Hi,

I've recently started using Ensembl for help in designing a gene panel for NGS. 

Each time I select a gene on Ensembl it comes up with different available transcripts for that gene. 

What defines a transcript? Is it literally just a different version of the gene in different individuals (but if so, how come some of the transcripts appear to be so different in terms of bp length and amino acid number)

Any help in explaining would be most gratefully received!


This is more of a comment, possibly a rant. In my opinion the concept of gene is obsolete and we would be better off if we ditched the concept of "gene" altogether. 

Genes made sense when it was thought that there were these discrete units (genes) which produced each a single transcript and a single protein. However, a single gene can produce multiple transcripts and these can be very different one from the other (see for example the table of transcripts of the [Actin gene][1], there are several coding and non coding transcripts). So when we say gene X has a mutation it is not clear what we are referring to. How many transcripts are affected by this mutation? Are they coding or pseudogenes? In my opinion it would be simpler to think in "transcript space" and forget about genes. 

Another way if seeing this is to consider that while transcripts exist, genes don't exist. When you do mRNA extraction you isolate transcripts, not genes, you can't isolate genes. You could have a restriction enzyme that cuts left and right of a "gene", but this is also not true. You have an enzyme that cuts at positions A and B, which happen to include a bunch of transcripts. If the definition of that gene (and transcripts) change, the enzyme still cuts there because it doesn't "see" genes, it sees DNA sequence.

I think "genes" hang around because they make some statements simpler ("Mutation at position A hits gene X" as opposed to "Mutation at position A hits an intron of transcripts X, an exon of transcript Y, and a UTR of Z"), but they are at best incomplete statements.

Any thoughts?

  [1]: http://www.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000075624;r=7:5527151-5563784