I have sequenced about a 700 bp gene fragment of protease from genomic DNA. Now I would like to know the coding regions and whether it has any introns? Which software should I use?
Can you look into sequenced and annotated genomes of related species?
Otherwise I would isolate RNA, make cDNA and sequence the cDNA with gene specific primers. Then you can compare the genomic DNA and the cDNA sequences.
The methodology described above is the one which will give you definitive data. Anyway, if you are working on a protease whose sequence is supposed to be conserved across species, just do a BLASTx of your sequence at NCBI. In this case, the presence/absence of gaps should give you reasonable information obout the presence/absence of introns and their location.
MY serine protease is of Arthrobotrys conoides. The reported gene sequence is about 1150bp and my sequence is 700bp. My sequence showing 99% similarity with reported.
If you have 99% similarity, you can use the other known and described genes as a scaffold to make a prediction for your gene. For the ultimate proof you will not come around sequencing cDNA.
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