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
ZFLNCT00407 ZFLNCG00278 XR_001784911;
ZFLNCT11832 ZFLNCG07717 ENST00000452572; NONHSAT191431; ENSMUST00000119530; NONMMUT101445;
ZFLNCT09189 ZFLNCG05963 ENST00000411687; NONHSAT147714; ENSMUST00000118507; NONMMUT048455;
ZFLNCT03051 ZFLNCG02075 ENST00000416882; NONHSAT141041;
ZFLNCT12890 ZFLNCG08383 ENST00000601911;
ZFLNCT02753 ZFLNCG01878 NONHSAT053514;
ZFLNCT00021 ZFLNCG00017 NONMMUT112577;
ZFLNCT08551 ZFLNCG05528 NONMMUT041370;
ZFLNCT16920 ZFLNCG10934 NONHSAT151604;
ZFLNCT11529 ZFLNCG07534 ENSMUST00000171054; NONMMUT112267;
ZFLNCT15848 ZFLNCG10264 ENST00000399538;
ZFLNCT19632 ZFLNCG12723 NONHSAT182699;
ZFLNCT17052 ZFLNCG11027 ENST00000621765; NONHSAT095141;
ZFLNCT11441 ZFLNCG07471 NONMMUT095466;
ZFLNCT13524 ZFLNCG08769 NONHSAT004025;
ZFLNCT13561 ZFLNCG08784 NONHSAT173071; ENSMUST00000133337; NONMMUT129143;
ZFLNCT15380 ZFLNCG09983 ENST00000299671; NONHSAT173370;
ZFLNCT13970 ZFLNCG09085 NONHSAT058922; NONMMUT085119;
ZFLNCT06275 ZFLNCG04096 NONHSAT080219; NONMMUT110906;
ZFLNCT09412 ZFLNCG06098 ENST00000617175;
ZFLNCT04399 ZFLNCG02861 ENSMUST00000206208;
ZFLNCT15885 ZFLNCG10284 NONMMUT128195;
ZFLNCT10956 ZFLNCG07185 XR_870694;
ZFLNCT07453 ZFLNCG04825 ENST00000555580; NONHSAT035540;
ZFLNCT04157 ZFLNCG02682 ENST00000561698; NONHSAT067681;