1. A brief comment on nomenclature. A croe (coding region of an exon) is not exactly an exon Steve Mount ISMB SIG meeting on alternative splicing June 23, 2005. Detroit, Michigan

2. A block of sequence bounded by an initiation codon and a 5’ splice site, or a 3’ splice site and a stop codon, is a coding segment, but not an exon. These segments are often called exons, but they are not. I propose that there will be much less confusion on this point if they are given a name of their own.

3. Gene

4. mRNA

5. Exons

6. CDS

7. Croe (coding region of an exon)

8. An mRNA is composed of exons:

9. A CDS is composed of croes:

10. What to cite: Myles Axton. 2005. "Touching Base” Nature Genetics (January) 37, page 15 My own web site: SteveMount.com www.stevemount.com/Science.html

11. Another question: Different modes of alternative splicing have the same effect on the mRNA in that they create an indel between variants. Alternative 5’ splice sites Exon skipping vs. retention Alternative 3’ splice sites Intron retention Would it be useful to have a name for segments of this sort?

12. Summary: -- We need a word for segments of coding information within an exon because many people use the word exon to refer to these segments and it creates confusion. -- Miles Axton has proposed that croe be used for “coding region of an exon.” I think that it should apply even when the entire exon is coding. -- Another case is insertions in one cDNA with respect to another. Do we need a word for this?