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
ZFLNCT07676 ZFLNCG04961 NONHSAT125667; NONMMUT021354;
ZFLNCT16793 ZFLNCG10832 NONMMUT112932;
ZFLNCT09504 ZFLNCG06174 ENST00000520239; NONHSAT217178; ENSMUST00000153199; NONMMUT066111;
ZFLNCT16119 ZFLNCG10420 ENSMUST00000193146;
ZFLNCT05975 ZFLNCG03886 ENSMUST00000120719; NONMMUT072982;
ZFLNCT10582 ZFLNCG06910 NONMMUT125801;
ZFLNCT11349 ZFLNCG07407 NONMMUT088437;
ZFLNCT01605 ZFLNCG01103 ENST00000426903; NONHSAT087652;
ZFLNCT20035 ZFLNCG12919 ENSMUST00000137186; NONMMUT108793;
ZFLNCT08840 ZFLNCG05733 NONHSAT183856;
ZFLNCT08383 ZFLNCG05430 ENST00000584100;
ZFLNCT13746 ZFLNCG08914 ENST00000582538;
ZFLNCT05187 ZFLNCG03390 NONHSAT101419;
ZFLNCT02712 ZFLNCG01842 ENST00000623156; NONHSAT176183; NONMMUT011938;
ZFLNCT14441 ZFLNCG09389 XR_874820;
ZFLNCT06118 ZFLNCG04003 NONHSAT109003;
ZFLNCT04914 ZFLNCG03196 NONHSAT222807;
ZFLNCT11392 ZFLNCG07435 NONHSAT180755;
ZFLNCT03874 ZFLNCG02469 ENSMUST00000198842; NONMMUT121471;
ZFLNCT12167 ZFLNCG07937 NONMMUT031908;
ZFLNCT19550 ZFLNCG12666 ENST00000624347; NONHSAT150383; NONMMUT128143;
ZFLNCT09479 ZFLNCG06152 ENST00000510070;
ZFLNCT18214 ZFLNCG11752 NONHSAT176066; ENSMUST00000149865; NR_003282; NONMMUT083981;
ZFLNCT01077 ZFLNCG00727 NONMMUT098886;
ZFLNCT03728 ZFLNCG02390 NONMMUT136608;