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
ZFLNCT13915 ZFLNCG09043 NONHSAT159723; NONHSAT160790; NONHSAT024359; NONHSAT161539;
ZFLNCT13916 ZFLNCG09044 ENST00000623895; NONHSAT066734; NONHSAT159723; NONHSAT179793; NONHSAT179794; NONHSAT066733; NONHSAT066735; NONHSAT161539; NONHSAT066732; NONHSAT160790; NONHSAT024359;
ZFLNCT13917 ZFLNCG09044 ENST00000623895; NONHSAT066734; NONHSAT159723; NONHSAT179793; NONHSAT179794; NONHSAT066733; NONHSAT066735; NONHSAT161539; NONHSAT066732; NONHSAT160790; NONHSAT024359;
ZFLNCT14156 ZFLNCG09204 NONMMUT049453;
ZFLNCT14157 ZFLNCG09205 NONMMUT049453;
ZFLNCT14563 ZFLNCG09471 ENST00000426157; rna77744; rna77745; rna74621; rna66421; rna77746; NONHSAT189848; NONHSAT091535; NONHSAT220149; NONHSAT134676; NONHSAT160400; NONHSAT198950; rna80637; NONMMUT092169;
ZFLNCT14948 ZFLNCG09706 NONHSAT207507; NONHSAT207506; NONHSAT209330;
ZFLNCT14973 ZFLNCG09725 ENST00000475761; ENST00000405276;
ZFLNCT15007 ZFLNCG09744 ENST00000554629; NONHSAT037793;
ZFLNCT15025 ZFLNCG09758 rna6449;
ZFLNCT15026 ZFLNCG09758 rna6449;
ZFLNCT15071 ZFLNCG09788 ENST00000613982; ENST00000434147; ENST00000426157; rna90220; rna66421; rna74621; NONHSAT165736; NONHSAT004190; NONHSAT215736; NONHSAT192357; NONHSAT086680; NONHSAT004188; NONHSAT014037; NONHSAT192356; NONHSAT198950; NONHSAT004191; NONHSAT134676; NONHSAT147897; NONHSAT166789; NONHSAT086678; NONHSAT220149; NONHSAT147896; NONHSAT147894; NONHSAT033962; NONHSAT189848; NONHSAT155667; NONHSAT091535; rna80637; NONMMUT129855; NONMMUT092169;
ZFLNCT15105 ZFLNCG09814 ENST00000576490; ENST00000597230; ENST00000500612; ENST00000494214; ENST00000569752; ENST00000573447; ENST00000446262; ENST00000597158; ENST00000623035; ENST00000599190; ENST00000476474; ENST00000593270; ENST00000590111; ENST00000496160; ENST00000586338; ENST00000576590; ENST00000594379; ENST00000383942; ENST00000571449; ENST00000575139; ENST00000594865; ENST00000457283; ENST00000595301; ENST00000486926; ENST00000570901; ENST00000634951; ENST00000619673; ENST00000363309; ENST00000598561; ENST00000469492; ENST00000571963; ENST00000595422; ENST00000588040; ENST00000477141; ENST00000492040; ENST00000589671; ENST00000575089; ENST00000396799; ENST00000573414; ENST00000612939; ENST00000572691; ENST00000589551; ENST00000412789; ENST00000596451; ENST00000406892; ENST00000489336; ENST00000519852; ENST00000592296; ENST00000592245; ENST00000465341; ENST00000518073; ENST00000567341; ENST00000595094; ENST00000588047; ENST00000517411; ENST00000384113; ENST00000592087; ENST00000592880; ENST00000604303; ENST00000614138; ENST00000577163; ENST00000569728; ENST00000594562; ENST00000586394; ENST00000524335; ENST00000456718; ENST00000591177; ENST00000521207; ENST00000598051; ENST00000616184; ENST00000495324; ENST00000569091; ENST00000523031; ENST00000634630; rna119547; rna101309; rna122291; rna69739; rna122191; rna119528; rna117583; rna118615; rna119549; rna122190; rna101315; rna117581; rna117582; rna117580; rna61646; rna119548; rna61647; rna117584; rna117579; rna122189; rna123184; rna119562; rna120635; rna119534; rna117578; rna123312; rna122192; rna101310; NONHSAT180384; NONHSAT067564; NONHSAT066011; NONHSAT180621; NONHSAT147961; NONHSAT180564; NONHSAT141770; NONHSAT068285; NONHSAT068124; NONHSAT147976; NONHSAT129556; NONHSAT068334; NONHSAT129555; NONHSAT180382; NONHSAT189872; NONHSAT066155; NONHSAT061207; NONHSAT129558; NONHSAT179931; NONHSAT147962; NONHSAT067637; NONHSAT217782; NONHSAT068244; NONHSAT147971; NONHSAT173232; NONHSAT072465; NONHSAT068341; NONHSAT068245; NONHSAT129557; NONHSAT067565; NONHSAT147975; NONHSAT129553; NONHSAT067569; NONHSAT067560; NONHSAT060961; NONHSAT063614; NONHSAT179784; NONHSAT180620; NONHSAT179990; NONHSAT124124; NONHSAT141763; NONHSAT066010; NONHSAT068255; NONHSAT147969; NONHSAT061208; NONHSAT179716; NONHSAT068335; NONHSAT147960; NONHSAT217811; NONHSAT147966; NONHSAT147967; NONHSAT061212; NONHSAT067532; NONHSAT141765; NONHSAT180618; NONHSAT179923; NONHSAT141764; NONHSAT219049; NONHSAT179783; NONHSAT032162; NONHSAT147970; NONHSAT061210; NONHSAT129554; NONHSAT066004; NONHSAT067510; NONHSAT147964; NONHSAT147973; NONHSAT066053; NONHSAT066006; NONHSAT173545; NONHSAT068440; NONHSAT066059; NONHSAT147965; NONHSAT161786; NONHSAT067639; NONHSAT129839; NONHSAT068346; NONHSAT217809; NONHSAT180623; NONHSAT147968; NONHSAT141771; NONHSAT068125; NONHSAT061211; NONHSAT068312; NONHSAT143481; NONHSAT066646; NONHSAT032163; NONHSAT129559; NONHSAT179920; NONHSAT061203; NONHSAT155389; NONHSAT068344; NONHSAT067693; NONHSAT060959; NONHSAT068238; NONHSAT179786; NONHSAT066052; NONHSAT066009; NONHSAT143480; NONHSAT179420; NONHSAT179928; NONHSAT068239; NONHSAT032175; NONHSAT032161; NONHSAT068345; NONHSAT066019; NONHSAT180252; NONHSAT179932; NONHSAT108460; NONHSAT180395; NONHSAT063615; NONHSAT180619; NONHSAT067638; NONHSAT067570; NONHSAT068337; NONHSAT067512; NONHSAT066677; NONHSAT217810; NONHSAT063743; NONHSAT068259; NONHSAT066145; NONHSAT180624; NONHSAT068313; NONHSAT147963; NONHSAT147974; NONHSAT061206; NONHSAT179719; NONHSAT179459; NONHSAT147977; NONHSAT129560; NONHSAT012799; NONHSAT212439; NONHSAT147972; NONHSAT061209; NONHSAT068439; NONHSAT189871; NONHSAT068342; NONHSAT180000; NONHSAT180552; NONHSAT122291; ENSMUST00000205272; ENSMUST00000180846; ENSMUST00000049518; ENSMUST00000143812; ENSMUST00000199837; rna39617; rna39612; rna77966; NONMMUT018127; NONMMUT054960; NONMMUT068237; NONMMUT126426; NONMMUT068232; NONMMUT126427; NONMMUT059839; NONMMUT068239; NONMMUT122901; NONMMUT124878; NONMMUT009632; NONMMUT060530; NONMMUT029150; NONMMUT068235; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT122900; NONMMUT068236; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT132117; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT122898; NONMMUT122899; NONMMUT060997; NONMMUT018128; NONMMUT090167; NONMMUT068226; NONMMUT068238; NONMMUT126528;
