Breast Cancer Long Read Transcriptome


This web portal provides tools for querying, visualizing, and downloading data from a collection of breast cancer samples profiled by full-length RNA sequencing (PacBio SMRT sequencing).



Quick User Guide


Isoforms Tab: query full-length (FL) isoforms and open-reading frames (ORFs) by gene

  1. Summary Tab: overview of FL isoforms and ORFs
  2. Protein Browser Tab: visualize ORF protein features, such as domains, transmembrane regions and MS/MS peptides
  3. Protein Alignment Tab: compare FL isoform to UniProt canonical

IGV Browser Tab

Visualize FL isoforms using the IGV Genome Browser (hg38)

Reference

Long-read sequencing reveals the full-length isoform diversity in breast cancer.

Veiga et al., (2020) Submitted.
Developed by Diogo Veiga at the Jacskon Laboratory for Genomic Medicine.

Make selections and click "Retrieve isoforms" to update dataset and graphs







Transcript sequences

Splice category of full-length transcripts

ORF sequences

ORF identity to Uniprot

Protein Features

Click on the table to display protein features

Results - Protein Features

Protein Sequence Alignment

FASTA

Click on the table to perform alignment between PacBio ORF and closest Uniprot match.

Results - Pairwise Global Alignment


ORF sequences