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
Black 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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3154,967,598 - 154,969,917 (-)EnsemblGRCr8
mRatBN7.23134,514,368 - 134,517,243 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3134,515,039 - 134,516,505 (-)EnsemblmRatBN7.2
Rnor_6.03141,303,341 - 141,305,489 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3141,304,005 - 141,305,471 (-)Ensemblrn6Rnor6.0
Rnor_5.03147,721,612 - 147,723,156 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43135,729,476 - 135,731,300 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3133,377,533 - 133,379,681 (-)NCBICelera
RGSC_v3.13135,634,855 - 135,636,873 (-)NCBI
Cytogenetic Map3q41NCBI
JBrowse:




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

Genomics

Comparative Map Data
Nkx2-4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83154,968,252 - 154,970,300 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3154,967,598 - 154,969,917 (-)EnsemblGRCr8
mRatBN7.23134,514,368 - 134,517,243 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3134,515,039 - 134,516,505 (-)EnsemblmRatBN7.2
Rnor_6.03141,303,341 - 141,305,489 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3141,304,005 - 141,305,471 (-)Ensemblrn6Rnor6.0
Rnor_5.03147,721,612 - 147,723,156 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43135,729,476 - 135,731,300 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3133,377,533 - 133,379,681 (-)NCBICelera
RGSC_v3.13135,634,855 - 135,636,873 (-)NCBI
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 (-)Ensemblhg38GRCh38
GRCh372021,376,003 - 21,378,164 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362021,324,005 - 21,326,047 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm382147,083,337 - 147,085,439 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2147,083,316 - 147,085,445 (-)Ensemblmm10GRCm38
MGSCv372146,909,612 - 146,911,081 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha242,063,214 - 2,064,662 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0242,442,402 - 2,443,857 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_Cfam_GSD_1.0
NKX2-4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1729,199,618 - 29,201,133 (-)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474121,769,147 - 21,775,554 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Nkx2-4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v15126,680,045 - 126,681,588 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Nkx2-4
11 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3141555229186555229Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141555229186555229Rat
1582233Insul10Insulin level QTL 105.40.0015blood insulin amount (VT:0001560)serum insulin level times blood glucose level (CMO:0002040)3133259579178259579Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3141555229186555229Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3141555229186555229Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3129154923182114333Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3141555229186555229Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3141555229186555229Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3133134628178134628Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3141508991166376254Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)3112250810157250810Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3142898802187898802Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)3145335553189428310Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3117537367162537367Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3125116475170116475Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3110225882155225882Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3136091420155634702Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3139299381184299381Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3122395989167395989Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3141508991177728348Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)3131036586176036586Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3137114333182114333Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)3131036586176036586Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)398651826167012663Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3110634702155634702Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3141555229186555229Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3116188400161188400Rat

Markers in Region
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
2 4 63 11 4 2 4 2 1 22 13 60 5 44 2 2 2

Sequence


Ensembl Acc Id: ENSRNOT00000016915   ⟹   ENSRNOP00000016915
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3154,967,598 - 154,969,917 (-)Ensembl
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 Sequences
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)
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTX2-F1-model_v2 AlphaFold D3ZTX2 1-353 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:1304985 AgrOrtholog
BioCyc Gene G2FUF-47556 BioCyc
Ensembl Genes ENSRNOG00000012647 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016915 ENTREZGENE
  ENSRNOT00000016915.6 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


Nomenclature History
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