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
ZFLNCT01097 ZFLNCG00744 ENST00000591177; ENST00000604665; ENST00000590111; ENST00000383942; ENST00000589671; ENST00000384113; ENST00000592296; ENST00000599190; ENST00000603829; ENST00000597780; ENST00000600253; ENST00000595508; ENST00000595010; ENST00000412789; rna122103; rna123184; rna119562; rna120635; rna122291; rna69739; NONHSAT066345; NONHSAT066052; NONHSAT067510; NONHSAT179928; NONHSAT032161; NONHSAT066053; NONHSAT179918; NONHSAT066344; NONHSAT179932; NONHSAT067638; NONHSAT180619; NONHSAT180395; NONHSAT067500; NONHSAT180564; NONHSAT180620; NONHSAT179990; NONHSAT068285; NONHSAT067497; NONHSAT068124; NONHSAT066677; NONHSAT066145; NONHSAT067639; NONHSAT067498; NONHSAT067499; NONHSAT067509; NONHSAT179716; NONHSAT068125; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT012799; NONHSAT067508; NONHSAT068244; NONHSAT180618; NONHSAT155389; NONHSAT067693; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000205272; ENSMUST00000203998; ENSMUST00000180846; rna40907; rna39617; rna35197; rna35194; rna39612; NONMMUT056827; NONMMUT060396; NONMMUT054960; NONMMUT068237; NONMMUT126426; NONMMUT123726; NONMMUT068232; NONMMUT126427; NONMMUT059839; NONMMUT068239; NONMMUT124878; NONMMUT060530; NONMMUT009632; NONMMUT056825; NONMMUT068235; NONMMUT126588; NONMMUT126529; NONMMUT068236; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT132117; NONMMUT060539; NONMMUT056826; NONMMUT124678; NONMMUT060997; NONMMUT068226; NONMMUT068238; NONMMUT126528;
ZFLNCT01134 ZFLNCG00767 NONHSAT101123;
ZFLNCT01228 ZFLNCG00832 NONHSAT102457; NONHSAT202813;
ZFLNCT01230 ZFLNCG00834 NONMMUT048490;
ZFLNCT01325 ZFLNCG00909 ENST00000613982; ENST00000434147; ENST00000426157; rna90220; rna66421; rna74621; NONHSAT086680; NONHSAT189848; NONHSAT165736; NONHSAT166789; NONHSAT183945; NONHSAT155667; NONHSAT192357; NONHSAT086678; NONHSAT220149; NONHSAT134676; NONHSAT014037; NONHSAT192356; NONHSAT198950; NONHSAT033962; rna80637; NONMMUT092169; NONMMUT069646;
ZFLNCT01432 ZFLNCG00988 rna125076; NONHSAT079463; NONHSAT189594; NONHSAT079464; ENSMUST00000145346; ENSMUST00000187147; ENSMUST00000145021; ENSMUST00000185798; ENSMUST00000181782; rna81789; rna81781; rna81790; rna81782; rna81787; rna81788; rna81791; NONMMUT092967; NONMMUT020955; NONMMUT020946; NONMMUT020956; NONMMUT020950; NONMMUT020948; NONMMUT092964; NONMMUT092965; NONMMUT020954; NONMMUT010285; NONMMUT092966; NONMMUT020947; NONMMUT020949;
ZFLNCT01433 ZFLNCG00989 rna125076; NONHSAT079463; NONHSAT189594; NONHSAT079464; ENSMUST00000145346; ENSMUST00000187147; ENSMUST00000145021; ENSMUST00000185798; ENSMUST00000181782; rna81789; rna81781; rna81790; rna81782; rna81787; rna81788; rna81791; NONMMUT092967; NONMMUT020955; NONMMUT020946; NONMMUT020956; NONMMUT020950; NONMMUT020948; NONMMUT092964; NONMMUT092965; NONMMUT020954; NONMMUT010285; NONMMUT092966; NONMMUT020947; NONMMUT020949;
ZFLNCT01605 ZFLNCG01103 ENST00000589195; NONHSAT053926; NONMMUT084397; NONMMUT084396;
ZFLNCT01606 ZFLNCG01104 ENST00000589195; NONHSAT053926; NONMMUT084397; NONMMUT084396;
