Mouse Gene Tgfbrap1 (ENSMUST00000186694.6) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus transforming growth factor, beta receptor associated protein 1 (Tgfbrap1), transcript variant 2, mRNA. (from RefSeq NM_001357299)
Gencode Transcript: ENSMUST00000186694.6
Gencode Gene: ENSMUSG00000070939.9
Transcript (Including UTRs)
   Position: mm10 chr1:43,047,220-43,092,729 Size: 45,510 Total Exon Count: 12 Strand: -
Coding Region
   Position: mm10 chr1:43,049,659-43,075,938 Size: 26,280 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:43,047,220-43,092,729)mRNA (may differ from genome)Protein (860 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: TGFA1_MOUSE
DESCRIPTION: RecName: Full=Transforming growth factor-beta receptor-associated protein 1; Short=TGF-beta receptor-associated protein 1; Short=TRAP-1; Short=TRAP1;
FUNCTION: Plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling. May recruit SMAD4 to the vicinity of the receptor complex and facilitate its interaction with receptor-regulated Smads, such as SMAD2 (By similarity).
SUBUNIT: Interacts with TGFBR2 and ACVR2B; in the absence of ligand stimulation. Interacts with TGFBR1, ACVRL1, BMPR1A and ACVR1B; in the absence of ligand stimulation and to a less extent. Interacts with SMAD4; the interaction seems to be mutually exclusive with the interaction of SMAD4 and phosphorylated SMAD2. May interact with ALOX5 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Note=Colocalizes with TGF-beta receptors in the absence of signaling (By similarity).
SIMILARITY: Belongs to the TRAP1 family.
SIMILARITY: Contains 1 CNH 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 -217.30363-0.599 Picture PostScript Text
3' UTR -774.372439-0.317 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
IPR001180 - Citron
IPR000547 - Clathrin_H-chain/VPS_repeat
IPR019452 - VPS39/TGF_beta_rcpt-assoc_1
IPR019453 - VPS39/TGF_beta_rcpt-assoc_2

Pfam Domains:
PF00637 - Region in Clathrin and VPS
PF00780 - CNH domain
PF10366 - Vacuolar sorting protein 39 domain 1
PF10367 - Vacuolar sorting protein 39 domain 2

SCOP Domains:
48371 - ARM repeat

ModBase Predicted Comparative 3D Structure on Q3UR70
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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     
 RGDEnsembl   
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005160 transforming growth factor beta receptor binding
GO:0046332 SMAD binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0006886 intracellular protein transport
GO:0007165 signal transduction
GO:0008333 endosome to lysosome transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0034058 endosomal vesicle fusion

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0016020 membrane
GO:0033263 CORVET complex
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK141742 - Mus musculus 9 days embryo whole body cDNA, RIKEN full-length enriched library, clone:D030049N14 product:tansforming growth factor, beta receptor associated protein 1, full insert sequence.
BC030488 - Mus musculus transforming growth factor, beta receptor associated protein 1, mRNA (cDNA clone IMAGE:5373084), with apparent retained intron.
AK014063 - Mus musculus 13 days embryo head cDNA, RIKEN full-length enriched library, clone:3110018K12 product:unclassifiable, full insert sequence.
BC072608 - Mus musculus transforming growth factor, beta receptor associated protein 1, mRNA (cDNA clone IMAGE:6834730).
BC138866 - Mus musculus transforming growth factor, beta receptor associated protein 1, mRNA (cDNA clone MGC:170493 IMAGE:8861888), complete cds.
BC138867 - Mus musculus transforming growth factor, beta receptor associated protein 1, mRNA (cDNA clone MGC:170494 IMAGE:8861889), complete cds.
AK082918 - Mus musculus 7 days embryo whole body cDNA, RIKEN full-length enriched library, clone:C430019A16 product:TGF BETA RECEPTOR ASSOCIATED PROTEIN-1 homolog [Homo sapiens], full insert sequence.
AK159332 - Mus musculus osteoclast-like cell cDNA, RIKEN full-length enriched library, clone:I420016G06 product:Hypothetical prenyl group binding site, full insert sequence.
AK051333 - Mus musculus 12 days embryo spinal ganglion cDNA, RIKEN full-length enriched library, clone:D130035M05 product:hypothetical Prenyl group binding site (CAAX box) containing protein, full insert sequence.
LF192638 - JP 2014500723-A/141: Polycomb-Associated Non-Coding RNAs.
MA428215 - JP 2018138019-A/141: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001357299, Q3UR70, Q8BKN4, TGFA1_MOUSE, uc007ave.1, uc007ave.2
UCSC ID: uc007ave.2
RefSeq Accession: NM_001357299
Protein: Q3UR70 (aka TGFA1_MOUSE)
CCDS: CCDS14920.1

-  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.