Gsx2 (GS homeobox 2) - Rat Genome Database

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Gene: Gsx2 (GS homeobox 2) Rattus norvegicus
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Symbol: Gsx2
Name: GS homeobox 2
RGD ID: 1308047
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Predicted to be involved in generation of neurons and olfactory bulb development. Predicted to act upstream of or within several processes, including nervous system development; positive regulation of oligodendrocyte differentiation; and regulation of respiratory gaseous exchange by nervous system process. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human GSX2 (GS homeobox 2); INTERACTS WITH bisphenol A; Cuprizon; 1,2-dichloroethane (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: genomic screened homeo box 2; Gsh2; LOC364140
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
mRatBN7.21433,123,799 - 33,126,151 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1433,124,381 - 33,126,105 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1433,474,374 - 33,476,721 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01434,782,183 - 34,784,530 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01433,267,435 - 33,269,782 (-)NCBIRnor_WKY
Rnor_6.01435,650,985 - 35,652,709 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1435,650,985 - 35,652,709 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01435,479,361 - 35,481,085 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41435,489,441 - 35,491,165 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11435,489,434 - 35,491,334 (-)NCBI
Celera1432,394,600 - 32,396,324 (-)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7619729   PMID:9398437   PMID:11060228   PMID:11124115   PMID:11731457   PMID:12724834   PMID:12930780   PMID:15930101   PMID:16715081   PMID:18701439   PMID:23042297   PMID:31412107  


Genomics

Comparative Map Data
Gsx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21433,123,799 - 33,126,151 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1433,124,381 - 33,126,105 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1433,474,374 - 33,476,721 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01434,782,183 - 34,784,530 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01433,267,435 - 33,269,782 (-)NCBIRnor_WKY
Rnor_6.01435,650,985 - 35,652,709 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1435,650,985 - 35,652,709 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01435,479,361 - 35,481,085 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41435,489,441 - 35,491,165 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11435,489,434 - 35,491,334 (-)NCBI
Celera1432,394,600 - 32,396,324 (-)NCBICelera
Cytogenetic Map14p11NCBI
GSX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38454,100,163 - 54,102,498 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl454,099,523 - 54,102,498 (+)EnsemblGRCh38hg38GRCh38
GRCh37454,966,330 - 54,968,665 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36454,660,955 - 54,662,879 (+)NCBINCBI36Build 36hg18NCBI36
Celera452,465,927 - 52,467,801 (+)NCBICelera
Cytogenetic Map4q12NCBI
HuRef450,913,211 - 50,915,085 (+)NCBIHuRef
CHM1_1455,001,958 - 55,003,832 (+)NCBICHM1_1
T2T-CHM13v2.0457,587,414 - 57,589,749 (+)NCBIT2T-CHM13v2.0
Gsx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39575,236,262 - 75,238,554 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl575,236,262 - 75,238,554 (+)EnsemblGRCm39 Ensembl
GRCm38575,075,601 - 75,077,893 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl575,075,601 - 75,077,893 (+)EnsemblGRCm38mm10GRCm38
MGSCv37575,471,626 - 75,473,918 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36575,357,298 - 75,359,590 (+)NCBIMGSCv36mm8
Celera572,359,931 - 72,362,223 (+)NCBICelera
Cytogenetic Map5C3.3NCBI
cM Map539.55NCBI
Gsx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495544716,714,870 - 16,715,757 (-)NCBIChiLan1.0ChiLan1.0
GSX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1476,397,771 - 76,399,715 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl476,397,180 - 76,399,715 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0469,837,643 - 69,840,101 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
GSX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11346,640,172 - 46,642,405 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1346,640,172 - 46,641,546 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1346,597,718 - 46,599,873 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01347,250,450 - 47,252,604 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1347,250,428 - 47,252,675 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11346,923,091 - 46,925,239 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01346,455,303 - 46,457,455 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01347,328,642 - 47,330,797 (+)NCBIUU_Cfam_GSD_1.0
Gsx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528529,591,982 - 29,594,299 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648216,704,193 - 16,705,729 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493648216,703,936 - 16,706,224 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GSX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl840,881,552 - 40,883,995 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1840,880,093 - 40,883,928 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2842,924,085 - 42,926,267 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GSX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1714,436,848 - 14,446,197 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl714,439,371 - 14,440,944 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606615,277,429 - 15,279,859 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gsx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476115,387,674 - 15,389,229 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476115,387,217 - 15,389,404 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gsx2
16 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:80
Count of miRNA genes:65
Interacting mature miRNAs:70
Transcripts:ENSRNOT00000003080
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat

Markers in Region
Gsh2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21433,125,835 - 33,126,117 (+)MAPPERmRatBN7.2
Rnor_6.01435,652,440 - 35,652,721NCBIRnor6.0
Rnor_5.01435,480,816 - 35,481,097UniSTSRnor5.0
RGSC_v3.41435,490,896 - 35,491,177UniSTSRGSC3.4
Celera1432,396,055 - 32,396,336UniSTS
Cytogenetic Map14p11UniSTS


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

endocrine system hemolymphoid system integumental system musculoskeletal system nervous system reproductive system appendage
High
Medium
Low 34 3
Below cutoff 5 8 2 2 15 10 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003080   ⟹   ENSRNOP00000003080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1433,124,381 - 33,126,105 (-)Ensembl
Rnor_6.0 Ensembl1435,650,985 - 35,652,709 (-)Ensembl
RefSeq Acc Id: NM_001137563   ⟹   NP_001131035
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21433,123,799 - 33,126,151 (-)NCBI
Rnor_6.01435,650,985 - 35,652,709 (-)NCBI
Rnor_5.01435,479,361 - 35,481,085 (-)NCBI
RGSC_v3.41435,489,441 - 35,491,165 (-)RGD
Celera1432,394,600 - 32,396,324 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001131035   ⟸   NM_001137563
- UniProtKB: B6RGM2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003080   ⟸   ENSRNOT00000003080
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B6RGM2-F1-model_v2 AlphaFold B6RGM2 1-305 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:1308047 AgrOrtholog
BioCyc Gene G2FUF-15922 BioCyc
Ensembl Genes ENSRNOG00000002266 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003080 ENTREZGENE
  ENSRNOP00000003080.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003080 ENTREZGENE
  ENSRNOT00000003080.5 UniProtKB/TrEMBL
InterPro GSH2 UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_region UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:364140 UniProtKB/TrEMBL
NCBI Gene 364140 ENTREZGENE
PANTHER PTHR47421 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Gsx2 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt B6RGM1_RAT UniProtKB/TrEMBL
  B6RGM2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Gsx2  GS homeobox 2  Gsx2  GS homeobox 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Gsx2  GS homeobox 2  Gsh2_predicted  genomic screened homeo box 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Gsh2_predicted  genomic screened homeo box 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED