Mouse Gene Gsc (ENSMUST00000021513.5) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus goosecoid homeobox (Gsc), mRNA. (from RefSeq NM_010351)
Gencode Transcript: ENSMUST00000021513.5
Gencode Gene: ENSMUSG00000021095.5
Transcript (Including UTRs)
   Position: mm10 chr12:104,471,209-104,473,330 Size: 2,122 Total Exon Count: 3 Strand: -
Coding Region
   Position: mm10 chr12:104,471,491-104,473,115 Size: 1,625 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:104,471,209-104,473,330)mRNA (may differ from genome)Protein (256 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Homeobox protein goosecoid;
FUNCTION: Regulates chordin (CHRD). May play a role in spatial programing within discrete embryonic fields or lineage compartments during organogenesis (By similarity). In concert with NKX3-2, plays a role in defining the structural components of the middle ear; required for the development of the entire tympanic ring. Goosecoid-expressing regions of the gastrulating mouse egg cylinder have organizer-like activity when transplanted into Xenopus embryos.
TISSUE SPECIFICITY: In early gastrulation, expressed in the dorsal lip. In later stages of development found in head, limbs and body wall.
INDUCTION: By activin.
SIMILARITY: Belongs to the paired homeobox family. Bicoid subfamily.
SIMILARITY: Contains 1 homeobox DNA-binding domain.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -110.30215-0.513 Picture PostScript Text
3' UTR -113.00282-0.401 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

SCOP Domains:
81822 - RuBisCo LSMT C-terminal, substrate-binding domain
46689 - Homeodomain-like
53613 - Ribokinase-like

ModBase Predicted Comparative 3D Structure on Q02591
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001085 RNA polymerase II transcription factor binding
GO:0001103 RNA polymerase II repressing transcription factor binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0009653 anatomical structure morphogenesis
GO:0014036 neural crest cell fate specification
GO:0021904 dorsal/ventral neural tube patterning
GO:0023019 signal transduction involved in regulation of gene expression
GO:0030178 negative regulation of Wnt signaling pathway
GO:0030900 forebrain development
GO:0042474 middle ear morphogenesis
GO:0043583 ear development
GO:0048644 muscle organ morphogenesis
GO:0048704 embryonic skeletal system morphogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005667 transcription factor complex
GO:0016604 nuclear body

-  Descriptions from all associated GenBank mRNAs
  Y13149 - Mus musculus mRNA for goosecoid homeobox protein, clone cDNA-D.
Y13150 - Mus musculus mRNA for goosecoid homeobox protein, clone cDNA-E.
X99239 - M.muscsulus mRNA for goosecoid homeobox.
AB221548 - Mus musculus cDNA pooled tissues:(tissue_type=brain,dev_stage=8-12 days neonate,strain=BALB/c),(tissue_type=testis,dev_stage=adult, strain=C57BL/6J), clone:V01X003I13.
BC160213 - Synthetic construct Mus musculus clone IMAGE:100063861, MGC:193328 goosecoid homeobox (Gsc) mRNA, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: GSC_MOUSE, NM_010351, Q02591, uc007oxh.1, uc007oxh.2
UCSC ID: uc007oxh.2
RefSeq Accession: NM_010351
Protein: Q02591 (aka GSC_MOUSE)
CCDS: CCDS26153.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.