This might help! https://www.youtube.com/watch?v=0EP5wQ0pyvU
On genome.ucsc.edu, you can visualise if predicted genes / exons match with actually detected RNAs or ESTs (which is more trustworthy than just prediction), then download the corresponding sequences.
(but some of the tools mentioned above may already check this?)
FGENESH can be optimized for different organisms (e.g. fungi).
Sequencing of cDNA libraries followed by mapping to the genome sequence would be a genome wide experimental approach, where you also get information about splice variants.
If the gene structure is annotated you can look it up in the corresponding browser or gff file as suggested by others. However, If you just have the product of your gene and the raw genome sequence, you can align it with BLAT, for instance. If you have the protein product of a homologous gene I would suggest you run Exonerate.
If you have cDNA and gDNA sequences, Spidey at NCBI would infer the exon-intron boundaries. If you have the gDNA only, GeneScan (http://genes.mit.edu/GENSCAN.html) would recognize probable boundaries.
you can use intron prediction algoithms and alignment vs coding sequence (EST,cDNA) as previously suggested. For validation check the splicing sites ( | ). Most of splicing site are 5' G| GTR .... YAG|G 3'
Good luck
If you are interested in many/all genes of your organism, use NGS sequencing of mRNA isolated from cells grown under different conditions (maximise expression of genes) followed by mapping to the genome sequence. This will give you most intron/exon borders, splice variants and 3'- and 5'-regions.
This will be helpful..
https://www.youtube.com/watch?v=_asGjfCTLNE
Dear,
I use this: http://www.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind.
Good luck!
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