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
ZFLNCT05105 ZFLNCG03325 NONMMUT008765;
ZFLNCT06323 ZFLNCG04125 ENSMUST00000138361; NR_132444; NONMMUT117875;
ZFLNCT05118 ZFLNCG03333 ENSMUST00000177185;
ZFLNCT15716 ZFLNCG10183 ENST00000501397; NR_133571;
ZFLNCT05165 ZFLNCG03371 ENST00000407765; NONHSAT114914;
ZFLNCT09554 ZFLNCG06212 NONMMUT046865;
ZFLNCT03035 ZFLNCG02069 NONHSAT056602;
ZFLNCT20541 ZFLNCG13238 NONMMUT076891;
ZFLNCT05927 ZFLNCG03848 ENSMUST00000177136; NONMMUT000741;
ZFLNCT18359 ZFLNCG11842 NONMMUT080519;
ZFLNCT00869 ZFLNCG00602 ENSMUST00000117121;
ZFLNCT06921 ZFLNCG04496 NONHSAT159202;
ZFLNCT07637 ZFLNCG04933 ENSMUST00000184377;
ZFLNCT09515 ZFLNCG06184 NONHSAT204155;
ZFLNCT04656 ZFLNCG03035 ENST00000579003; NONHSAT054945;
ZFLNCT12156 ZFLNCG07929 ENST00000406003;
ZFLNCT05309 ZFLNCG03472 ENST00000607486; NONHSAT204415;
ZFLNCT02403 ZFLNCG01643 ENST00000407852; NONHSAT113226; ENSMUST00000195269;
ZFLNCT04032 ZFLNCG02583 NONMMUT133211;
ZFLNCT03008 ZFLNCG02045 NONHSAT160034;
ZFLNCT08780 ZFLNCG05687 XR_001749929;
ZFLNCT04290 ZFLNCG02774 NONMMUT127488;
ZFLNCT13834 ZFLNCG08990 NONMMUT057062;
ZFLNCT20808 ZFLNCG13384 NONHSAT017210; NONMMUT064161;
ZFLNCT13049 ZFLNCG08479 ENSMUST00000185538; NONMMUT132403;