ZFLNCT01616 ZFLNCG01112 ENST00000437825; ENST00000588766; ENST00000415255; ENST00000534006; ENST00000585832; ENST00000570175; ENST00000623762; ENST00000589281; ENST00000586610; rna98819; rna98818; rna3458; rna116102; rna116103; rna68511; rna114672; rna68512; NONHSAT002587; NONHSAT179871; NONHSAT180036; NONHSAT058988; NONHSAT200129; NONHSAT200128; NONHSAT200132; NONHSAT047077; NONHSAT097164; NONHSAT176593; NONHSAT130474; NONHSAT058987; NONHSAT175408; NONHSAT067151; NONHSAT105523; NONHSAT056077; NONHSAT176592; NONHSAT129665; NONHSAT058985; NONHSAT176591; NONHSAT021250; NONHSAT216652; NONHSAT060245; NONHSAT175635; NONHSAT058984; NONHSAT011398; NONHSAT071474; NONHSAT060252; NONHSAT060247; NONHSAT021251; NONHSAT180037; NONHSAT200130; NONHSAT060248; NONHSAT184939; NONHSAT217414; rna36350; NONMMUT053279; NONMMUT057750; NONMMUT048698; NONMMUT048697; NONMMUT057758; NONMMUT038423; NONMMUT048080; NONMMUT063810; NONMMUT038424; NONMMUT048699;
ZFLNCT01617 ZFLNCG01113 ENST00000534006; NONHSAT216652; NONHSAT129665;
ZFLNCT01618 ZFLNCG01113 ENST00000534006; NONHSAT216652; NONHSAT129665;
ZFLNCT01685 ZFLNCG01161 NONHSAT149936;
ZFLNCT01712 ZFLNCG01183 NONHSAT169068; ENSMUST00000167763; rna81738; NONMMUT020926; NONMMUT092958;
ZFLNCT01845 ZFLNCG01265 ENST00000369989; ENST00000417241; rna6547; rna6546; NONHSAT152056; NONHSAT005004; NONHSAT005003; NONHSAT149515;
ZFLNCT01941 ZFLNCG01330 ENST00000634876; NONHSAT119938; NONHSAT119939; NONHSAT119940;
ZFLNCT02089 ZFLNCG01412 ENST00000446875; ENST00000436779; ENST00000497954; ENST00000602963; ENST00000503314; NONHSAT136243; NONHSAT136238; NONHSAT105888; NONHSAT136235; NONHSAT136245; NONHSAT136242; NONHSAT017687; NONHSAT105887; NONHSAT136239; NONHSAT136237; NONHSAT053811; NONHSAT136241; NONHSAT010014; NONHSAT150681; NONHSAT010018; NONHSAT105925; ENSMUST00000139019; ENSMUST00000144738; ENSMUST00000154810; ENSMUST00000152031; rna106216; rna44782; rna44789; rna44787; rna44786; rna44788; NONMMUT074719; NONMMUT137627; NONMMUT102071; NONMMUT137628; NONMMUT074721; NONMMUT063076; NONMMUT063075; NONMMUT074720; NONMMUT074716; NONMMUT125922; NONMMUT074723; NONMMUT029575; NONMMUT125923;
ZFLNCT02090 ZFLNCG01413 ENST00000446875; ENST00000436779; ENST00000602963; ENST00000503314; NONHSAT136238; NONHSAT105888; NONHSAT136235; NONHSAT017687; NONHSAT105887; NONHSAT136239; NONHSAT136237; NONHSAT136241; NONHSAT010014; NONHSAT150681; NONHSAT010018; NONHSAT105925; ENSMUST00000152031; ENSMUST00000139019; rna44782; rna44789; rna44787; rna44786; rna44788; NONMMUT063076; NONMMUT125922; NONMMUT125923; NONMMUT063075;
ZFLNCT02091 ZFLNCG01413 ENST00000446875; ENST00000436779; ENST00000602963; ENST00000503314; NONHSAT136238; NONHSAT105888; NONHSAT136235; NONHSAT017687; NONHSAT105887; NONHSAT136239; NONHSAT136237; NONHSAT136241; NONHSAT010014; NONHSAT150681; NONHSAT010018; NONHSAT105925; ENSMUST00000152031; ENSMUST00000139019; rna44782; rna44789; rna44787; rna44786; rna44788; NONMMUT063076; NONMMUT125922; NONMMUT125923; NONMMUT063075;
ZFLNCT02107 ZFLNCG01422 ENSMUST00000056774; ENSMUST00000174778; ENSMUST00000174094; ENSMUST00000173025; ENSMUST00000172895; ENSMUST00000174261; ENSMUST00000173809; rna94057; NONMMUT029517; NONMMUT029515; NONMMUT029514; NONMMUT029522; NONMMUT100988; NONMMUT029516;
ZFLNCT02386 ZFLNCG01631 rna68470;
ZFLNCT02392 ZFLNCG01635 ENST00000579256; ENST00000623613; NONHSAT053415; NONHSAT176169; NONHSAT053416; NONHSAT074969; NONHSAT182932;
ZFLNCT02393 ZFLNCG01636 ENST00000579256; ENST00000623613; NONHSAT053415; NONHSAT176169; NONHSAT053416; NONHSAT074969; NONHSAT182932;
ZFLNCT02395 ZFLNCG01638 rna109153; NONHSAT053426; ENSMUST00000123784; NONMMUT084322; NONMMUT084321; NONMMUT011843;
ZFLNCT02439 ZFLNCG01668 ENST00000589195; NONHSAT053926; NONMMUT084397; NONMMUT084396;