If you have a transcriptome that has been assembled from shotgun reads the TSA (Transcriptome Shotgun Assembly) database is a good place to put it so that it can be widely accessed.
This guide assumes that you simply want to submit the assembled sequences from your transcriptome without annotations. NCBI sets a high bar for inclusion of annotations so for most non-model organisms they are probably not going to meet the criteria.
To create a TSA submission take a look at the ncbi guidelines. This gist is based on those guidelines.
