Hello,
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
Can you show a browser screenshot for any gene ? If you think it is snorna, you can probably check iCLIP data for snoRNP complex, i think it was paper in genome biology.
Update: Honestly, not sure, what is going on there. However i would check few things
1) Is this one of the case, or there are handful of such cases. If it is only a single case, probably not very interesting and likley some sequencing artifact, but if have hundreds of such loci, you can look for some features.
2) I see that in the screenshot, in the boundary of small RNAs reads, there is a different color in the corresponding exonic region, which is marking something. Check the color code document in the UCSC.
3) Look for RNA-binding protein from ENCODE data.
4) If you see low CAGE signals on exons, check here https://www.ncbi.nlm.nih.gov/pubmed/24002785 that shows CAGE signals on exons are post-transcriptionally processed signals. Look if you find similar sequence enrichment in CAGE tags.
Thanks this is very helpful.