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
ZFLNCT06688 ZFLNCG04349 ENST00000403259; ENST00000404269; ENST00000402707; ENST00000405418; NONHSAT108234; NONHSAT207010; NONHSAT108409; NONHSAT208927; NONHSAT207011; NONHSAT208920; NONHSAT206983; NONHSAT108412; NONHSAT208904; NONHSAT208926; NONHSAT210351; NONHSAT108411; NONHSAT006252; ENSMUST00000146857; rna75746; NONMMUT016573; NONMMUT089374; NONMMUT089375; NONMMUT016667; NONMMUT016666; NONMMUT016574; NONMMUT016665; NONMMUT089373;
ZFLNCT06796 ZFLNCG04408 ENST00000454509; ENST00000429821; ENST00000434742; rna76127; NONMMUT038973; NONMMUT038972;
ZFLNCT06885 ZFLNCG04472 ENST00000548810; ENST00000550837; ENST00000415255; ENST00000589281; rna3458; NONHSAT002587; NONHSAT037539; NONHSAT058984; NONHSAT184505; NONHSAT159282; NONHSAT022341; NONHSAT058985; NONHSAT021251; NONHSAT013400; NONHSAT184506; NONHSAT176593; NONHSAT130474; NONHSAT022337; NONHSAT021250; ENSMUST00000178699; ENSMUST00000195512; rna99358; rna99359; rna99350; NONMMUT033512; NONMMUT033513; NONMMUT033508; NONMMUT038423; NONMMUT048080; NONMMUT033517; NONMMUT033516; NONMMUT038424;
ZFLNCT06886 ZFLNCG04472 ENST00000548810; ENST00000550837; ENST00000415255; ENST00000589281; rna93892; rna3458; NONHSAT168605; NONHSAT002587; NONHSAT021250; NONHSAT058984; NONHSAT184505; NONHSAT159282; NONHSAT037539; NONHSAT184939; NONHSAT168606; NONHSAT071474; NONHSAT022341; NONHSAT058985; NONHSAT021251; NONHSAT168604; NONHSAT013400; NONHSAT184506; NONHSAT130474; NONHSAT022337; NONHSAT037537; NONHSAT168607; ENSMUST00000178699; ENSMUST00000195512; rna99358; rna99359; rna99350; NONMMUT033512; NONMMUT057750; NONMMUT033513; NONMMUT033508; NONMMUT070332; NONMMUT038423; NONMMUT048080; NONMMUT033517; NONMMUT033516; NONMMUT038424; NONMMUT070331;
ZFLNCT06888 ZFLNCG04474 NONHSAT022016; NONHSAT160415; NONMMUT033698;
ZFLNCT06891 ZFLNCG04477 NONMMUT115735;
ZFLNCT06922 ZFLNCG04497 NONHSAT159200;
ZFLNCT07139 ZFLNCG04633 NONMMUT109660;
ZFLNCT07152 ZFLNCG04642 NONHSAT017441; NONHSAT152740; NONHSAT180588; NONHSAT152739; NONHSAT152741; NONHSAT180587; NONHSAT008736; NONHSAT152742; NONHSAT152743; NONHSAT180589; NONHSAT158732;
ZFLNCT07277 ZFLNCG04702 NONMMUT134576;
ZFLNCT07565 ZFLNCG04894 ENST00000611953; ENST00000403259; ENST00000608318; ENST00000454320; ENST00000362070; ENST00000635439; ENST00000404269; ENST00000369385; ENST00000564237; ENST00000498492; ENST00000402707; ENST00000405418; rna44644; rna44654; NONHSAT108234; NONHSAT108206; NONHSAT207010; NONHSAT206984; NONHSAT206983; NONHSAT206979; NONHSAT149773; NONHSAT210353; NONHSAT010024; NONHSAT208927; NONHSAT208920; NONHSAT208904; NONHSAT210351; NONHSAT108411; NONHSAT210352; NONHSAT006253; NONHSAT006252; NONHSAT208905; NONHSAT108409; NONHSAT153071; NONHSAT210354; NONHSAT207011; NONHSAT006254; NONHSAT108412; NONHSAT208926; NONHSAT108251; ENSMUST00000176742; ENSMUST00000176760; ENSMUST00000139822; ENSMUST00000193036; ENSMUST00000146857; ENSMUST00000118168; ENSMUST00000176275; ENSMUST00000090779; ENSMUST00000177796; ENSMUST00000176143; rna75934; rna18414; rna18415; rna75746; NONMMUT016573; NONMMUT113658; NONMMUT044249; NONMMUT044254; NONMMUT044255; NONMMUT016666; NONMMUT113659; NONMMUT016574; NONMMUT089373; NONMMUT113660; NONMMUT044253; NONMMUT016664; NONMMUT089375; NONMMUT016572; NONMMUT044251; NONMMUT016667; NONMMUT111673; NONMMUT016665; NONMMUT044256; NONMMUT113661; NONMMUT089374; NONMMUT090997; NONMMUT016675;