ZFLNCT15106 ZFLNCG09815 ENST00000596451; ENST00000614138; ENST00000500612; ENST00000446262; ENST00000597158; ENST00000592296; ENST00000599190; ENST00000619673; ENST00000567341; ENST00000456718; ENST00000598561; ENST00000469492; ENST00000591177; ENST00000590111; ENST00000477141; ENST00000616184; ENST00000496160; ENST00000569091; ENST00000586338; ENST00000594379; ENST00000383942; ENST00000462960; ENST00000589671; ENST00000384113; ENST00000396799; ENST00000594865; ENST00000600253; ENST00000595010; ENST00000412789; rna122103; rna122189; rna123184; rna119562; rna120635; rna119534; rna122291; rna122192; rna69739; rna54192; rna122216; rna122190; rna122191; rna54193; rna54194; NONHSAT067569; NONHSAT066052; NONHSAT066009; NONHSAT143480; NONHSAT067510; NONHSAT067564; NONHSAT179928; NONHSAT214884; NONHSAT032161; NONHSAT066011; NONHSAT179982; NONHSAT066053; NONHSAT179918; NONHSAT067560; NONHSAT179932; NONHSAT180621; NONHSAT067638; NONHSAT180619; NONHSAT180395; NONHSAT067500; NONHSAT179784; NONHSAT067570; NONHSAT180564; NONHSAT180552; NONHSAT180620; NONHSAT179990; NONHSAT066059; NONHSAT067512; NONHSAT068285; NONHSAT067497; NONHSAT068124; NONHSAT217810; NONHSAT161786; NONHSAT066677; NONHSAT063743; NONHSAT189872; NONHSAT066145; NONHSAT219049; NONHSAT180382; NONHSAT068313; NONHSAT129839; NONHSAT067639; NONHSAT066010; NONHSAT179783; NONHSAT067498; NONHSAT067499; NONHSAT217809; NONHSAT179716; NONHSAT217811; NONHSAT068125; NONHSAT068312; NONHSAT143481; NONHSAT179931; NONHSAT066646; NONHSAT032163; NONHSAT179719; NONHSAT129832; NONHSAT067637; NONHSAT012799; NONHSAT068244; NONHSAT179920; NONHSAT067532; NONHSAT068195; NONHSAT173232; NONHSAT155389; NONHSAT179923; NONHSAT180618; NONHSAT189871; NONHSAT180551; NONHSAT180615; NONHSAT067693; NONHSAT216673; NONHSAT067565; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna40907; rna39617; rna39612; NONMMUT060396; NONMMUT068237; NONMMUT063768; NONMMUT126426; NONMMUT068232; NONMMUT126427; NONMMUT059839; NONMMUT068239; NONMMUT124878; NONMMUT060530; NONMMUT009632; NONMMUT029150; NONMMUT068235; NONMMUT126588; NONMMUT126529; NONMMUT068236; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT132117; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT068226; NONMMUT063770; NONMMUT068238; NONMMUT126528;
ZFLNCT15424 ZFLNCG10016 ENSMUST00000159142; ENSMUST00000161024; NONMMUT066766; NONMMUT066764; NONMMUT129230; NONMMUT131475;
ZFLNCT15777 ZFLNCG10223 ENST00000599050; NONHSAT179749; NONHSAT066384;
