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
ZFLNCT10376 ZFLNCG06785 NONHSAT189608; NONHSAT189609; NONMMUT040730;
ZFLNCT10377 ZFLNCG06785 NONHSAT189608; NONHSAT189609; NONMMUT040730;
ZFLNCT10839 ZFLNCG07092 rna70630;
ZFLNCT11251 ZFLNCG07349 NONMMUT064076;
ZFLNCT12257 ZFLNCG08008 NONHSAT222775;
ZFLNCT12532 ZFLNCG08168 NONMMUT009434; NONMMUT009435;
ZFLNCT14071 ZFLNCG09151 ENST00000606913; NONHSAT207704;
ZFLNCT14072 ZFLNCG09151 ENST00000606913; NONHSAT207704;
ZFLNCT14539 ZFLNCG09454 NONMMUT014214; NONMMUT014213;
ZFLNCT14848 ZFLNCG09642 ENST00000549515; rna92398; NONHSAT036198; rna72444;
ZFLNCT14849 ZFLNCG09642 ENST00000549515; rna92398; NONHSAT036198; rna72444;
ZFLNCT15031 ZFLNCG09761 NONHSAT169357; NONHSAT037051; NONHSAT037050; NONMMUT094346;
ZFLNCT15032 ZFLNCG09761 NONHSAT169357; NONHSAT037051; NONHSAT037050; NONMMUT094346;
ZFLNCT15392 ZFLNCG09993 rna61835; rna61836;
ZFLNCT15994 ZFLNCG10319 NONHSAT213247;
ZFLNCT16230 ZFLNCG10481 ENST00000521197; ENST00000467897; rna51647; NONHSAT119683; ENSMUST00000131502; rna35395; NONMMUT056950;
ZFLNCT16521 ZFLNCG10655 NONHSAT127684;
ZFLNCT16634 ZFLNCG10716 ENST00000458352; ENST00000437331; ENST00000605417; NONHSAT122129; NONHSAT122136; NONHSAT122133; NONHSAT122127; ENSMUST00000159568; rna33878; NONMMUT055660; NONMMUT055657;
ZFLNCT16951 ZFLNCG10956 NONHSAT168995; NONHSAT168994; NONMMUT015967;
ZFLNCT16952 ZFLNCG10956 NONHSAT168995; NONHSAT168994; NONMMUT015967;
ZFLNCT18081 ZFLNCG11661 NONMMUT031986;
ZFLNCT18774 ZFLNCG12157 NONHSAT008696; NONHSAT150290; NONHSAT008694; ENSMUST00000180797; NONMMUT002780; NONMMUT078897; NONMMUT002781; NONMMUT002786;
ZFLNCT18955 ZFLNCG12270 NONMMUT034732;
ZFLNCT19020 ZFLNCG12302 ENST00000487240; ENST00000626948; ENST00000493521; ENST00000460739; rna30825; rna30826; NONHSAT194974; NONHSAT093465; NONHSAT093470; NONHSAT093469; NONHSAT093468; ENSMUST00000196793; ENSMUST00000198032; ENSMUST00000196243; NONMMUT042500; NONMMUT042498; NONMMUT042499; NONMMUT042501; NONMMUT042497;
ZFLNCT19022 ZFLNCG12302 ENST00000470817; ENST00000487240; ENST00000481234; ENST00000597347; ENST00000626948; ENST00000493521; ENST00000460739; ENST00000482559; ENST00000493116; rna30825; rna30826; NONHSAT194974; NONHSAT093465; NONHSAT093470; NONHSAT093473; NONHSAT093469; NONHSAT093468; NONHSAT093472; NONHSAT093482; NONHSAT093480; NONHSAT196623; NONHSAT093481; ENSMUST00000188411; ENSMUST00000196793; ENSMUST00000196058; ENSMUST00000198032; ENSMUST00000196243; rna16172; NONMMUT042504; NONMMUT042497; NONMMUT042500; NONMMUT042498; NONMMUT113082; NONMMUT042499; NONMMUT042501; NONMMUT042503; NONMMUT113081;