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
ZFLNCT12833 ZFLNCG08345 NONMMUT037021;
ZFLNCT07135 ZFLNCG04629 ENST00000570636;
ZFLNCT16140 ZFLNCG10436 NONMMUT017189;
ZFLNCT16822 ZFLNCG10857 NONHSAT178331;
ZFLNCT15263 ZFLNCG09913 NONHSAT173926;
ZFLNCT13937 ZFLNCG09058 NONHSAT124124;
ZFLNCT10012 ZFLNCG06539 NONMMUT081391;
ZFLNCT16866 ZFLNCG10893 NONMMUT004325;
ZFLNCT02758 ZFLNCG01881 ENSMUST00000121864; NONMMUT109707;
ZFLNCT03974 ZFLNCG02537 ENST00000458361;
ZFLNCT17636 ZFLNCG11381 ENST00000584772; NR_104607; NONHSAT145702;
ZFLNCT19454 ZFLNCG12601 ENST00000544920; NONHSAT101518; ENSMUST00000086236; XR_383892; NONMMUT022236;
ZFLNCT18951 ZFLNCG12267 ENST00000515547; XR_001745255; NONHSAT123119; NONMMUT058362;
ZFLNCT11039 ZFLNCG07232 ENST00000453841; NONHSAT136396;
ZFLNCT05661 ZFLNCG03668 ENSMUST00000187154; NONMMUT079011;
ZFLNCT02764 ZFLNCG01887 ENST00000511386; ENSMUST00000185254;
ZFLNCT05956 ZFLNCG03872 ENST00000629188; NONHSAT184903;
ZFLNCT05080 ZFLNCG03310 ENST00000518409; NONHSAT221317; ENSMUST00000204855;
ZFLNCT10606 ZFLNCG06927 ENST00000547655; NONHSAT163523;
ZFLNCT11794 ZFLNCG07695 NONMMUT087911;
ZFLNCT19560 ZFLNCG12673 XR_001751685;
ZFLNCT15026 ZFLNCG09758 ENST00000440059; ENSMUST00000120184;
ZFLNCT03167 ZFLNCG02140 NONMMUT082028;
ZFLNCT00720 ZFLNCG00500 XR_931373; NONHSAT027048; NONMMUT123153;
ZFLNCT14027 ZFLNCG09121 NONHSAT152385; ENSMUST00000118023;