[BiO BB] Intron/Exon Analysis

[shashikanth marri]

Hai Oscar Medina,
I have seen your question in bio bulletin board forum. i would like
give suggestions to your query.
Just by seeing the mRNA sequence we cannot say whether it is a
alternatively spliced or not if it is a new sequence. we cannot say
whether it is spliced or not unless we compare it with  the genomic
DNA.
If you are comparing with the genomic DNA we predict the exons. the
best tools now avialble online are SIM4
(http://pbil.univ-lyon1.fr/sim4.php) and
SPIDEY (http://www.ncbi.nih.gov/IEB/Research/Ostell/Spidey/).
wether it is spliced or not we cannot confirm just by aligning. If any
previous related mRNA are present in that system has to be known (you
get either from literature search or just do the blast search and find
related mRNA). which is annotated.

then align your mRNA and annotated mRNA on genomic sequence and
observe the exon regions. if any exon is missing in annotated one
compared to the your mRNA then you can say it is spliced. in other
words your mRNA sequence lies in intronic region of the annotated mRNA
on genomic DNA then you can say it as spliced form.

If want to do for whole mRNA then take EST sequences and compare your
mRNA sequence on genomic DNA. then observe any exon lies on intron
region, or any 5' exonic region extenstion then you say it as spliced
form.