id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-311066-62edsbfc	Cox, Brian J.	Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2	2020-06-24		.txt	text/plain	2926	172	61	Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5'-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. Some RNAs, especially non-coding RNAs, generally lack a poly-A tail, which could explain poor detection of TRS independent sgmRNAs. Using published sequencing data of ribosome depleted total RNA from SARS-CoV-2 infected cells and animals (Blanco-Melo et al., 2020) , I aligned these against the viral genome (Figure 2) . Using the aligned reads, I generated transcript models using stringtie, which identified multiple spliced species that aligned with the TRS-L templated events (Figure 2) . Split reads also identified TRS-independent sgmRNAs. In support of my observations on SARS-CoV-2, I also assessed SARS-CoV and MERs transcriptional data, two other human pathogenic CoV. I also identified the TIR motif, a novel sequence element (ATTGGC) flanking the spliced regions of TRS independent sgmRNAs in both SARS-CoV-2 and SARS-CoV.	./cache/cord-311066-62edsbfc.txt	./txt/cord-311066-62edsbfc.txt