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Table 1 Summary of sno-lncRNAs identified from human, rhesus and mouse ESCs

From: Species-specific alternative splicing leads to unique expression of sno-lncRNAs

Species Cell line Location Expression level (RPKM) snoRNA caps Parent gene Validated by NB Notes
Human ESC (H9) chr15:25310171-25313030 142 SNORD116-6, SORD116-7 SNURF-SNRPN Yes sno-IncRNA1
chr15:25324203-25325381 829 SNORD116-13, SNORD116-14 SNURF-SNRPN Yes sno-IncRNA2
chr15:25330530-25331766 2319 SNORD116-18, SNORD116-19 SNURF-SNRPN Yes sno-IncRNA3
chr15:25332807-25334043 1012 SNORD116-20, SNORD116-21 SNURF-SNRPN Yes sno-IncRNA4
chr15:25344644-25346814 113 SNORD116-26, SNORD116-27 SNURF-SNRPN Yes sno-IncRNA5
chr7:45143947-45144641 186 SNORA5A, SNORA5C TBRG4 Yes sno-Inc5AC
chr17:16342822-16343420 106 SNORD49B, SNORD49A C17orf76-AS1 Yes Additional file 1
chr11:93463680-93464265 18 SNORA25, SNORA32 TAF1D Yes Additional file 2
ENCODE Cell Lines chr1:173833312-173833583 29 SNORD81, SNORD47 GAS5 N/A N/A
chr9:136216948-136217382 14 SNORD36B, Snord36A RPL7A N/A N/A
chr11:93466393-93466763 8 SNORD5, SNORA18* TAD1D N/A N/A
Rhesus ESC chr1:204218457-204219170 14 SNORD78, SNORD77 GAS5 N/A N/A
chr1:204219672-204220510 18 SNORD75, SNORD74 GAS5 N/A N/A
chr7:2838589-2840464 83 SNORD116, SNORD116 SNURF-SNRPN N/A human sno-IncRNA3 homologue
chr7:2850511-2851734 34 SNORD116, SNORD116 SNURF-SNRPN N/A human sno-IncRNA4 homologue
chr7:164873802-164874792 29 SNORD114, SNORD114 N/A N/A N/A
chr10:15174906-15176653 13 SNORD12B, SNORD12C ZFAS1 N/A N/A
chr19:55523975-55524331 12 SNORD33, SNORD34 RPL13A N/A RPL13A region sno-IncRNA homologue
Mouse ESC (R1) chr7:52381972-52382315 146 SNORD33, SNORD34 RPL13A Yes RPL13A region sno-IncRNA
  1. 19 sno-lncRNAs identified in this study were listed with their species source, cell line source, genomic locations, expression level (RPKM), snoRNA ends, parent genes, validation and other notes. It includes eight sno-lncRNAs in human ESCs, three in ENCODE human cell lines, seven in rhesus ESCs and one in mouse ESCs. Expression levels of sno-lncRNAs were evaluated using RPKM in relevant cell lines (the ENCODE GM12878 cell line was used). Due to the poor annotation, host genes and snoRNA ends in rhesus were predicted from human and/or mouse homologous sequences. *one sno-lncRNA that contains a box C/D snoRNA at one end and a box H/ACA snoRNA at the other end was highlighted with asterisk.