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
ZFLNCT18429 ZFLNCG11901 ENST00000596451; ENST00000597230; ENST00000614138; ENST00000500612; ENST00000597158; ENST00000594562; ENST00000595301; ENST00000588382; ENST00000592296; ENST00000592245; ENST00000599190; ENST00000634951; ENST00000619673; ENST00000567341; ENST00000363309; ENST00000456718; ENST00000598561; ENST00000469492; ENST00000591177; ENST00000595422; ENST00000477141; ENST00000616184; ENST00000496160; ENST00000569091; ENST00000594379; ENST00000383942; ENST00000384113; ENST00000587121; ENST00000634630; ENST00000594865; ENST00000412789; rna122189; rna119680; rna123184; rna119562; rna120635; rna122291; rna123312; rna118615; rna122192; rna69739; rna122190; rna122191; NONHSAT067569; NONHSAT180384; NONHSAT143480; NONHSAT066052; NONHSAT067510; NONHSAT067564; NONHSAT179420; NONHSAT179928; NONHSAT068239; NONHSAT068345; NONHSAT032161; NONHSAT066053; NONHSAT067560; NONHSAT060961; NONHSAT067638; NONHSAT180619; NONHSAT180621; NONHSAT180395; NONHSAT179784; NONHSAT067570; NONHSAT180564; NONHSAT066059; NONHSAT180620; NONHSAT179990; NONHSAT068337; NONHSAT068285; NONHSAT067512; NONHSAT219049; NONHSAT066677; NONHSAT063743; NONHSAT068334; NONHSAT066145; NONHSAT180624; NONHSAT068313; NONHSAT067639; NONHSAT179783; NONHSAT068255; NONHSAT068346; NONHSAT180623; NONHSAT179716; NONHSAT068335; NONHSAT068238; NONHSAT212853; NONHSAT068312; NONHSAT066141; NONHSAT143481; NONHSAT066646; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT066142; NONHSAT012799; NONHSAT179920; NONHSAT067532; NONHSAT180618; NONHSAT173232; NONHSAT155389; NONHSAT068344; NONHSAT179923; NONHSAT180551; NONHSAT068341; NONHSAT068342; NONHSAT180000; NONHSAT180552; NONHSAT067565; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna40907; rna39617; rna39612; NONMMUT060396; NONMMUT054960; NONMMUT068237; NONMMUT126426; NONMMUT126427; NONMMUT059839; NONMMUT068239; NONMMUT124878; NONMMUT009632; NONMMUT060530; NONMMUT029150; NONMMUT068235; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT068236; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT132117; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT090167; NONMMUT068226; NONMMUT068238; NONMMUT126528;
ZFLNCT18430 ZFLNCG11901 ENST00000596451; ENST00000597230; ENST00000500612; ENST00000614138; ENST00000597158; ENST00000594562; ENST00000595301; ENST00000588382; ENST00000592296; ENST00000592245; ENST00000599190; ENST00000634951; ENST00000619673; ENST00000567341; ENST00000363309; ENST00000456718; ENST00000598561; ENST00000469492; ENST00000591177; ENST00000595422; ENST00000477141; ENST00000616184; ENST00000496160; ENST00000569091; ENST00000594379; ENST00000383942; ENST00000384113; ENST00000587121; ENST00000634630; ENST00000594865; ENST00000412789; rna122189; rna119680; rna123184; rna119562; rna120635; rna122291; rna123312; rna118615; rna122192; rna69739; rna122190; rna122191; NONHSAT067569; NONHSAT180384; NONHSAT143480; NONHSAT066052; NONHSAT067510; NONHSAT067564; NONHSAT179420; NONHSAT179928; NONHSAT068239; NONHSAT068345; NONHSAT032161; NONHSAT066053; NONHSAT067560; NONHSAT060961; NONHSAT067638; NONHSAT180619; NONHSAT180621; NONHSAT180395; NONHSAT179784; NONHSAT067570; NONHSAT180564; NONHSAT066059; NONHSAT180620; NONHSAT179990; NONHSAT068337; NONHSAT068285; NONHSAT067512; NONHSAT219049; NONHSAT066677; NONHSAT063743; NONHSAT068334; NONHSAT066145; NONHSAT180624; NONHSAT068313; NONHSAT067639; NONHSAT179783; NONHSAT068255; NONHSAT068346; NONHSAT180623; NONHSAT179716; NONHSAT068335; NONHSAT068238; NONHSAT212853; NONHSAT068312; NONHSAT066141; NONHSAT143481; NONHSAT066646; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT066142; NONHSAT012799; NONHSAT179920; NONHSAT067532