Alternative splicing analysis - anyone know good programs for analysis (Dec/13/2006 )
Hi, I'm working in a project in which I want to find out if there is alternative splicing of a protein sequence.
We already have one of the isoforms, which is a transmembrane protein, caracterized at our laboratory; and we know, due to the results of a NB analysis, that there are at least two more mRNAs. But our transcript is not the longer one, so I don't know how far away should I start analizing sequence looking for new exons.
We know the location on the rat genome and my idea is to analyze the sequence and boundaries of this ORF.
Can anyone give me any suggestions of programs that analyze sequences and give this kind of information, splicing information, promoter and regulatory sites prediction, etc.?
The transcript involves the sequence of 6 contigs on the genome and I started studying the 5' contig trying to find other exons, a promoter sequence and so forth.
If anyone can help me I'll be more than thankful!!
We already have one of the isoforms, which is a transmembrane protein, caracterized at our laboratory; and we know, due to the results of a NB analysis, that there are at least two more mRNAs. But our transcript is not the longer one, so I don't know how far away should I start analizing sequence looking for new exons.
We know the location on the rat genome and my idea is to analyze the sequence and boundaries of this ORF.
Can anyone give me any suggestions of programs that analyze sequences and give this kind of information, splicing information, promoter and regulatory sites prediction, etc.?
The transcript involves the sequence of 6 contigs on the genome and I started studying the 5' contig trying to find other exons, a promoter sequence and so forth.
If anyone can help me I'll be more than thankful!!
I don't know any program that can help you with your special needs.
My suggestions:
1. I agree, looking into mouse gene will help. It can help to identify new exons, but this might not be complete, depends on the homology of the gene btw human and mouse.
2. I suggest to look into EST data, where information of expressed sequence tags. EST data are what we use to assemble and discover splicing variants, so I guess this is the best way to go.
3. Microarray data (probe sequences) might also help.
Let me know if I can be of any further help.