROTEIN 1 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Nkx1-1 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005113 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt M0R5R8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-14 Nkx1-1  NK1 homeobox 1  Nkx1-1  NK1 transcription factor related, locus 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-05 Nkx1-1  NK1 transcription factor related, locus 1 (Drosophila)  Nkx1-1  NK1 homeobox 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Nkx1-1  NK1 transcription factor related, locus 1 (Drosophila)  RGD1564874_predicted  similar to homeodomain protein Sax2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564874_predicted  similar to homeodomain protein Sax2 (predicted)  LOC298981  similar to homeodomain protein Sax2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC298981  similar to homeodomain protein Sax2      Symbol and Name status set to provisional 70820 PROVISIONAL