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
ZFLNCT13027 ZFLNCG08477 ENST00000566278; ENSMUST00000189975;
ZFLNCT19313 ZFLNCG12499 ENST00000439523;
ZFLNCT09860 ZFLNCG06438 ENST00000513542; NR_126371; NONHSAT098631; ENSMUST00000204187; NONMMUT128916;
ZFLNCT08654 ZFLNCG05603 NONHSAT191586;
ZFLNCT16104 ZFLNCG10406 ENST00000416636;
ZFLNCT14090 ZFLNCG09161 ENST00000423940; NONHSAT005498;
ZFLNCT14569 ZFLNCG09477 NONMMUT088433;
ZFLNCT16972 ZFLNCG10970 ENST00000555937;
ZFLNCT10094 ZFLNCG06591 ENSMUST00000194822; NONMMUT076659;
ZFLNCT03677 ZFLNCG02362 ENSMUST00000069489;
ZFLNCT14735 ZFLNCG09555 ENST00000509840; NONHSAT099057; ENSMUST00000120816;
ZFLNCT15695 ZFLNCG10169 XR_380276; NONMMUT025494;
ZFLNCT00071 ZFLNCG00048 ENST00000545710; NONHSAT219163; ENSMUST00000117862; NONMMUT105391;
ZFLNCT01777 ZFLNCG01221 ENST00000394662; NONHSAT149318; ENSMUST00000198870;
ZFLNCT17930 ZFLNCG11560 ENSMUST00000197115; NONMMUT053324;
ZFLNCT12514 ZFLNCG08153 ENSMUST00000203885;
ZFLNCT20686 ZFLNCG13319 NONHSAT163953;
ZFLNCT11049 ZFLNCG07239 NONHSAT157531;
ZFLNCT14053 ZFLNCG09138 ENST00000418783; NR_038893; NONHSAT081952; ENSMUST00000120147; NONMMUT037327;
ZFLNCT09637 ZFLNCG06268 NONHSAT216876; ENSMUST00000120252; NONMMUT093175;
ZFLNCT03443 ZFLNCG02263 NONMMUT081408;
ZFLNCT20595 ZFLNCG13264 ENSMUST00000198417; NONMMUT054357;
ZFLNCT11806 ZFLNCG07703 ENSMUST00000153581; NONMMUT039363;
ZFLNCT19298 ZFLNCG12487 ENST00000587528; NONHSAT058885; NONMMUT031675;
ZFLNCT19189 ZFLNCG12400 NONMMUT040691;