Nkx2-4 (NK2 homeobox 4) - Rat Genome Database

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Gene: Nkx2-4 (NK2 homeobox 4) Rattus norvegicus
Analyze
Symbol: Nkx2-4
Name: NK2 homeobox 4
RGD ID: 1304985
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 be active in nucleus. Orthologous to human NKX2-4 (NK2 homeobox 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; gentamycin; indole-3-methanol.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: homeobox protein Nkx-2.4; LOC366213; NK2 transcription factor related, locus 4; NK2 transcription factor related, locus 4 (Drosophila)
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83154,968,252 - 154,970,300 (-)NCBIGRCr8
mRatBN7.23134,514,368 - 134,517,243 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3134,515,039 - 134,516,505 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.03141,303,341 - 141,305,489 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3141,304,005 - 141,305,471 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03147,721,612 - 147,723,156 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43135,729,476 - 135,731,300 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13135,634,855 - 135,636,873 (-)NCBI
Celera3133,377,533 - 133,379,681 (-)NCBICelera
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Nkx2-4Ratfamilial hyperinsulinemic hypoglycemia 1  ISONKX2-4 (Homo sapiens)8554872ClinVar Annotator: match by term: Hyperinsulinemic hypoglycemia more ...ClinVarPMID:38605124

1 to 20 of 22 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Nkx2-4Rat1,2-dimethylhydrazine decreases expressionISONkx2-4 (Mus musculus)64804641 and 2-Dimethylhydrazine results in decreased expression of NKX2-4 mRNACTDPMID:22206623
Nkx2-4Rat2,3,7,8-tetrachlorodibenzodioxine affects expressionISONkx2-4 (Mus musculus)6480464Tetrachlorodibenzodioxin affects the expression of NKX2-4 mRNACTDPMID:24058054
Nkx2-4Rat2,3,7,8-tetrachlorodibenzodioxine increases expressionEXP 6480464Tetrachlorodibenzodioxin results in increased expression of NKX2-4 mRNACTDPMID:33387578
Nkx2-4Rataflatoxin B1 decreases methylationISONKX2-4 (Homo sapiens)6480464Aflatoxin B1 results in decreased methylation of NKX2-4 geneCTDPMID:27153756
Nkx2-4Ratall-trans-retinoic acid multiple interactionsISONkx2-4 (Mus musculus)6480464[mono-(2-ethylhexyl)phthalate co-treated with Tretinoin] results in increased expression of NKX2-4 mRNACTDPMID:36189433
Nkx2-4Ratbenzo[a]pyrene decreases methylationISONKX2-4 (Homo sapiens)6480464Benzo(a)pyrene results in decreased methylation of NKX2-4 promoterCTDPMID:27901495
Nkx2-4Ratbis(2-ethylhexyl) phthalate increases expressionISONkx2-4 (Mus musculus)6480464Diethylhexyl Phthalate results in increased expression of NKX2-4 mRNACTDPMID:34319233
Nkx2-4Ratbisphenol A decreases methylationISONkx2-4 (Mus musculus)6480464bisphenol A results in decreased methylation of NKX2-4 promoterCTDPMID:27312807
Nkx2-4Ratbisphenol A affects methylationISONkx2-4 (Mus musculus)6480464bisphenol A affects the methylation of NKX2-4 promoterCTDPMID:27334623
Nkx2-4Ratbutanal increases expressionISONKX2-4 (Homo sapiens)6480464butyraldehyde results in increased expression of NKX2-4 mRNACTDPMID:26079696
Nkx2-4Ratcadmium atom increases expressionISONKX2-4 (Homo sapiens)6480464Cadmium results in increased expression of NKX2-4 mRNACTDPMID:24376830
Nkx2-4Ratchlorpyrifos increases expressionISONkx2-4 (Mus musculus)6480464Chlorpyrifos results in increased expression of NKX2-4 mRNACTDPMID:32715474
Nkx2-4RatFR900359 increases phosphorylationISONKX2-4 (Homo sapiens)6480464FR900359 results in increased phosphorylation of NKX2-4 proteinCTDPMID:37730182
Nkx2-4Ratgentamycin increases expressionEXP 6480464Gentamicins results in increased expression of NKX2-4 mRNACTDPMID:33387578
Nkx2-4Ratindole-3-methanol multiple interactionsEXP 6480464[indole-3-carbinol co-treated with Diethylnitrosamine] results in increased expression of NKX2-4 mRNACTDPMID:22129741
Nkx2-4Ratmono(2-ethylhexyl) phthalate multiple interactionsISONkx2-4 (Mus musculus)6480464[mono-(2-ethylhexyl)phthalate co-treated with Tretinoin] results in increased expression of NKX2-4 mRNACTDPMID:36189433
Nkx2-4RatN-nitrosodiethylamine multiple interactionsEXP 6480464[indole-3-carbinol co-treated with Diethylnitrosamine] results in increased expression of NKX2-4 mRNACTDPMID:22129741
Nkx2-4Ratparacetamol increases expressionEXP 6480464Acetaminophen results in increased expression of NKX2-4 mRNACTDPMID:33387578
Nkx2-4Ratpotassium dichromate increases expressionISONkx2-4 (Mus musculus)6480464Potassium Dichromate results in increased expression of NKX2-4 mRNACTDPMID:23608068
Nkx2-4Rattitanium dioxide increases methylationISONkx2-4 (Mus musculus)6480464titanium dioxide results in increased methylation of NKX2-4 geneCTDPMID:35295148

