Human Gene GSC (ENST00000238558.5_6) from GENCODE V47lift37
  Description: goosecoid homeobox (from RefSeq NM_173849.3)
Gencode Transcript: ENST00000238558.5_6
Gencode Gene: ENSG00000133937.5_8
Transcript (Including UTRs)
   Position: hg19 chr14:95,234,560-95,236,450 Size: 1,891 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr14:95,234,828-95,236,352 Size: 1,525 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:95,234,560-95,236,450)mRNA (may differ from genome)Protein (257 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GSC_HUMAN
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. 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 (By similarity).
SUBCELLULAR LOCATION: Nucleus.
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


-  MalaCards Disease Associations
  MalaCards Gene Search: GSC
Diseases sorted by gene-association score: short stature, auditory canal atresia, mandibular hypoplasia, skeletal abnormalities* (1270), synostosis (5), auditory neuropathy (5), cornelia de lange syndrome (4), velocardiofacial syndrome (2)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.32 RPKM in Breast - Mammary Tissue
Total median expression: 15.55 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -48.9098-0.499 Picture PostScript Text
3' UTR -87.60268-0.327 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 - Homeodomain

SCOP Domains:
46689 - Homeodomain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2DMU - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P56915
FrontTopSide
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details  Gene Details 
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, 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: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:0007369 gastrulation
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
  LP895956 - Sequence 820 from Patent EP3253886.
BC063580 - Homo sapiens goosecoid homeobox, mRNA (cDNA clone MGC:75223 IMAGE:4370088), complete cds.
AY177407 - Homo sapiens homeobox protein goosecoid mRNA, complete cds.
JD462901 - Sequence 443925 from Patent EP1572962.
JD051363 - Sequence 32387 from Patent EP1572962.
KJ895581 - Synthetic construct Homo sapiens clone ccsbBroadEn_04975 GSC gene, encodes complete protein.
AB463695 - Synthetic construct DNA, clone: pF1KB7536, Homo sapiens GSC gene for goosecoid homeobox, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000238558.1, ENST00000238558.2, ENST00000238558.3, ENST00000238558.4, GSC_HUMAN, NM_173849, P56915, Q86YR1, uc317edw.1, uc317edw.2
UCSC ID: ENST00000238558.5_6
RefSeq Accession: NM_173849.3
Protein: P56915 (aka GSC_HUMAN)

-  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.