All transcripts were divided into PCGs and non-coding transcripts after the reference genome annotation. A non-coding transcript that overlapped with PCGs, shorter than 200 nucleotides and containing single exon were filtered out. Then filtered transcripts were aligned against to the NCBI NR database (www.ncbi.nlm.nih.gov/protein) and UniProt rat_10116 protein database (www.uniprot.org) [83]; any transcripts which shown sequence similarity with any of these proteins with a cut-off E value of 10− 5 were removed. After these two filtering steps, the software CNCI version 2 [84], PLEK version 1.2 [85], CPAT version 2.0 [86] were used to predict the coding potential of transcripts. The candidate transcripts with no putative coding potential (CNCI score < 0), PLEK score < 0, and coding probability cut-off value of CPAT < 0.44 were considered as final lncRNAs. Furthermore, the final lncRNAs only identified in at least two samples were used for further analyses.

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