Nkx3-2 (NK3 homeobox 2) - Rat Genome Database
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Gene: Nkx3-2 (NK3 homeobox 2) Mus musculus
Analyze
Symbol: Nkx3-2
Name: NK3 homeobox 2
RGD ID: 1621641
MGI Page MGI
Description: Exhibits DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including animal organ development; intestinal epithelial cell development; and negative regulation of chondrocyte differentiation. Predicted to localize to nucleus. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and limb. Orthologous to human NKX3-2 (NK3 homeobox 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: bagpipe homeobox gene 1 homolog; bagpipe homeobox protein homolog 1; Bap; Bapx1; homeobox protein NK-3 homolog B; homeobox protein Nkx-3.2; homeodomain protein Nkx-3.2; Nkx-3.; Nkx-3.2; NKX3.2
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39541,918,826 - 41,921,563 (-)NCBIGRCm39mm39
GRCm39 Ensembl541,918,826 - 41,921,844 (-)Ensembl
GRCm38541,761,483 - 41,764,220 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl541,761,483 - 41,764,501 (-)EnsemblGRCm38mm10GRCm38
MGSCv37542,152,722 - 42,155,459 (-)NCBIGRCm37mm9NCBIm37
MGSCv36542,049,696 - 42,052,468 (-)NCBImm8
Celera539,220,946 - 39,223,683 (-)NCBICelera
Cytogenetic Map5B3NCBI
cM Map522.58NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal axial skeleton morphology  (IAGP)
abnormal basicranium morphology  (IAGP)
abnormal basioccipital bone morphology  (IAGP)
abnormal basisphenoid bone morphology  (IAGP)
abnormal bone ossification  (IAGP)
abnormal cartilage development  (IAGP)
abnormal cartilage morphology  (IAGP)
abnormal cervical atlas morphology  (IAGP)
abnormal cervical axis morphology  (IAGP)
abnormal cervical vertebrae morphology  (IAGP)
abnormal craniofacial bone morphology  (IAGP)
abnormal cranium morphology  (IAGP)
abnormal digestive organ placement  (IAGP)
abnormal digestive system development  (IAGP)
abnormal digestive system morphology  (IAGP)
abnormal enteric neuron morphology  (IAGP)
abnormal enterocyte proliferation  (IAGP)
abnormal exoccipital bone morphology  (IAGP)
abnormal forestomach-glandular stomach junction morphology  (IAGP)
abnormal gastric parietal cell morphology  (IAGP)
abnormal hyoid bone body morphology  (IAGP)
abnormal intervertebral disk morphology  (IAGP)
abnormal intestinal enteroendocrine cell morphology  (IAGP)
abnormal intestinal goblet cell morphology  (IAGP)
abnormal intestinal smooth muscle morphology  (IAGP)
abnormal intestine development  (IAGP)
abnormal intestine physiology  (IAGP)
abnormal left-right axis patterning  (IAGP)
abnormal lumbar vertebrae morphology  (IAGP)
abnormal malleus morphology  (IAGP)
abnormal middle ear morphology  (IAGP)
abnormal middle ear ossicle morphology  (IAGP)
abnormal neurocranium morphology  (IAGP)
abnormal notochord morphology  (IAGP)
abnormal odontoid process morphology  (IAGP)
abnormal pancreas development  (IAGP)
abnormal rib morphology  (IAGP)
abnormal sclerotome morphology  (IAGP)
abnormal skeleton morphology  (IAGP)
abnormal stomach epithelium morphology  (IAGP)
abnormal stomach glandular epithelium morphology  (IAGP)
abnormal stomach morphology  (IAGP)
abnormal stomach pyloric region morphology  (IAGP)
abnormal stomach smooth muscle circular layer morphology  (IAGP)
abnormal supraoccipital bone morphology  (IAGP)
abnormal thoracic cavity morphology  (IAGP)
abnormal thoracic vertebrae morphology  (IAGP)
abnormal tympanic ring morphology  (IAGP)
abnormal vertebrae development  (IAGP)
abnormal vertebrae morphology  (IAGP)
abnormal vertebral arch development  (IAGP)
abnormal vertebral arch morphology  (IAGP)
abnormal vertebral body development  (IAGP)
abnormal vertebral body morphology  (IAGP)
abnormal vertebral column morphology  (IAGP)
absent arcus anterior  (IAGP)
absent basioccipital bone  (IAGP)
absent basisphenoid bone  (IAGP)
absent gonial bone  (IAGP)