; NONHSAT180618; NONHSAT173232; NONHSAT155389; NONHSAT068344; NONHSAT179923; NONHSAT180551; NONHSAT068341; NONHSAT068342; NONHSAT180000; NONHSAT180552; NONHSAT067565; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna40907; rna39617; rna39612; NONMMUT060396; NONMMUT054960; NONMMUT068237; NONMMUT126426; NONMMUT126427; NONMMUT059839; NONMMUT068239; NONMMUT124878; NONMMUT009632; NONMMUT060530; NONMMUT029150; NONMMUT068235; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT068236; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT132117; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT090167; NONMMUT068226; NONMMUT068238; NONMMUT126528;
ZFLNCT18431 ZFLNCG11902 ENST00000596451; ENST00000597230; ENST00000500612; ENST00000597158; ENST00000595301; ENST00000592296; ENST00000592245; ENST00000599190; ENST00000634951; ENST00000567341; ENST00000456718; ENST00000598561; ENST00000591177; ENST00000594379; ENST00000383942; ENST00000384113; ENST00000634630; ENST00000594865; ENST00000412789; rna122189; rna123184; rna119562; rna120635; rna122291; rna123312; rna118615; rna122192; rna69739; rna122190; rna122191; NONHSAT067569; NONHSAT180384; NONHSAT143480; NONHSAT067564; NONHSAT179420; NONHSAT179928; NONHSAT068345; NONHSAT032161; NONHSAT066053; NONHSAT060961; NONHSAT067638; NONHSAT180395; NONHSAT067570; NONHSAT180564; NONHSAT180620; NONHSAT179990; NONHSAT068337; NONHSAT219049; NONHSAT066677; NONHSAT063743; NONHSAT068334; NONHSAT066145; NONHSAT180624; NONHSAT067639; NONHSAT068255; NONHSAT068346; NONHSAT180623; NONHSAT179716; NONHSAT068335; NONHSAT143481; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT012799; NONHSAT067532; NONHSAT180618; NONHSAT173232; NONHSAT155389; NONHSAT068344; NONHSAT179923; NONHSAT068341; NONHSAT068342; NONHSAT180000; NONHSAT180552; NONHSAT067565; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna39617; rna39612; NONMMUT029150; NONMMUT054960; NONMMUT060538; NONMMUT126426; NONMMUT126588; NONMMUT126427; NONMMUT060997; NONMMUT068229; NONMMUT126529; NONMMUT126530; NONMMUT090167; NONMMUT068226; NONMMUT124878; NONMMUT060530; NONMMUT053727; NONMMUT009632; NONMMUT060539; NONMMUT029153; NONMMUT124678; NONMMUT126528;
ZFLNCT18432 ZFLNCG11903 ENST00000596451; ENST00000614138; ENST00000500612; ENST00000597158; ENST00000592296; ENST00000592245; ENST00000599190; ENST00000634951; ENST00000619673; ENST00000567341; ENST00000363309; ENST00000456718; ENST00000598561; ENST00000591177; ENST00000616184; ENST00000496160; ENST00000569091; ENST00000594379; ENST00000383942; ENST00000384113; ENST00000634630; ENST00000594865; ENST00000412789; rna122189; rna123184; rna119562; rna120635; rna122291; rna118615; rna122192; rna69739; rna122190; rna122191; NONHSAT067569; NONHSAT180384; NONHSAT143480; NONHSAT066052; NONHSAT067510; NONHSAT067564; NONHSAT179420; NONHSAT179928; NONHSAT032161; NONHSAT066053; NONHSAT060961; NONHSAT067638; NONHSAT180619; NONHSAT180395; NONHSAT179784; NONHSAT067570; NONHSAT180564; NONHSAT066059; NONHSAT180620; NONHSAT179990; NONHSAT067512; NONHSAT068285; NONHSAT219049; NONHSAT066677; NONHSAT063743; NONHSAT066145; NONHSAT067639; NONHSAT179783; NONHSAT068255; NONHSAT179716; NONHSAT143481; NONHSAT066646; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT012799; NONHSAT179920; NONHSAT067532; NONHSAT180618; NONHSAT173232; NONHSAT155389; NONHSAT179923; NONHSAT180551; NONHSAT180552; NONHSAT067565; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna40907; rna39617; rna39612; NONMMUT060396; NONMMUT054960; NONMMUT068237; NONMMUT063768; NONMMUT126426; NONMMUT068232; NONMMUT126427; NONMMUT059839; NONMMUT068239; NONMMUT124878; NONMMUT009632; NONMMUT060530; NONMMUT029150; NONMMUT068235; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT068236; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT132117; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT090167; NONMMUT068226; NONMMUT063770; NONMMUT068238; NONMMUT126528;
