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
ZFLNCT19664 ZFLNCG12734 XR_384507;
ZFLNCT03089 ZFLNCG02099 ENSMUST00000165827; XR_876039;
ZFLNCT11671 ZFLNCG07633 ENST00000427229; NONHSAT181851;
ZFLNCT06338 ZFLNCG04137 XR_932357; NONHSAT200801;
ZFLNCT02491 ZFLNCG01697 NONMMUT011677;
ZFLNCT12050 ZFLNCG07858 XR_001779570;
ZFLNCT01690 ZFLNCG01165 NONHSAT093170; ENSMUST00000180833; NONMMUT113011;
ZFLNCT16513 ZFLNCG10649 NONHSAT217403;
ZFLNCT11435 ZFLNCG07466 XR_001739099;
ZFLNCT07896 ZFLNCG05089 ENST00000419766; NR_033665; NONHSAT213379; NONMMUT094711;
ZFLNCT10416 ZFLNCG06812 NONMMUT094478;
ZFLNCT01415 ZFLNCG00977 ENST00000439038; NONHSAT180029; ENSMUST00000199413;
ZFLNCT10029 ZFLNCG06547 NR_037612;
ZFLNCT20008 ZFLNCG12902 NONHSAT166058; NONMMUT033356;
ZFLNCT05116 ZFLNCG03332 ENST00000588490; XR_001746503; NONHSAT097885; ENSMUST00000118791; NONMMUT066804;
ZFLNCT02392 ZFLNCG01635 ENST00000430731; NONHSAT084375;
ZFLNCT02421 ZFLNCG01653 NONHSAT211617; NONMMUT121609;
ZFLNCT02034 ZFLNCG01376 ENST00000467614;
ZFLNCT07018 ZFLNCG04561 NONHSAT171627;
ZFLNCT20384 ZFLNCG13129 NONMMUT039701;
ZFLNCT12685 ZFLNCG08238 NONMMUT047033;
ZFLNCT02508 ZFLNCG01699 ENSMUST00000187566;
ZFLNCT20278 ZFLNCG13065 ENST00000493291; NONHSAT093212; ENSMUST00000051985;
ZFLNCT13201 ZFLNCG08567 NONHSAT023109;
ZFLNCT14003 ZFLNCG09106 ENST00000411857; NONHSAT007861;