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
ZFLNCT09183 ZFLNCG05960 NONMMUT127699;
ZFLNCT00175 ZFLNCG00115 NONHSAT176477; NONMMUT084483;
ZFLNCT06497 ZFLNCG04227 ENST00000506407; NONHSAT092125; ENSMUST00000195492;
ZFLNCT18427 ZFLNCG11899 NONHSAT180249;
ZFLNCT05421 ZFLNCG03534 NONMMUT029108;
ZFLNCT18303 ZFLNCG11800 ENST00000406025; NONHSAT017730; ENSMUST00000162504; NONMMUT038364;
ZFLNCT12175 ZFLNCG07943 ENSMUST00000133742; XR_001784569; NONMMUT115745;
ZFLNCT18884 ZFLNCG12229 XR_872852;
ZFLNCT10672 ZFLNCG06977 NONHSAT149138;
ZFLNCT05724 ZFLNCG03715 NONMMUT090204;
ZFLNCT19521 ZFLNCG12639 ENST00000448913; NONHSAT078524; ENSMUST00000117876;
ZFLNCT01847 ZFLNCG01267 NONHSAT149513;
ZFLNCT16098 ZFLNCG10400 NONHSAT197190; NONMMUT104279;
ZFLNCT05146 ZFLNCG03358 ENST00000401029; NONHSAT179707;
ZFLNCT00429 ZFLNCG00295 NONHSAT098860;
ZFLNCT06887 ZFLNCG04473 ENST00000521717;
ZFLNCT07454 ZFLNCG04826 ENST00000547785; ENSMUST00000187682; NONMMUT000812;
ZFLNCT05549 ZFLNCG03611 ENSMUST00000155951;
ZFLNCT07907 ZFLNCG05097 NONHSAT009985;
ZFLNCT14758 ZFLNCG09574 NONHSAT101961; XR_872672;
ZFLNCT08318 ZFLNCG05384 ENST00000486414; XR_001747591; NONHSAT047228; ENSMUST00000120318; XR_001781424; NONMMUT045070;
ZFLNCT03623 ZFLNCG02330 ENST00000445336; NONHSAT095490; NONMMUT056549;
ZFLNCT13617 ZFLNCG08827 ENST00000603272; NONHSAT207766;
ZFLNCT11358 ZFLNCG07412 NONMMUT104143;
ZFLNCT11666 ZFLNCG07634 NONMMUT133928;