Intersect gene annotation with specific position or genomic interval

Hi,

I've several genomic interval and I want to check if they are overlapping with known gene. I've a gtf file with the coordinates of gene exons. My idea was to use intersectBed from bedtools but I've a little problem with small genomic interval that are are overlapping intron coordinates and not exons ( it do ot report me the gene where this interval is). Is it possible to specifiy to intersectBed to take into account introns ? or is there an another tool ?

Thanks

N.