absent intervertebral disk  (IAGP)
absent spleen  (IAGP)
absent supraoccipital bone  (IAGP)
absent ventral tubercle of atlas  (IAGP)
absent vertebral body  (IAGP)
axial skeleton hypoplasia  (IAGP)
barrel chest  (IAGP)
basioccipital bone hypoplasia  (IAGP)
basisphenoid bone hypoplasia  (IAGP)
decreased body height  (IAGP)
decreased body length  (IAGP)
decreased cell proliferation  (IAGP)
gonial bone hypoplasia  (IAGP)
kinked tail  (IAGP)
lethality throughout fetal growth and development, complete penetrance  (IAGP)
neonatal lethality, complete penetrance  (IAGP)
no abnormal phenotype detected  (IAGP)
perinatal lethality, complete penetrance  (IAGP)
persistence of notochord tissue  (IAGP)
respiratory distress  (IAGP)
short tail  (IAGP)
short vertebral column  (IAGP)
small basioccipital bone  (IAGP)
small basisphenoid bone  (IAGP)
small caudal vertebrae  (IAGP)
small exoccipital bone  (IAGP)
small forestomach  (IAGP)
small stomach  (IAGP)
small vertebrae  (IAGP)
thick tail  (IAGP)
vertebral body hypoplasia  (IAGP)
vertebral compression  (IAGP)
References

Additional References at PubMed
PMID:9256352   PMID:9271676   PMID:9271679   PMID:9344671   PMID:9621431   PMID:10449756   PMID:10469600   PMID:10572046   PMID:10843805   PMID:10886375   PMID:10926756   PMID:10944221  
PMID:11440720   PMID:11517919   PMID:11523821   PMID:12163410   PMID:12204261   PMID:12441295   PMID:12477932   PMID:12490554   PMID:12646629   PMID:12746429   PMID:14504237   PMID:14681479  
PMID:14973294   PMID:15024065   PMID:15329346   PMID:15618518   PMID:15703179   PMID:15829524   PMID:15944191   PMID:15951842   PMID:16221728   PMID:16251273   PMID:16421188   PMID:16602821  
PMID:16678811   PMID:16791844   PMID:16912273   PMID:17078065   PMID:17310243   PMID:17477400   PMID:17586487   PMID:17855428   PMID:18287559   PMID:18452913   PMID:19208343   PMID:19217813  
PMID:19306868   PMID:19325248   PMID:19520072   PMID:19762422   PMID:20430747   PMID:21267068   PMID:21303853   PMID:21307095   PMID:21606193   PMID:21677750   PMID:21750033   PMID:21873635  
PMID:21909240   PMID:21913311   PMID:22093831   PMID:22216134   PMID:22507129   PMID:22511961   PMID:22768305   PMID:22902530   PMID:23473983   PMID:23645682   PMID:24948604   PMID:24952961  
PMID:25902370   PMID:26057579   PMID:27253464   PMID:27381226   PMID:27892540   PMID:27986952   PMID:28479297   PMID:28943241   PMID:29031732   PMID:29246974   PMID:29700203   PMID:30630826  
PMID:30771302   PMID:31167144   PMID:31604927   PMID:31953387   PMID:32155439   PMID:32857951   PMID:33057429  


Genomics

Comparative Map Data
Nkx3-2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39541,918,826 - 41,921,563 (-)NCBIGRCm39mm39
GRCm39 Ensembl541,918,826 - 41,921,844 (-)Ensembl
GRCm38541,761,483 - 41,764,220 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl541,761,483 - 41,764,501 (-)EnsemblGRCm38mm10GRCm38
MGSCv37542,152,722 - 42,155,459 (-)NCBIGRCm37mm9NCBIm37
MGSCv36542,049,696 - 42,052,468 (-)NCBImm8
Celera539,220,946 - 39,223,683 (-)NCBICelera
Cytogenetic Map5B3NCBI
cM Map522.58NCBI
NKX3-2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl413,540,830 - 13,544,508 (-)EnsemblGRCh38hg38GRCh38
GRCh38413,540,830 - 13,544,508 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37413,542,454 - 13,546,132 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36413,151,552 - 13,155,212 (-)NCBINCBI36hg18NCBI36
Build 34413,218,722 - 13,222,307NCBI
Celera414,008,663 - 14,012,323 (-)NCBI
Cytogenetic Map4p15.33NCBI
HuRef412,880,106 - 12,883,766 (-)NCBIHuRef
CHM1_1413,541,051 - 13,544,711 (-)NCBICHM1_1
Nkx3-2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21469,183,795 - 69,186,182 (+)NCBI
Rnor_6.0 Ensembl1473,813,528 - 73,815,757 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01473,813,531 - 73,818,489 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01473,825,360 - 73,828,802 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1468,115,963 - 68,118,823 (+)NCBICelera
