Gsc2 (goosecoid homeobox 2) - Rat Genome Database

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Gene: Gsc2 (goosecoid homeobox 2) Rattus norvegicus
Analyze
Symbol: Gsc2
Name: goosecoid homeobox 2
RGD ID: 1305333
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 regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human GSC2 (goosecoid homeobox 2); INTERACTS WITH bisphenol A; 1,2-dichloroethane (ortholog); 1,2-dimethylhydrazine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: goosecoid-like; Gscl; homeobox protein goosecoid-2; LOC363831
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
GRCr81196,576,424 - 96,578,412 (+)NCBIGRCr8
mRatBN7.21183,070,784 - 83,075,874 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,072,138 - 83,074,126 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,800,750 - 91,802,738 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01184,461,884 - 84,463,872 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01183,515,499 - 83,517,487 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01187,220,618 - 87,222,606 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,220,618 - 87,222,606 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,312,181 - 90,314,169 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,060,271 - 85,062,259 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11185,100,906 - 85,102,374 (+)NCBI
Celera1181,848,147 - 81,850,135 (+)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9603426   PMID:9700206   PMID:10822263   PMID:23332764  


Genomics

Comparative Map Data
Gsc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81196,576,424 - 96,578,412 (+)NCBIGRCr8
mRatBN7.21183,070,784 - 83,075,874 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,072,138 - 83,074,126 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,800,750 - 91,802,738 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01184,461,884 - 84,463,872 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01183,515,499 - 83,517,487 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01187,220,618 - 87,222,606 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,220,618 - 87,222,606 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,312,181 - 90,314,169 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,060,271 - 85,062,259 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11185,100,906 - 85,102,374 (+)NCBI
Celera1181,848,147 - 81,850,135 (+)NCBICelera
Cytogenetic Map11q23NCBI
GSC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382219,146,993 - 19,150,292 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2219,146,993 - 19,150,292 (-)EnsemblGRCh38hg38GRCh38
GRCh372219,134,506 - 19,137,805 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362217,516,504 - 17,517,796 (-)NCBINCBI36Build 36hg18NCBI36
Build 342217,511,057 - 17,512,350NCBI
Celera222,988,450 - 2,989,742 (-)NCBICelera
Cytogenetic Map22q11.21NCBI
CHM1_12219,136,007 - 19,137,299 (-)NCBICHM1_1
T2T-CHM13v2.02219,521,533 - 19,524,832 (-)NCBIT2T-CHM13v2.0
Gsc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391617,730,978 - 17,732,891 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1617,730,971 - 17,732,923 (-)EnsemblGRCm39 Ensembl
GRCm381617,913,114 - 17,915,027 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1617,913,107 - 17,915,059 (-)EnsemblGRCm38mm10GRCm38
MGSCv371617,913,647 - 17,915,152 (-)NCBIGRCm37MGSCv37mm9NCBIm37
Celera1618,486,619 - 18,488,124 (-)NCBICelera
Cytogenetic Map16A3NCBI
cM Map1611.1NCBI
Gsc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544218,823,495 - 18,825,760 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544218,824,187 - 18,825,760 (+)NCBIChiLan1.0ChiLan1.0
GSC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22328,766,957 - 28,770,180 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12231,314,549 - 31,317,772 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0221,901,389 - 1,904,671 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12217,581,449 - 17,584,239 (-)NCBIpanpan1.1PanPan1.1panPan2
GSC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12630,033,185 - 30,034,174 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2629,987,283 - 29,988,471 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02631,433,426 - 31,437,346 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2631,434,465 - 31,436,086 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12629,482,654 - 29,485,525 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02629,106,059 - 29,108,277 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02630,193,559 - 30,198,109 (+)NCBIUU_Cfam_GSD_1.0
Gsc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118139,595,069 - 139,599,230 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366193,157,228 - 3,174,086 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366193,154,834 - 3,158,654 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GSC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1450,957,991 - 50,960,193 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11450,956,315 - 50,960,424 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21454,523,278 - 54,527,379 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GSC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1196,598,246 - 6,601,230 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl196,598,259 - 6,599,532 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666085331,282 - 334,587 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gsc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624945172,345 - 176,191 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624945172,345 - 176,453 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gsc2
2 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:71
Count of miRNA genes:56
Interacting mature miRNAs:66
Transcripts:ENSRNOT00000041975
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
2302043Pia27Pristane induced arthritis QTL 2718.60.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)118256654583440803Rat

Markers in Region
UniSTS:256469  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,072,798 - 83,073,646 (+)MAPPERmRatBN7.2
Rnor_6.01187,221,279 - 87,222,126NCBIRnor6.0
Rnor_5.01190,312,842 - 90,313,689UniSTSRnor5.0
RGSC_v3.41185,060,932 - 85,061,779UniSTSRGSC3.4
Celera1181,848,808 - 81,849,655UniSTS
Cytogenetic Map11q23UniSTS
UniSTS:495797  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,072,120 - 83,073,712 (+)MAPPERmRatBN7.2
Rnor_6.01187,220,601 - 87,222,192NCBIRnor6.0
Rnor_5.01190,312,164 - 90,313,755UniSTSRnor5.0
RGSC_v3.41185,060,254 - 85,061,845UniSTSRGSC3.4
Celera1181,848,130 - 81,849,721UniSTS
Cytogenetic Map11q23UniSTS


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 nervous system reproductive system respiratory system
High
Medium
Low 8 17
Below cutoff 1 21 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041975   ⟹   ENSRNOP00000046863
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,072,138 - 83,074,126 (+)Ensembl
Rnor_6.0 Ensembl1187,220,618 - 87,222,606 (+)Ensembl
RefSeq Acc Id: NM_001108846   ⟹   NP_001102316
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,576,424 - 96,578,412 (+)NCBI
mRatBN7.21183,072,138 - 83,074,126 (+)NCBI
Rnor_6.01187,220,618 - 87,222,606 (+)NCBI
Rnor_5.01190,312,181 - 90,314,169 (+)NCBI
RGSC_v3.41185,060,271 - 85,062,259 (+)RGD
Celera1181,848,147 - 81,850,135 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102316 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL77912 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000046863
  ENSRNOP00000046863.3
Reference Protein Sequences
RefSeq Acc Id: NP_001102316   ⟸   NM_001108846
- UniProtKB: D3Z9R9 (UniProtKB/TrEMBL),   A6JSJ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000046863   ⟸   ENSRNOT00000041975
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z9R9-F1-model_v2 AlphaFold D3Z9R9 1-214 view protein structure

Transcriptome

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

Promoters
RGD ID:13698313
Promoter ID:EPDNEW_R8838
Type:single initiation site
Name:Gsc2_1
Description:goosecoid homeobox 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01187,220,561 - 87,220,621EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305333 AgrOrtholog
BioCyc Gene G2FUF-20621 BioCyc
Ensembl Genes ENSRNOG00000000282 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041975 ENTREZGENE
  ENSRNOT00000041975.4 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:363831 UniProtKB/TrEMBL
NCBI Gene 363831 ENTREZGENE
PANTHER HOMEOBOX PROTEIN GOOSECOID-2 UniProtKB/TrEMBL
  HOMEOBOX PROTEIN GOOSECOID-RELATED UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Gsc2 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000282 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6JSJ5 ENTREZGENE, UniProtKB/TrEMBL
  D3Z9R9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-20 Gsc2  goosecoid homeobox 2  Gscl  goosecoid-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Gscl  goosecoid-like   Gscl_predicted  goosecoid-like (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Gscl_predicted  goosecoid-like (predicted)      Symbol and Name status set to approved 70820 APPROVED