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
ZFLNCT01715 ZFLNCG01186 NONMMUT000506;
ZFLNCT11712 ZFLNCG07657 NONHSAT156006;
ZFLNCT10375 ZFLNCG06785 ENST00000397254; NONHSAT136776; ENSMUST00000119414; NONMMUT059121;
ZFLNCT11007 ZFLNCG07220 ENSMUST00000160999;
ZFLNCT08685 ZFLNCG05624 XR_389388;
ZFLNCT08252 ZFLNCG05335 NONHSAT164108;
ZFLNCT15689 ZFLNCG10166 NONHSAT170783;
ZFLNCT19409 ZFLNCG12566 ENST00000635687; NR_132742;
ZFLNCT08890 ZFLNCG05760 NONMMUT127379;
ZFLNCT00050 ZFLNCG00037 NONHSAT007044;
ZFLNCT14935 ZFLNCG09696 ENST00000429211; NONHSAT184193;
ZFLNCT18341 ZFLNCG11830 ENST00000244820; NR_135202; NONHSAT179471;
ZFLNCT10338 ZFLNCG06766 XR_867753;
ZFLNCT13230 ZFLNCG08583 NONMMUT010965;
ZFLNCT01688 ZFLNCG01163 ENSMUST00000191834; NONMMUT079302;
ZFLNCT05773 ZFLNCG03740 NONMMUT000334;
ZFLNCT05947 ZFLNCG03863 NONMMUT067217;
ZFLNCT09346 ZFLNCG06057 ENST00000454082; NONHSAT079405; ENSMUST00000086596; NONMMUT002519;
ZFLNCT00871 ZFLNCG00604 NONHSAT160506;
ZFLNCT06000 ZFLNCG03907 ENSMUST00000180862; NONMMUT119050;
ZFLNCT09007 ZFLNCG05838 NONHSAT183384; ENSMUST00000178708; NONMMUT066295;
ZFLNCT15105 ZFLNCG09814 NONMMUT053705;
ZFLNCT12439 ZFLNCG08121 NONHSAT223580;
ZFLNCT01721 ZFLNCG01192 ENSMUST00000120466; NONMMUT050674;
ZFLNCT04573 ZFLNCG02993 NONHSAT201693;