Table 1 Overview of selected lncRNAs and other candidates. Summary of the 4 selected lncRNAs in this study in addition to supplemental candidates with interesting characteristics that could not be studied extensively. Information on genomic localisation, number of co-expressed genes, average expression level and comments on the reason of their selection have been displayed
From: RNA-Seq analysis reveals the long noncoding RNAs associated with immunity in wild Myotis myotis bats
id | Alternative name or orthologue | Module | Reason for selection and comments | Average TMM | nb co-expressed genes | genome_contig | start (principal isoform) | stop (principal isoform) | Orientation | lncRNA_type | Length (principal isoform) | GC_percent (principal isoform) | nb_exons (principal isoform) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
BatLnc_Mmyo_Intergenic.scaffold_m19_p_11G5906 | BatLnc1 | ME1 | Highest number of co-expressed genes | 421.7794 | 505 | scaffold_m19_p_11 | 51860350 | 51873439 | - | Intergenic lncRNA (lincRNA) | 1381 | 54.89 | 9 |
BatLnc_Mmyo_Intergenic.scaffold_m19_p_20G211 | TUG1 | ME1 | Second highest number of co-expressed genes | 203.5984 | 482 | scaffold_m19_p_20 | 585143 | 594776 | - | Intergenic lncRNA (lincRNA) | 6970 | 43.74 | 6 |
BatLnc_Mmyo_Intergenic.scaffold_m19_p_10G9343 | MALAT1 | ME3 | Very high maximum expression | 14764.89 | 226 | scaffold_m19_p_10 | 78761846 | 78767310 | - | Intergenic lncRNA (lincRNA) | 4695 | 41.68 | 4 |
BatLnc_Mmyo_Intergenic.scaffold_m19_p_10G9375 | NEAT1:25 | ME3 | Very high maximum expression | 219.5041 | 317 | scaffold_m19_p_10 | 78820282 | 78822192 | - | Intergenic lncRNA (lincRNA) | 1584 | 58.52 | 3 |
BatLnc_Mmyo_Intergenic.scaffold_m19_p_2G8635 | ME1 | Close to GBP6 (Interferon (IFN)-inducible GTPase), fourth highest number of co-expressed genes | 28.0283 | 459 | scaffold_m19_p_2 | 67195941 | 67199810 | - | Intergenic lncRNA (lincRNA) | 709 | 46.83 | 4 | |
BatLnc_Mmyo_OA.scaffold_m19_p_1G16694 | ME1 | Overlap RORA, an important gene for the function of Th4 and Th17 cells (10.1371/journal.pone.0251233 , https://www.nature.com/articles/s41467-020–20385-9) | 15.24445 | 224 | scaffold_m19_p_1 | 176262064 | 176279643 | + | Overlapping Antisens lncRNA (loancRNA) | 3085 | 45.41 | 3 | |
BatLnc_Mmyo_Intergenic.scaffold_m19_p_18G6167 | ME3 | Ex-aequo highest number of co-expressed genes in ME3 | 68.93299 | 367 | scaffold_m19_p_18 | 32961501 | 32969028 | - | Intergenic lncRNA (lincRNA) | 7527 | 46.45 | 1 | |
BatLnc_Mmyo_OA.scaffold_m19_p_8G519 | ME3 | Ex-aequo highest number of co-expressed genes in ME3, overlap HECW2 | 21.4605 | 367 | scaffold_m19_p_8 | 6154728 | 6156175 | + | Overlapping Antisens lncRNA (loancRNA) | 927 | 53.83 | 2 | |
BatLnc_Mmyo_Intergenic.scaffold_m19_p_7G3451 | ME3 | Fragment of an low antisens expression coming from the promoter of (Interferon gamma receptor 1) | 33.14992 | 248 | scaffold_m19_p_7 | 25080813 | 25086933 | + | Intergenic lncRNA (lincRNA) | 6120 | 42.79 | 1 | |