1 to 20 of 22 rows

Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Nkx2-4Ratbiological_process  ND 159840711/2009: no relevant rat dataRGD 
Nkx2-4Ratcell differentiation involved_inIBAFB:FBgn0000576 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Nkx2-4Ratregulation of DNA-templated transcription involved_inIEAInterPro:IPR0179701600115GO_REF:0000002InterProGO_REF:0000002
Nkx2-4Ratregulation of transcription by RNA polymerase II involved_inIBAFB:FBgn0002941 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Nkx2-4Ratnucleus is_active_inIBAFB:FBgn0000576 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Nkx2-4Ratnucleus located_inIEAUniProtKB-SubCell:SL-01911600115GO_REF:0000044UniProtGO_REF:0000044
Nkx2-4Ratnucleus located_inIEAUniProtKB-KW:KW-05391600115GO_REF:0000043UniProtGO_REF:0000043
Nkx2-4Ratnucleus located_inIEAUniRule:UR0004010371600115GO_REF:0000104UniProtGO_REF:0000104

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Nkx2-4RatDNA binding enablesIEAInterPro:IPR001356 and InterPro:IPR0204791600115GO_REF:0000002InterProGO_REF:0000002
Nkx2-4RatDNA binding enablesIEAUniRule:UR0004010371600115GO_REF:0000104UniProtGO_REF:0000104
Nkx2-4RatDNA binding enablesIEAUniProtKB-KW:KW-0238 and UniProtKB-KW:KW-03711600115GO_REF:0000043UniProtGO_REF:0000043
Nkx2-4RatDNA-binding transcription factor activity, RNA polymerase II-specific enablesIEAInterPro:IPR0179701600115GO_REF:0000002InterProGO_REF:0000002
Nkx2-4RatDNA-binding transcription factor activity, RNA polymerase II-specific enablesIBAFB:FBgn0004110 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033
Nkx2-4Ratprotein binding enablesISONKX2-4 (Homo sapiens)1624291UniProtKB:A8MTQ0 and PMID:32296183RGDPMID:32296183
Nkx2-4RatRNA polymerase II cis-regulatory region sequence-specific DNA binding enablesIBAFB:FBgn0000576 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033


#
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Comprehensive gene review and curation RGD comprehensive gene curation


