Smooth Muscle Transcriptome Browser

Department of Physiology and Cell Biology

The Smooth Muscle Transcriptome Browser offers expression profiles, isoforms, and cDNAs (ORFs: open reading frames) of each gene expressed in the key cell populations and GI tissues for functional studies.

Access the Smooth Muscle Transcriptome Browser
Opens in new window

Applications

  1. Searching for isoforms (transcriptional variants) and genomic structure (promoter, exons and introns) for each expressed gene in cell and tissue types
  2. Displaying expression levels (FPKM) of each isoform in cell and tissue types
  3. Downloading the cDNA sequence for each isoform
  4. Predicting open rereading frames of authentic and potential peptide(s) resulting from a selected isoform

Search instructions

  1. Go to "Select Track" and select a reference mouse genome: mm9 (NCBI37, July 2007) and mm10 (GRCm38, Dec. 2011). Select a cell and/or tissue type(s) under the transcripts section.
  2. Click "Browser" or "Back to Browser".
  3. To search expressed transcriptional variants of a gene, type in a gene symbol (overwrite it on the chromosome location), and click "Search".
  4. Select a displayed gene on the list of reference transcripts.
  5. Navigate display options in Overview, Region, and Details in left sidebar.
  6. Optimize the view using the Scroll/Zoom or Flip options above the browser.
  7. Click a desired transcriptional variant to see expression profiles (expression levels and number of variants) in cell and tissue types, chromosomal location and DNA sequences of exons and introns.
  8. To access cDNA information, click "Download cDNA Sequence" in upper right "Fasta" panel and download will begin.
  9. To access translated protein information, click "Search Open Reading Frames".
  10. Copy the cDNA sequence and paste it into the NCBI ORF Finder (link in window) and click "submit" on ORFinder page.
  11. Evaluate feasibility of ORFs found by NCBI ORF Finder using "SmartBLAST" or "BLAST" to find potential protein(s) (generally, the longest ORF is an authentic peptide).

For more information and detailed instructions on how to use the browser, see the reference paper below.

Reference

Breland A, Ha S, Jorgensen BG, Gardner TA, Sanders KM, Ro S. Smooth Muscle Transcriptome Browser: offering genome-wide references and expression profiles of transcripts expressed in intestinal SMC, ICC, and PDGFRα+ cells (SIP syncytium). In review