Conserved lncRNA

We used three methods (that are direct BLASTN, collinearity with conserved coding gene, and overlap with multi-species ultra-conserved non-coding elements (UCNE)) to find the counterparts of zebrafish lncRNAs in human or mouse. In direct comparison of zebrafish lncRNA and human/mouse lncRNA with BLASTN, bidirectional best hits using a relatively non-stringent threshold (E-value<=10-5) were considered as orthologs. In collinearity method, we compared the coding genes of zebrafish with those of human or mouse using BLASTP as anchor points. We assumed that those lncRNAs with more than 5 anchor points in the 20k upstream/downstream region are orthologs. In UCNE method, if two lncRNAs from different species overlap with at least one UCNE, as another anchor point, they were considered as orthologs. Finally, we obtained 2,156 zebrafish lncRNA genes that have the counterpart in human or mouse.

Zebrafish lncRNA Transcript Zebrafish lncRNA Gene Human lncRNA Transcript Mouse lncRNA Transcript
ZFLNCT02892 ZFLNCG01971 ENST00000369387; NONHSAT097860; ENSMUST00000119546; XR_001779565; NONMMUT076842;
ZFLNCT09916 ZFLNCG06472 NONHSAT176391;
ZFLNCT03347 ZFLNCG02230 ENSMUST00000176552; NONMMUT015351;
ZFLNCT20251 ZFLNCG13045 ENST00000517961; XR_001750619;
ZFLNCT15871 ZFLNCG10279 ENSMUST00000202206;
ZFLNCT06206 ZFLNCG04064 ENST00000396021; NONHSAT223375;
ZFLNCT08856 ZFLNCG05745 ENST00000508433; NONHSAT096408; NONMMUT000852;
ZFLNCT03797 ZFLNCG02412 ENST00000603395; ENSMUST00000152147; NR_015608; NONMMUT056353;
ZFLNCT12048 ZFLNCG07857 NONMMUT077716;
ZFLNCT11705 ZFLNCG07652 NONHSAT155999; NONMMUT105596;
ZFLNCT05646 ZFLNCG03657 NONHSAT220701;
ZFLNCT01818 ZFLNCG01245 ENST00000532834; NONHSAT018235;
ZFLNCT01502 ZFLNCG01035 NONHSAT027457; NONMMUT086784;
ZFLNCT02769 ZFLNCG01892 ENST00000407031; NONHSAT175770;
ZFLNCT01227 ZFLNCG00831 NONHSAT149356;
ZFLNCT03931 ZFLNCG02508 NONMMUT082932;
ZFLNCT10356 ZFLNCG06773 NONMMUT023682;
ZFLNCT04661 ZFLNCG03038 ENST00000488261; NONHSAT017156;
ZFLNCT04152 ZFLNCG02678 XR_876659;
ZFLNCT07210 ZFLNCG04664 ENSMUST00000096485;
ZFLNCT12116 ZFLNCG07901 NONHSAT198150;
ZFLNCT16524 ZFLNCG10658 NONHSAT147544;
ZFLNCT12528 ZFLNCG08164 NONMMUT034292;
ZFLNCT07127 ZFLNCG04626 ENST00000423374; NONHSAT138053;
ZFLNCT02299 ZFLNCG01559 NONHSAT063083;