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
ZFLNCT00117 ZFLNCG00079 NONHSAT183457; NONHSAT076575; NONHSAT183458; ENSMUST00000181595; NONMMUT001260; NONMMUT001261; NONMMUT075590;
ZFLNCT00118 ZFLNCG00080 NONHSAT183457; NONHSAT076575; NONHSAT183458; ENSMUST00000181595; NONMMUT001260; NONMMUT001261; NONMMUT075590;
ZFLNCT00648 ZFLNCG00439 NONHSAT099505; NONMMUT065509; NONMMUT065510;
ZFLNCT00734 ZFLNCG00509 NONHSAT166348;
ZFLNCT03087 ZFLNCG02097 NONHSAT175358; NONMMUT011580; NONMMUT011581;
ZFLNCT03432 ZFLNCG02254 ENST00000415146; NONHSAT122831; NONHSAT213860; NONMMUT123446;
ZFLNCT03802 ZFLNCG02416 NONMMUT124584; NONMMUT059401; NONMMUT059400; NONMMUT059399; NONMMUT059402;
ZFLNCT03887 ZFLNCG02478 NONHSAT011397;
ZFLNCT05923 ZFLNCG03846 NONHSAT182284;
ZFLNCT05997 ZFLNCG03906 NONMMUT119052;
ZFLNCT06000 ZFLNCG03907 ENSMUST00000131029; rna30552; rna30553; NONMMUT053539; NONMMUT119050; NONMMUT119049;
ZFLNCT06336 ZFLNCG04136 NONHSAT207201; NONHSAT207199;
ZFLNCT06568 ZFLNCG04269 NONHSAT222655;
ZFLNCT06796 ZFLNCG04408 NONMMUT038972;
ZFLNCT07411 ZFLNCG04808 NONMMUT063272;
ZFLNCT07412 ZFLNCG04808 NONMMUT063272;
ZFLNCT08566 ZFLNCG05540 NONHSAT185887; NONMMUT109177; NONMMUT037825; NONMMUT109178; NONMMUT037826;
ZFLNCT08569 ZFLNCG05540 NONHSAT185887; NONMMUT109177; NONMMUT037825; NONMMUT109178; NONMMUT037826;
ZFLNCT08570 ZFLNCG05540 NONHSAT185887; NONMMUT109177; NONMMUT037825; NONMMUT109178; NONMMUT037826;
ZFLNCT08925 ZFLNCG05783 NONHSAT183457; NONHSAT076575; NONHSAT183458; ENSMUST00000181595; NONMMUT001260; NONMMUT001261; NONMMUT075590;
ZFLNCT09276 ZFLNCG06015 NONMMUT037503;
ZFLNCT09521 ZFLNCG06190 NONHSAT134595; NONMMUT036927;
ZFLNCT09522 ZFLNCG06191 NONHSAT134595; NONMMUT036927;
ZFLNCT09523 ZFLNCG06191 NONHSAT134595; NONMMUT036927;
ZFLNCT09524 ZFLNCG06191 NONHSAT134595; NONMMUT036927;