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
ZFLNCT06376 ZFLNCG04159 NONMMUT058165;
ZFLNCT18290 ZFLNCG11789 NONHSAT053328; NONMMUT098680;
ZFLNCT20479 ZFLNCG13191 ENST00000315707; NR_026951; NONHSAT145510; NONMMUT085385;
ZFLNCT09947 ZFLNCG06483 ENST00000419794;
ZFLNCT17439 ZFLNCG11266 XR_001747325;
ZFLNCT16024 ZFLNCG10344 ENST00000509326; NONHSAT099109;
ZFLNCT09425 ZFLNCG06108 ENST00000587610; NONHSAT192632;
ZFLNCT14734 ZFLNCG09554 NR_027063; NONHSAT073175;
ZFLNCT06166 ZFLNCG04033 NONMMUT048288;
ZFLNCT11596 ZFLNCG07579 NONMMUT131887;
ZFLNCT20885 ZFLNCG13442 NONHSAT139084;
ZFLNCT05089 ZFLNCG03315 NONHSAT169075;
ZFLNCT12820 ZFLNCG08334 ENST00000464884;
ZFLNCT18328 ZFLNCG11818 NONHSAT151359; NONMMUT080124;
ZFLNCT07855 ZFLNCG05074 NONHSAT179463; NONMMUT118921;
ZFLNCT01503 ZFLNCG01036 NONHSAT151628;
ZFLNCT19489 ZFLNCG12625 NONHSAT214133;
ZFLNCT19610 ZFLNCG12705 ENSMUST00000119445;
ZFLNCT19907 ZFLNCG12851 NONMMUT093668;
ZFLNCT15461 ZFLNCG10037 ENSMUST00000159536;
ZFLNCT08063 ZFLNCG05211 ENST00000406314; NONHSAT114000; ENSMUST00000119463; NONMMUT013365;
ZFLNCT11421 ZFLNCG07457 XR_001744464;
ZFLNCT13464 ZFLNCG08727 XR_244242;
ZFLNCT05236 ZFLNCG03419 NONHSAT130919; ENSMUST00000120233;
ZFLNCT20245 ZFLNCG13042 NONHSAT126961;