ZFLNCT15818 ZFLNCG10246 ENST00000415679; ENST00000435580; ENST00000562313; ENST00000531824; rna81546; rna111894; rna9391; rna81545; NONHSAT055614; NONHSAT007037; NONHSAT007036; NONHSAT176509; NONHSAT055613; NONHSAT025076; NONHSAT160893; NONHSAT161624; NONHSAT160894; NONHSAT025078; NONHSAT159877; NONHSAT007038; NONHSAT161625;
ZFLNCT15998 ZFLNCG10322 ENST00000497954; ENST00000503314; ENST00000505151; ENST00000514784; ENST00000499096; ENST00000446875; ENST00000506340; ENST00000436779; ENST00000417281; ENST00000602963; ENST00000511331; rna44721; rna43609; rna43554; NONHSAT033784; NONHSAT136235; NONHSAT205133; NONHSAT010014; NONHSAT150681; NONHSAT105939; NONHSAT033783; NONHSAT105938; NONHSAT136242; NONHSAT105887; NONHSAT146402; NONHSAT105885; NONHSAT105940; NONHSAT136238; NONHSAT105888; NONHSAT136245; NONHSAT017687; NONHSAT136239; NONHSAT136237; NONHSAT105937; NONHSAT136241; NONHSAT105925; NONHSAT105936; NONHSAT136243; NONHSAT053811; NONHSAT010018; ENSMUST00000139019; ENSMUST00000144738; ENSMUST00000154810; ENSMUST00000152031; rna106216; rna44782; rna44789; rna44787; rna44786; rna44788; NONMMUT074719; NONMMUT137627; NONMMUT102071; NONMMUT137628; NONMMUT074721; NONMMUT063076; NONMMUT063075; NONMMUT074720; NONMMUT074716; NONMMUT125922; NONMMUT074723; NONMMUT029575; NONMMUT125923;
ZFLNCT15999 ZFLNCG10323 ENST00000497954; ENST00000503314; ENST00000505151; ENST00000514784; ENST00000499096; ENST00000446875; ENST00000506340; ENST00000436779; ENST00000417281; ENST00000602963; ENST00000511331; rna44721; rna43609; rna43554; NONHSAT033784; NONHSAT136235; NONHSAT205133; NONHSAT010014; NONHSAT150681; NONHSAT105939; NONHSAT033783; NONHSAT105938; NONHSAT136242; NONHSAT105887; NONHSAT146402; NONHSAT105885; NONHSAT105940; NONHSAT136238; NONHSAT105888; NONHSAT136245; NONHSAT017687; NONHSAT136239; NONHSAT136237; NONHSAT105937; NONHSAT136241; NONHSAT105925; NONHSAT105936; NONHSAT136243; NONHSAT053811; NONHSAT010018; ENSMUST00000139019; ENSMUST00000144738; ENSMUST00000154810; ENSMUST00000152031; rna106216; rna44782; rna44789; rna44787; rna44786; rna44788; NONMMUT074719; NONMMUT137627; NONMMUT102071; NONMMUT137628; NONMMUT074721; NONMMUT063076; NONMMUT063075; NONMMUT074720; NONMMUT074716; NONMMUT125922; NONMMUT074723; NONMMUT029575; NONMMUT125923;
ZFLNCT16000 ZFLNCG10324 ENST00000497954; ENST00000503314; ENST00000505151; ENST00000514784; ENST00000499096; ENST00000446875; ENST00000506340; ENST00000436779; ENST00000417281; ENST00000602963; ENST00000511331; rna44721; rna43609; rna43554; NONHSAT033784; NONHSAT136235; NONHSAT205133; NONHSAT010014; NONHSAT150681; NONHSAT105939; NONHSAT033783; NONHSAT105938; NONHSAT136242; NONHSAT105887; NONHSAT146402; NONHSAT105885; NONHSAT105940; NONHSAT136238; NONHSAT105888; NONHSAT136245; NONHSAT017687; NONHSAT136239; NONHSAT136237; NONHSAT105937; NONHSAT136241; NONHSAT105925; NONHSAT105936; NONHSAT136243; NONHSAT053811; NONHSAT010018; ENSMUST00000139019; ENSMUST00000144738; ENSMUST00000154810; ENSMUST00000152031; rna106216; rna44782; rna44789; rna44787; rna44786; rna44788; NONMMUT074719; NONMMUT137627; NONMMUT102071; NONMMUT137628; NONMMUT074721; NONMMUT063076; NONMMUT063075; NONMMUT074720; NONMMUT074716; NONMMUT125922; NONMMUT074723; NONMMUT029575; NONMMUT125923;
ZFLNCT16001 ZFLNCG10325 ENST00000497954; ENST00000503314; ENST00000505151; ENST00000514784; ENST00000499096; ENST00000446875; ENST00000506340; ENST00000436779; ENST00000417281; ENST00000602963; ENST00000511331; rna44721; rna43609; rna43554; NONHSAT033784; NONHSAT136235; NONHSAT205133; NONHSAT010014; NONHSAT150681; NONHSAT105939; NONHSAT033783; NONHSAT105938; NONHSAT136242; NONHSAT105887; NONHSAT146402; NONHSAT105885; NONHSAT105940; NONHSAT136238; NONHSAT105888; NONHSAT136245; NONHSAT017687; NONHSAT136239; NONHSAT136237; NONHSAT105937; NONHSAT136241; NONHSAT105925; NONHSAT105936; NONHSAT136243; NONHSAT053811; NONHSAT010018; ENSMUST00000139019; ENSMUST00000144738; ENSMUST00000154810; ENSMUST00000152031; rna106216; rna44782; rna44789; rna44787; rna44786; rna44788; NONMMUT074719; NONMMUT137627; NONMMUT102071; NONMMUT137628; NONMMUT074721; NONMMUT063076; NONMMUT063075; NONMMUT074720; NONMMUT074716; NONMMUT125922; NONMMUT074723; NONMMUT029575; NONMMUT125923;
ZFLNCT16014 ZFLNCG10336 ENST00000491732; NONHSAT180143; NONHSAT060835;
ZFLNCT16024 ZFLNCG10344 ENST00000497954; ENST00000503314; ENST00000505151; ENST00000514784; ENST00000499096; ENST00000446875; ENST00000506340; ENST00000436779; ENST00000417281; ENST00000602963; ENST00000511331; rna44721; rna43609; rna43554; NONHSAT033784; NONHSAT136235; NONHSAT205133; NONHSAT010014; NONHSAT150681; NONHSAT105939; NONHSAT033783; NONHSAT105938; NONHSAT136242; NONHSAT105887; NONHSAT146402; NONHSAT105885; NONHSAT105940; NONHSAT136238; NONHSAT105888; NONHSAT136245; NONHSAT017687; NONHSAT136239; NONHSAT136237; NONHSAT105937; NONHSAT136241; NONHSAT105925; NONHSAT105936; NONHSAT136243; NONHSAT053811; NONHSAT010018; ENSMUST00000139019; ENSMUST00000144738; ENSMUST00000154810; ENSMUST00000152031; rna106216; rna44782; rna44789; rna44787; rna44786; rna44788; NONMMUT074719; NONMMUT074716; NONMMUT137627; NONMMUT043652; NONMMUT102071; NONMMUT137628; NONMMUT074721; NONMMUT063076; NONMMUT063075; NONMMUT074720; NONMMUT043650; NONMMUT125922; NONMMUT074723; NONMMUT029575; NONMMUT125923;
ZFLNCT16030 ZFLNCG10347 ENST00000437753; rna3955; NONHSAT002824; NONHSAT221352; NONHSAT194208; NONHSAT160879; rna8740;
ZFLNCT16036 ZFLNCG10352 NONMMUT063765; NONMMUT127783; NONMMUT126215; NONMMUT127782; NONMMUT126216; NONMMUT063766; NONMMUT126214;