ZFLNCT07566 ZFLNCG04895 ENST00000611953; ENST00000403259; ENST00000608318; ENST00000454320; ENST00000404269; ENST00000369385; ENST00000564237; ENST00000498492; ENST00000405418; rna44644; NONHSAT108234; NONHSAT108206; NONHSAT206984; NONHSAT206983; NONHSAT206979; NONHSAT149773; NONHSAT210353; NONHSAT010024; NONHSAT208927; NONHSAT208920; NONHSAT208904; NONHSAT210351; NONHSAT108411; NONHSAT210352; NONHSAT006253; NONHSAT006252; NONHSAT208905; NONHSAT108409; NONHSAT153071; NONHSAT210354; NONHSAT006254; NONHSAT208926; ENSMUST00000176742; ENSMUST00000176760; ENSMUST00000139822; ENSMUST00000193036; ENSMUST00000146857; ENSMUST00000118168; ENSMUST00000176275; ENSMUST00000090779; ENSMUST00000177796; ENSMUST00000176143; rna75934; rna18414; rna75746; rna18415; NONMMUT016573; NONMMUT113658; NONMMUT044249; NONMMUT044254; NONMMUT044255; NONMMUT016666; NONMMUT113659; NONMMUT016574; NONMMUT089373; NONMMUT113660; NONMMUT044253; NONMMUT016664; NONMMUT089375; NONMMUT016572; NONMMUT044251; NONMMUT111673; NONMMUT016665; NONMMUT044256; NONMMUT113661; NONMMUT089374; NONMMUT090997; NONMMUT016675;
ZFLNCT07596 ZFLNCG04909 rna40631;
ZFLNCT07754 ZFLNCG05001 NONMMUT136678; NONMMUT071751;
ZFLNCT07755 ZFLNCG05002 NONMMUT136678; NONMMUT071751;
ZFLNCT07756 ZFLNCG05002 NONMMUT136678; NONMMUT071751;
ZFLNCT07910 ZFLNCG05100 NONMMUT112458;
ZFLNCT07911 ZFLNCG05100 NONMMUT112458;
ZFLNCT07965 ZFLNCG05134 ENST00000428747; ENST00000439788; NONHSAT151158; NONHSAT151159; NONHSAT001024; NONHSAT151161; NONHSAT001023; NONHSAT151160;
ZFLNCT08044 ZFLNCG05195 ENST00000431955; NONHSAT005064; NONHSAT149521; ENSMUST00000163675; ENSMUST00000138472; ENSMUST00000154329; ENSMUST00000133570; ENSMUST00000135512; ENSMUST00000144591; ENSMUST00000131345; ENSMUST00000198085; ENSMUST00000145191; ENSMUST00000137970; ENSMUST00000146337; ENSMUST00000137800; ENSMUST00000152663; rna19056; NONMMUT111925; NONMMUT044741; NONMMUT044738; NONMMUT044736; NONMMUT044733; NONMMUT044728; NONMMUT113828; NONMMUT044739; NONMMUT044732; NONMMUT044737; NONMMUT044729; NONMMUT044735; NONMMUT044734; NONMMUT044740;
ZFLNCT08133 ZFLNCG05248 NONHSAT219861; ENSMUST00000180734; rna77743; NONMMUT017936; NONMMUT017933; NONMMUT091629; NONMMUT091630; NONMMUT017934; NONMMUT017945; NONMMUT017935; NONMMUT017937;
ZFLNCT08329 ZFLNCG05394 ENST00000414339; rna3762; NONHSAT148816; NONHSAT002746; ENSMUST00000195276; NONMMUT049192; NONMMUT117196;
ZFLNCT08330 ZFLNCG05394 ENST00000414339; rna3762; NONHSAT148816; NONHSAT002746; ENSMUST00000195276; NONMMUT049192; NONMMUT117196;
ZFLNCT08365 ZFLNCG05420 ENST00000448389; NONHSAT219723; NONHSAT132767; NONHSAT220913; NONHSAT220912; NONMMUT089975;
ZFLNCT08366 ZFLNCG05420 ENST00000448389; NONHSAT219723; NONHSAT132767; NONHSAT220913; NONHSAT220912; NONMMUT089975;