Hi everyone!
Can anyone help me to give me idea how to identify Introns and exonic sequences in the genomic DNA sequence for a particular gene, say FLT3 gene which i am working on.

One way to do it is to blast mRNA sequence with genome sequence for this gene. But you can do it easy on ensemble website. For example I did it for you for human flt3 (you didn't specify the species): http://www.ensembl.org/Homo_sapiens/exonview?db=core;transcript=ENST00000204637
So, if you go to http://www.ensembl.org, choose animal, put name of gene, then go to trtanscript, and then to exons.

At Gene Tools, we regularly target Morpholino oligos to exon/intron and intron/exon boundaries in order to modify splicing. The easiest resource we have worked with is the Ensembl website, as Marina suggested.

However, mRNA is often subject to alternative splicing. If you need to know the specific splicoform in your specific organism/tissue/developmental stage, you might need to isolate the mRNA and do a Northern blot for your messenger of interest; if the mass information from the Northern is not enough to determine the splicoform, you can go on to RT-PCR and/or sequencing. The surest way to determine splice sites is to compare the messenger's sequence with the genomic sequence -- but if you can accept some uncertainty, using a resource like Ensembl can save lots of time!

Best regards,

- Jon

Jon D. Moulton, Ph.D.
Gene Tools, LLC

Another method that will work for un-annotated genes (maybe you have a novel mRNA in your hands) is to use BLAT (available on the UCSC website). BLAT will align a spliced sequence to the genome, so you can visually see where the introns and exons lie. The BLAT output also gives you the exact alignment boundaries.

Try it out:

http://genome.ucsc.edu/cgi-bin/hgBlat