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
ZFLNCT01229 ZFLNCG00833 ENSMUST00000099331; NR_028314; NONMMUT018623;
ZFLNCT05623 ZFLNCG03648 NONHSAT150067;
ZFLNCT07203 ZFLNCG04660 ENSMUST00000161126; NONMMUT077849;
ZFLNCT04536 ZFLNCG02970 ENSMUST00000204451; NONMMUT057018;
ZFLNCT07253 ZFLNCG04692 ENST00000619697;
ZFLNCT05688 ZFLNCG03688 NONHSAT135491; ENSMUST00000133808; NONMMUT036290;
ZFLNCT05368 ZFLNCG03502 NONHSAT202714;
ZFLNCT03800 ZFLNCG02414 NONHSAT152775;
ZFLNCT07801 ZFLNCG05030 ENST00000514280; NONHSAT135241; ENSMUST00000153600; NONMMUT036498;
ZFLNCT04709 ZFLNCG03063 NONHSAT060336;
ZFLNCT02683 ZFLNCG01820 ENSMUST00000118491;
ZFLNCT20607 ZFLNCG13273 NONMMUT040051;
ZFLNCT06144 ZFLNCG04015 NONHSAT196855;
ZFLNCT20058 ZFLNCG12937 ENSMUST00000057752;
ZFLNCT06953 ZFLNCG04510 NONHSAT209343; NONMMUT068005;
ZFLNCT15868 ZFLNCG10279 NONHSAT215765; XR_871462;
ZFLNCT15214 ZFLNCG09886 XR_922313; XR_867369;
ZFLNCT18185 ZFLNCG11727 ENST00000505398; NONHSAT096496;
ZFLNCT12980 ZFLNCG08437 NONHSAT067289;
ZFLNCT19400 ZFLNCG12562 NONHSAT197629; XR_001780686;
ZFLNCT08845 ZFLNCG05737 ENST00000425462; NONHSAT084715;
ZFLNCT02813 ZFLNCG01926 ENST00000398050; ENSMUST00000120024; NONMMUT111148;
ZFLNCT19339 ZFLNCG12516 NONMMUT046578;
ZFLNCT16727 ZFLNCG10795 ENST00000568522; ENSMUST00000205237;
ZFLNCT17299 ZFLNCG11176 NR_037634; NONHSAT006050;