The transport of rice glutelin storage proteins to the storage vacuoles requires Rab5 and its cognate guanine nucleotide exchange factor (Rab5-GEF). Loss of function of these membrane vesicular trafficking factors results in the initial secretion of storage proteins and later their partial engulfment by the plasma membrane to form an extracellular paramural body (PMB); an aborted endosome complex. Here we show that in the Rab5-GEF mutant glup6 line, glutelin RNAs are specifically mis-localized from their normal location on the cisternal-ER to the protein body-ER and also apparently translocated to the PMBs. We substantiated the association of mRNAs with this aborted endosome complex by RNA-seq of PMBs purified by flow cytometry. Two PMB-associated RNA groups are readily resolved: those that are specifically enriched in this aborted complex and those that are highly expressed in the cytoplasm. Examination of the PMB-enriched RNAs indicates that they were not a random sampling of the glup6 transcriptome but, instead, encompassed only a few functional mRNA classes. Although specific autophagy is also an alternative mechanism, these studies support the view that RNA localization may co-opt membrane vesicular trafficking and that many RNAs, which share function or intracellular location, are co-transported in developing rice seeds.