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
ZFLNCT07226 ZFLNCG04675 ENSMUST00000117401;
ZFLNCT20982 ZFLNCG13518 ENST00000514441; NONHSAT096734;
ZFLNCT19532 ZFLNCG12649 NONMMUT115471;
ZFLNCT01545 ZFLNCG01073 ENST00000540463; NONHSAT217213; ENSMUST00000203107; NR_040766; NONMMUT070348;
ZFLNCT02320 ZFLNCG01573 ENSMUST00000184540;
ZFLNCT18844 ZFLNCG12206 ENST00000574705; NONHSAT148122;
ZFLNCT20250 ZFLNCG13045 ENST00000523257; ENSMUST00000117840;
ZFLNCT06939 ZFLNCG04499 NONMMUT102978;
ZFLNCT03729 ZFLNCG02391 ENST00000446783; NONHSAT001870;
ZFLNCT17424 ZFLNCG11257 NONHSAT184360; NONMMUT013248;
ZFLNCT18506 ZFLNCG11966 NONMMUT042546;
ZFLNCT17190 ZFLNCG11132 ENST00000423244; NONHSAT220733;
ZFLNCT06161 ZFLNCG04028 NONHSAT206209;
ZFLNCT13802 ZFLNCG08964 NONMMUT050266;
ZFLNCT05090 ZFLNCG03315 ENSMUST00000181782; NR_033497; NONMMUT020942;
ZFLNCT11089 ZFLNCG07261 ENST00000315132; NONHSAT175635;
ZFLNCT20404 ZFLNCG13142 NONHSAT178823;
ZFLNCT15365 ZFLNCG09973 NONHSAT152125; ENSMUST00000138430; NONMMUT088453;
ZFLNCT19303 ZFLNCG12492 ENSMUST00000178097;
ZFLNCT16045 ZFLNCG10359 ENST00000423841; NONHSAT175208; ENSMUST00000139408; NONMMUT021103;
ZFLNCT20701 ZFLNCG13327 NONHSAT160317; NONMMUT038482;
ZFLNCT19071 ZFLNCG12317 ENST00000439072; NONHSAT077403; ENSMUST00000188050;
ZFLNCT13191 ZFLNCG08559 NONHSAT066833; NONMMUT060117;
ZFLNCT20411 ZFLNCG13147 ENST00000426194; XR_935342; ENSMUST00000139804; NONMMUT031657;
ZFLNCT03521 ZFLNCG02299 ENST00000444527;