Assembled sequence submission to Genbank?

[Melissa]

Hi, I'm working on a paper about gene discovery in RNA-Seq. I have uploaded my NGS data to SRA but I'm not sure if I need to submit the assembled contigs I used in my analysis to Genbank. I'm a bit skeptical as these are not full length mRNAs and they contained gaps. Plus, I don't see any other paper doing that. Anyway, the sequences will be showed in the protein alignments as part of the additional files.

Does anyone know the standard procedure?

Thanks
Melissa