Cytogenetic Map14q21NCBI
Nkx3-2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495548010,213,761 - 10,216,860 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495548010,212,929 - 10,215,814 (+)NCBIChiLan1.0ChiLan1.0
NKX3-2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1413,258,949 - 13,262,458 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl413,258,949 - 13,262,458 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v047,958,218 - 7,961,844 (-)NCBIMhudiblu_PPA_v0panPan3
NKX3-2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1366,543,046 - 66,546,779 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl366,543,046 - 66,545,580 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha369,066,358 - 69,070,091 (+)NCBI
ROS_Cfam_1.0367,147,048 - 67,150,794 (+)NCBI
UMICH_Zoey_3.1366,524,627 - 66,528,359 (+)NCBI
UNSW_CanFamBas_1.0366,717,740 - 66,721,472 (+)NCBI
UU_Cfam_GSD_1.0367,087,659 - 67,091,382 (+)NCBI
Nkx3-2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_02440528560,297,353 - 60,300,979 (+)NCBI
SpeTri2.0NW_00493647713,999,045 - 14,001,659 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NKX3-2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl89,180,233 - 9,182,693 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.189,179,061 - 9,183,340 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.288,716,507 - 8,720,758 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NKX3-2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12736,641,837 - 36,647,917 (+)NCBI
ChlSab1.1 Ensembl2736,641,932 - 36,644,353 (+)Ensembl
Nkx3-2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475518,070,706 - 18,073,847 (+)NCBI

Position Markers
Bapx1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38541,763,994 - 41,764,198UniSTSGRCm38
MGSCv37542,155,233 - 42,155,437UniSTSGRCm37
Celera539,223,457 - 39,223,661UniSTS
Cytogenetic Map5B3UniSTS
cM Map523.0UniSTS
PMC22272P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38541,763,442 - 41,763,720UniSTSGRCm38
MGSCv37542,154,681 - 42,154,959UniSTSGRCm37
Celera539,222,905 - 39,223,183UniSTS
Cytogenetic Map5B3UniSTS
cM Map523.0UniSTS
Nkx3-2  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5B3UniSTS
cM Map523.0UniSTS
Bapx1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5B3UniSTS
cM Map523.0UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4141207Imrfq1_mimmune response to Factor IX QTL 1 (mouse)Not determined5791911941919241Mouse
1301693Sle6_msystemic lupus erythematosus susceptibility 6 (mouse)Not determined5884069387693978Mouse
14696730Kidlq1_mkidney weight, left QTL 1 (mouse)51340580847405808Mouse
1301685Estq2_mestradiol regulated response QTL 2 (mouse)Not determined51547674049476846Mouse
1300719Iba5_minduction of brown adipocytes 5 (mouse)Not determined52052964954529790Mouse
1301776Skts3_mskin tumor susceptibility 3 (mouse)Not determined52150995255510060Mouse
11537368Hmtb10_mhemostasis and thrombosis 10 (mouse)52189582554342976Mouse
11537367Hmtb11_mhemostasis and thrombosis 11 (mouse)52189582564649236Mouse
11341716Rvfs3_mRift Valley fever susceptibility 3 (mouse)526236236138457140Mouse
1300701Cd8ts1_mCD8 T cell subset 1 (mouse)Not determined52705800661058109Mouse
1301555Alcp10_malcohol preference locus 10 (mouse)Not determined53086693364867138Mouse
1301403Alcp9_malcohol preference locus 9 (mouse)Not determined53086693364867138Mouse
11353827Hplq1_mhot plate latency 1 (mouse)53141311665413116Mouse
4140990Lgq6_mlate growth QTL 6 (mouse)Not determined31975890100630065Mouse
4141219W10q16_mweight 10 weeks QTL 16 (mouse)Not determined31975890100630065Mouse
10043995Hbnr9_mHeligmosomoides bakeri nematode resistance 9 (mouse)Not determined53333132567331534Mouse
1301845Lxw4_mlupus BXSB x NZW 4 (mouse)Not determined53553712069537252Mouse
11049558Lmr24b_mleishmaniasis resistance 24b (mouse)53553712069537252Mouse
11049559Lmr24c_mleishmaniasis resistance 24c (mouse)53553712069537252Mouse
11049561Lmr24e_mleishmaniasis resistance 24e (mouse)53553712069537252Mouse
1301223Hdlq7_mHDL QTL 7 (mouse)Not determined53569722669697372Mouse
13464252Ahl10_mage related hearing loss, early onset 10 (mouse)53569722669697372Mouse
4141647Hrvhf1_mheart rate variability, high frequency 1 (mouse)Not determined3627608170276081Mouse
1301170Lith13_mlithogenic gene 13 (mouse)Not determined53633714470337256Mouse
36049766Ars22_mantibody response to SARS-CoV 22, day 29, IgG3 (mouse)53680000045300000Mouse
36049767Ars23_mantibody response to SARS-CoV 23, day 29, Total IgG (mouse)53680000045300000Mouse
36049768Ars24_mantibody response to SARS-CoV 24, 4 days post-rechallenge, IgG3 (mouse)53680000045300000Mouse
36049769Ars13_mantibody response to SARS-CoV 13, day 7, IgG2a+IgG2c (mouse)53680000045300000Mouse
36049770Ars14_mantibody response to SARS-CoV 14, day 7, IgG3 (mouse)53680000045300000Mouse
36049771Ars15_mantibody response to SARS-CoV 15, day 7, IgM (mouse)53680000045300000Mouse
36049772Ars20_mantibody response to SARS-CoV 20, day 15, Total IgG (mouse)53680000045300000Mouse
36049773Ars21_mantibody response to SARS-CoV 21, day 29, IgG2a+IgG2c (mouse)53680000045300000Mouse
36049774Ars16_mantibody response to SARS-CoV 16, day 7, Total IgG (mouse)53680000045300000Mouse
36049775Ars17_mantibody response to SARS-CoV 17, day 15, IgG2a+IgG2c (mouse)53680000045300000Mouse
36049776Ars18_mantibody response to SARS-CoV 18, day 15, IgG3 (mouse)53680000045300000Mouse
36049777Ars19_mantibody response to SARS-CoV 19, day 15, IgM (mouse)53680000045300000Mouse
35673310Ari4_mantibody response to influenza 4, day 15-45, IgG2b (mouse)53680000045300000Mouse
1300926Hpi2_mhepatic PMN infiltration 2 (mouse)Not determined53742414464649236Mouse
1301524Lmb2_mlupus in MRL and B6 F2 cross (mouse)Not determined537424144112317856Mouse
13464246Ahl11_mage related hearing loss, early onset 11 (mouse)53748643571486554Mouse
1300951Gbvq1_mgallstone bladder volume QTL 1 (mouse)Not determined53795433971954456Mouse
13464245Ahl12_mage related hearing loss, early onset 12 (mouse)53795433971954456Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:136
Count of miRNA genes:129
Interacting mature miRNAs:134
Transcripts:ENSMUST00000060820
Prediction methods: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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000060820   ⟹   ENSMUSP00000051990
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl541,761,483 - 41,764,501 (-)Ensembl
RefSeq Acc Id: NM_007524   ⟹   NP_031550
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39541,918,826 - 41,921,563 (-)NCBI
GRCm38541,761,483 - 41,764,220 (-)ENTREZGENE
MGSCv37542,152,722 - 42,155,459 (-)RGD
Celera539,220,946 - 39,223,683 (-)RGD
cM Map5 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_031550   ⟸   NM_007524
- UniProtKB: P97503 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000051990   ⟸   ENSMUST00000060820
Protein Domains
Homeobox

Promoters
RGD ID:6837950
Promoter ID:MM_KWN:42139
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney,   MEF_B4
Transcripts:UC008XHC.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36542,155,134 - 42,155,634 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:108015 AgrOrtholog
Ensembl Genes ENSMUSG00000049691 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000051990 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000060820 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:12020 UniProtKB/Swiss-Prot
MGD MGI:108015 ENTREZGENE
NCBI Gene 12020 ENTREZGENE
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nkx3-2 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NKX32_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  P97938_MOUSE UniProtKB/TrEMBL
UniProt Secondary A6H6G9 UniProtKB/Swiss-Prot