Transcript pages

The transcript page is the source of information relating to an RNA transcript of a gene. All transcript pages have a header section which summarizes the key information about the transcript:

This includes (top to bottom):

• Transcript id
• Short description (where available)
• Location of the transcript within the genome
• Additional information about the transcript including number of exons and domains and features
• Table of all transcripts for the source gene

The menu on the left-hand side allows you navigate through available data:

Available data are:

Summary

This is a summary view of the transcript

Splice variants

Displays all known splice variants as a table and in a browser view.

Sequence

This displays the nucleotide sequence of the gene. Exons are highlighted in pink/red:

This page also gives you the option of downloading the sequence in FASTA or RTF formats, or to BLAST the sequence using the WormBase ParaSite BLAST service.

External references

Links to external databases such as EntrezGene and WormBase.

Protein Information

Displays information about the protein product of the transcript.

Protein Summary

Displays a summary image of the protein domains and their location within the full-length protein.

Domains and Features

Displays all protein domains and features for the protein as a table, with links to the originating resource e.g. Panther or Pfam.

AlphaFold predicted model

The structure from AlphaFold DB for the selected transcript is viewable through the AlphaFold browser widget. For transcripts where a model is available, it is possible to highlight individual residues, variants, exon boundaries, and protein features on the predicted structure. This includes the ability to focus on one feature at a time, for example highlighting a single exon. By default, the structure is colour coded based on a pLDDT score, to show the confidence of the predictions.