aviable tools for gene collapsing

[tujchl]

Hi:
I am working on gene annotations from different groups such as Refseq, UCSC, vega and I want to collapse genes or transcripts generated by Alternative splicing or Alernative start site to unify gene list. Some things like UCSC canonical genes (one tanscripts ID represent many others)
I generated it by myself according to mRNA seq similarity but the output is not satisfied
So some one know some availble tools to do this thing?

Thanks