While comparing long vs small RNA-seq signal from uniquely mapping reads from the same cell type, I observed a handful of exonic regions where both signal data are highly expressed. The small RNA-seq reads are usually about 40nt long whereas the read length of the library is 75nt and the regions.
Also these exonic regions don't have supporting promoter signal from small RNA CAGE experiments, and the regions are not annotated for ncRNA, snoRNA or miRNA from GENCODE, RefSeq, and FANTOM5.
I am wondering if these small RNAs could be either excised exons, snoRNAs or miRNAs but I don't know how to validate these hypothesis hence my question:
How to determine the evidence of an excised exon? Is there a set of RNA binding protein, or sequence motif that I could look for?
EDIT following @Chirag Nepal comment: For example the exon of the SEC24C gene below has both long and short RNA expression and very low CAGE evidence at the exon start. Note that the expression values shown on all tracks are topped at 10 read per million (fushia lines above each signals). Thanks in advance for your time