Nkx2-4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83154,968,252 - 154,970,300 (-)NCBIGRCr8
mRatBN7.23134,514,368 - 134,517,243 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3134,515,039 - 134,516,505 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.03141,303,341 - 141,305,489 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3141,304,005 - 141,305,471 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03147,721,612 - 147,723,156 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43135,729,476 - 135,731,300 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13135,634,855 - 135,636,873 (-)NCBI
Celera3133,377,533 - 133,379,681 (-)NCBICelera
Cytogenetic Map3q41NCBI
NKX2-4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382021,395,365 - 21,397,526 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2021,395,365 - 21,397,526 (-)EnsemblGRCh38hg38GRCh38
GRCh372021,376,003 - 21,378,164 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362021,324,005 - 21,326,047 (-)NCBINCBI36Build 36hg18NCBI36
Celera2021,449,893 - 21,451,935 (-)NCBICelera
Cytogenetic Map20p11.22NCBI
HuRef2021,338,230 - 21,340,272 (-)NCBIHuRef
CHM1_12021,375,999 - 21,378,041 (-)NCBICHM1_1
T2T-CHM13v2.02021,452,023 - 21,454,184 (-)NCBIT2T-CHM13v2.0
Nkx2-4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392146,925,257 - 146,927,359 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2146,925,236 - 146,927,365 (-)EnsemblGRCm39 Ensembl
GRCm382147,083,337 - 147,085,439 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2147,083,316 - 147,085,445 (-)EnsemblGRCm38mm10GRCm38
MGSCv372146,909,612 - 146,911,081 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362146,775,317 - 146,776,786 (-)NCBIMGSCv36mm8
Celera2148,339,230 - 148,340,420 (-)NCBICelera
Cytogenetic Map2G2NCBI
cM Map272.63NCBI
NKX2-4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22122,283,750 - 22,302,727 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12022,280,586 - 22,283,157 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02021,352,472 - 21,356,074 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
NKX2-4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1242,034,963 - 2,036,434 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl242,035,811 - 2,036,434 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha242,063,214 - 2,064,662 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0242,442,402 - 2,443,857 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl242,442,425 - 2,443,857 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1242,039,433 - 2,040,875 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0242,142,783 - 2,144,244 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0242,419,729 - 2,421,179 (+)NCBIUU_Cfam_GSD_1.0
NKX2-4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1729,199,618 - 29,201,133 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11729,197,669 - 29,201,298 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21733,152,101 - 33,153,221 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NKX2-4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1250,374,867 - 50,381,509 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl250,380,003 - 50,381,490 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660785,178,874 - 5,180,825 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nkx2-4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474121,774,115 - 21,775,554 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474121,769,147 - 21,775,554 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

.

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Variants in Nkx2-4
6 total Variants

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:43
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000016915
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.


1 to 10 of 33 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat

1 to 10 of 33 rows
RH143254  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23134,516,652 - 134,516,922 (+)MAPPERmRatBN7.2
Rnor_6.03141,305,619 - 141,305,888NCBIRnor6.0
Rnor_5.03147,723,291 - 147,723,560UniSTSRnor5.0
RGSC_v3.43135,731,448 - 135,731,717UniSTSRGSC3.4
Celera3133,379,811 - 133,380,080UniSTS
RH 3.4 Map31094.9UniSTS
Cytogenetic Map3q41UniSTS
Nkx2-4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23134,515,046 - 134,515,395 (+)MAPPERmRatBN7.2
Rnor_6.03141,304,013 - 141,304,361NCBIRnor6.0
Rnor_5.03147,721,685 - 147,722,033UniSTSRnor5.0
RGSC_v3.43135,729,842 - 135,730,190UniSTSRGSC3.4
Celera3133,378,205 - 133,378,553UniSTS
Cytogenetic Map3q41UniSTS




alimentary part of gastrointestinal system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
2 59 11 4 2 1 2 1 10 6 54 41 2



Ensembl Acc Id: ENSRNOT00000016915   ⟹   ENSRNOP00000016915
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3134,515,039 - 134,516,505 (-)Ensembl
Rnor_6.0 Ensembl3141,304,005 - 141,305,471 (-)Ensembl
RefSeq Acc Id: XM_039106629   ⟹   XP_038962557
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83154,968,252 - 154,970,300 (-)NCBI
mRatBN7.23134,514,368 - 134,517,243 (-)NCBI
Protein RefSeqs XP_038962557 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL95117 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016915
  ENSRNOP00000016915.3
Ensembl Acc Id: ENSRNOP00000016915   ⟸   ENSRNOT00000016915
RefSeq Acc Id: XP_038962557   ⟸   XM_039106629
- UniProtKB: D3ZTX2 (UniProtKB/TrEMBL)
Homeobox

Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTX2-F1-model_v2 AlphaFold D3ZTX2 1-353 view protein structure


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



1 to 22 of 22 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-47556 BioCyc
Ensembl Genes ENSRNOG00000012647 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016915 ENTREZGENE
  ENSRNOT00000016915.5 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
  Homeobox_NK-like UniProtKB/TrEMBL
NCBI Gene 366213 ENTREZGENE
PANTHER HOMEOBOX PROTEIN NKX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN NKX-2.4 UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/TrEMBL
PhenoGen Nkx2-4 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012647 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt D3ZTX2 ENTREZGENE, UniProtKB/TrEMBL
1 to 22 of 22 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Nkx2-4  NK2 homeobox 4  Nkx2-4  NK2 transcription factor related, locus 4 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Nkx2-4  NK2 transcription factor related, locus 4 (Drosophila)   Nkx2-4_predicted  NK2 transcription factor related, locus 4 (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nkx2-4_predicted  NK2 transcription factor related, locus 4 (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED