Gbx2 (gastrulation brain homeobox 2) - Rat Genome Database

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Gene: Gbx2 (gastrulation brain homeobox 2) Rattus norvegicus
Analyze
Symbol: Gbx2
Name: gastrulation brain homeobox 2
RGD ID: 621866
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II core promoter sequence-specific DNA binding activity; and RNA polymerase II-specific DNA-binding transcription factor binding activity. Predicted to be involved in regulation of nervous system development and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including branching involved in blood vessel morphogenesis; nervous system development; and neural crest cell migration. Predicted to be active in nucleus. Orthologous to human GBX2 (gastrulation brain homeobox 2); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeobox protein GBX-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8997,957,304 - 97,959,883 (-)NCBIGRCr8
mRatBN7.2990,509,633 - 90,512,212 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl990,509,633 - 90,512,212 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx998,936,286 - 98,938,865 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09104,072,186 - 104,074,765 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09102,437,722 - 102,440,301 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0997,063,265 - 97,065,855 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl997,063,728 - 97,065,817 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0996,754,122 - 96,756,543 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4989,034,340 - 89,037,102 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1989,239,950 - 89,240,065 (-)NCBI
Celera988,058,118 - 88,060,697 (-)NCBICelera
Cytogenetic Map9q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. The homeobox gene GBX2, a target of the myb oncogene, mediates autocrine growth and monocyte differentiation. Kowenz-Leutz E, etal., Cell 1997 Oct 17;91(2):185-95.
4. Changing requirements for Gbx2 in development of the cerebellum and maintenance of the mid/hindbrain organizer. Li JY, etal., Neuron 2002 Sep 26;36(1):31-43.
5. Characterization and sequence analysis of the human homeobox-containing gene GBX2. Lin X, etal., Genomics 1996 Feb 1;31(3):335-42.
6. Regulation and function of FGF8 in patterning of midbrain and anterior hindbrain. Mason I, etal., Biochem Cell Biol 2000;78(5):577-84.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. Inhibition of constitutively activated Stat3 signaling pathway suppresses growth of prostate cancer cells. Ni Z, etal., Cancer Res 2000 Mar 1;60(5):1225-8.
10. GOA pipeline RGD automated data pipeline
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11967891   PMID:15829521   PMID:15996652   PMID:16651541   PMID:19279136   PMID:19700621   PMID:21048141   PMID:23144817  


Genomics

Comparative Map Data
Gbx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8997,957,304 - 97,959,883 (-)NCBIGRCr8
mRatBN7.2990,509,633 - 90,512,212 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl990,509,633 - 90,512,212 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx998,936,286 - 98,938,865 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09104,072,186 - 104,074,765 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09102,437,722 - 102,440,301 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0997,063,265 - 97,065,855 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl997,063,728 - 97,065,817 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0996,754,122 - 96,756,543 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4989,034,340 - 89,037,102 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1989,239,950 - 89,240,065 (-)NCBI
Celera988,058,118 - 88,060,697 (-)NCBICelera
Cytogenetic Map9q36NCBI
GBX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382236,161,340 - 236,168,386 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2236,165,236 - 236,168,386 (-)EnsemblGRCh38hg38GRCh38
GRCh372237,073,879 - 237,077,029 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362236,739,046 - 236,741,391 (-)NCBINCBI36Build 36hg18NCBI36
Build 342236,856,306 - 236,858,652NCBI
Celera2230,787,441 - 230,789,786 (-)NCBICelera
Cytogenetic Map2q37.2NCBI
HuRef2228,868,880 - 228,871,225 (-)NCBIHuRef
CHM1_12237,080,112 - 237,082,457 (-)NCBICHM1_1
T2T-CHM13v2.02236,651,067 - 236,658,113 (-)NCBIT2T-CHM13v2.0
Gbx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39189,855,684 - 89,858,898 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl189,855,678 - 89,858,901 (-)EnsemblGRCm39 Ensembl
GRCm38189,927,962 - 89,931,176 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl189,927,956 - 89,931,179 (-)EnsemblGRCm38mm10GRCm38
MGSCv37191,824,537 - 91,827,751 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36191,759,133 - 91,762,347 (-)NCBIMGSCv36mm8
Celera192,869,152 - 92,872,368 (-)NCBICelera
Cytogenetic Map1DNCBI
cM Map145.06NCBI
Gbx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955453538,280 - 540,306 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955453538,066 - 541,415 (+)NCBIChiLan1.0ChiLan1.0
GBX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213138,794,032 - 138,798,437 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B138,808,996 - 138,813,401 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B123,392,499 - 123,399,549 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
GBX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12547,005,509 - 47,008,367 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2547,005,504 - 47,008,512 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2547,508,245 - 47,511,037 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02547,359,565 - 47,362,361 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2547,359,543 - 47,362,930 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12547,267,592 - 47,270,382 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02547,061,156 - 47,063,938 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02547,291,077 - 47,293,871 (-)NCBIUU_Cfam_GSD_1.0
Gbx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303189,066,154 - 189,069,657 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365251,870,195 - 1,873,539 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365251,870,211 - 1,873,536 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GBX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15136,029,070 - 136,032,316 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115136,029,393 - 136,032,568 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215150,464,293 - 150,466,933 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GBX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110122,177,725 - 122,184,448 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10122,182,301 - 122,184,446 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604077,219,450 - 77,225,155 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gbx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248471,879,007 - 1,881,669 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248471,878,946 - 1,881,794 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gbx2
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:166
Count of miRNA genes:128
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000026419
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)98636963192058970Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)97927151191616855Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)97927151191616855Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat

Markers in Region
Gbx2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0996,754,122 - 96,754,504NCBIRnor5.0
RGSC_v3.4989,034,424 - 89,035,064UniSTSRGSC3.4
Celera988,057,981 - 88,058,621UniSTS
Cytogenetic Map9q35UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 10
Low 1 4 4 55 19
Below cutoff 1 19 14 6 14 6 2 2 5 11 10 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026419   ⟹   ENSRNOP00000026419
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl990,509,633 - 90,512,212 (-)Ensembl
Rnor_6.0 Ensembl997,063,728 - 97,065,817 (-)Ensembl
RefSeq Acc Id: NM_053708   ⟹   NP_446160
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8997,957,304 - 97,959,883 (-)NCBI
mRatBN7.2990,509,633 - 90,512,212 (-)NCBI
Rnor_6.0997,063,265 - 97,065,855 (-)NCBI
Rnor_5.0996,754,122 - 96,756,543 (-)NCBI
RGSC_v3.4989,034,340 - 89,037,102 (-)RGD
Celera988,058,118 - 88,060,697 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446160 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK70499 (Get FASTA)   NCBI Sequence Viewer  
  BAF44111 (Get FASTA)   NCBI Sequence Viewer  
  EDL92080 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000026419
  ENSRNOP00000026419.3
Reference Protein Sequences
RefSeq Acc Id: NP_446160   ⟸   NM_053708
- UniProtKB: G3V8J6 (UniProtKB/TrEMBL),   A6JQK7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026419   ⟸   ENSRNOT00000026419
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V8J6-F1-model_v2 AlphaFold G3V8J6 1-348 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:621866 AgrOrtholog
BioCyc Gene G2FUF-26766 BioCyc
Ensembl Genes ENSRNOG00000019495 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026419 ENTREZGENE
  ENSRNOT00000026419.7 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro GBX-1/2 UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:114500 UniProtKB/TrEMBL
NCBI Gene 114500 ENTREZGENE
PANTHER HOMEOBOX PROTEIN UNPLUGGED UniProtKB/TrEMBL
  PTHR24334 UniProtKB/TrEMBL
  PTHR24334:SF3 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Gbx2 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019495 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A1IJ65_RAT UniProtKB/TrEMBL
  A6JQK7 ENTREZGENE, UniProtKB/TrEMBL
  G3V8J6 ENTREZGENE, UniProtKB/TrEMBL
  Q91XM7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Gbx2  gastrulation brain homeobox 2      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Gbx2  gastrulation brain homeobox 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference