Isoform nomenclature question #217

Hi EGAPx team! I have some questions about the isoform nomenclature rules that EGAPx uses in product attributes. I've noticed three types of isoform product suffixes (where 'N' is a number):

1. isoform N (for mRNA/CDS features)
2. -TN (for mRNA/CDS features)
3. transcript variant XN (for transcript features)

Some observations about the suffixes:

• In some cases, the number used in the 'isoform' suffix and the '-T' suffix is different for the same isoform.
• For protein-coding isoforms, the transcript ID uses '-RN' instead of '-TN'.
• For transcript features, different rules for isoform naming are used.

My questions are:

1. Why are two separate suffixes used in the same product value for protein-coding isoforms?
2. Why do the numbers used in the separate suffixes sometimes differ for the same isoform?
3. Why use 'TN' for the protein-coding product suffix, 'RN' for the protein-coding transcript ID suffix, and 'XN' for transcript feature product suffixes?

Here are some examples from EGAPx runs (v0.4.1 and v0.5):

• product=heat shock protein 60A-like isoform 1-T1
• product=uncharacterized protein isoform 1-T2
• product=synaptotagmin 1 isoform 1-T3
• product=uncharacterized protein isoform 2-T3
• product=cramped chromatin regulator%2C transcript variant X5

Thanks for your help with this!