ZFLNCT18433 ZFLNCG11904 ENST00000598561; ENST00000591177; ENST00000614138; ENST00000569091; ENST00000383942; ENST00000384113; ENST00000592296; ENST00000592245; ENST00000599190; ENST00000634630; ENST00000634951; ENST00000594865; ENST00000412789; rna122291; rna123184; rna120635; rna69739; NONHSAT067510; NONHSAT179420; NONHSAT179928; NONHSAT032161; NONHSAT066053; NONHSAT060961; NONHSAT180395; NONHSAT067638; NONHSAT180564; NONHSAT180620; NONHSAT179990; NONHSAT067512; NONHSAT219049; NONHSAT066677; NONHSAT063743; NONHSAT066145; NONHSAT067639; NONHSAT179716; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT012799; NONHSAT179920; NONHSAT067532; NONHSAT180618; NONHSAT155389; NONHSAT180552; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna39617; rna39612; NONMMUT054960; NONMMUT126426; NONMMUT126427; NONMMUT059839; NONMMUT124878; NONMMUT060530; NONMMUT009632; NONMMUT029150; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT090167; NONMMUT068226; NONMMUT126528;
ZFLNCT18434 ZFLNCG11904 ENST00000598561; ENST00000591177; ENST00000614138; ENST00000569091; ENST00000383942; ENST00000384113; ENST00000592296; ENST00000592245; ENST00000599190; ENST00000634630; ENST00000634951; ENST00000594865; ENST00000412789; rna122291; rna123184; rna120635; rna69739; NONHSAT067510; NONHSAT179420; NONHSAT179928; NONHSAT032161; NONHSAT066053; NONHSAT060961; NONHSAT180395; NONHSAT067638; NONHSAT180564; NONHSAT180620; NONHSAT179990; NONHSAT067512; NONHSAT219049; NONHSAT066677; NONHSAT063743; NONHSAT066145; NONHSAT067639; NONHSAT179716; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT012799; NONHSAT179920; NONHSAT067532; NONHSAT180618; NONHSAT155389; NONHSAT180552; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna39617; rna39612; NONMMUT054960; NONMMUT126426; NONMMUT126427; NONMMUT059839; NONMMUT124878; NONMMUT060530; NONMMUT009632; NONMMUT029150; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT090167; NONMMUT068226; NONMMUT126528;
ZFLNCT18435 ZFLNCG11904 ENST00000598561; ENST00000591177; ENST00000614138; ENST00000569091; ENST00000383942; ENST00000384113; ENST00000592296; ENST00000592245; ENST00000599190; ENST00000634630; ENST00000634951; ENST00000594865; ENST00000412789; rna122291; rna123184; rna120635; rna69739; NONHSAT067510; NONHSAT179420; NONHSAT179928; NONHSAT032161; NONHSAT066053; NONHSAT060961; NONHSAT180395; NONHSAT067638; NONHSAT180564; NONHSAT180620; NONHSAT179990; NONHSAT067512; NONHSAT219049; NONHSAT066677; NONHSAT063743; NONHSAT066145; NONHSAT067639; NONHSAT179716; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT012799; NONHSAT179920; NONHSAT067532; NONHSAT180618; NONHSAT155389; NONHSAT180552; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna39617; rna39612; NONMMUT054960; NONMMUT126426; NONMMUT126427; NONMMUT059839; NONMMUT124878; NONMMUT060530; NONMMUT009632; NONMMUT029150; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT090167; NONMMUT068226; NONMMUT126528;
ZFLNCT18436 ZFLNCG11905 ENST00000614138; ENST00000500612; ENST00000594562; ENST00000588382; ENST00000592296; ENST00000592245; ENST00000599190; ENST00000634951; ENST00000567341; ENST00000598561; ENST00000591177; ENST00000595422; ENST00000569091; ENST00000594379; ENST00000383942; ENST00000384113; ENST00000587121; ENST00000634630; ENST00000594865; ENST00000412789; rna119680; rna123184; rna119562; rna120635; rna122291; rna118615; rna69739; NONHSAT180384; NONHSAT143480; NONHSAT067510; NONHSAT179420; NONHSAT179928; NONHSAT068239; NONHSAT032161; NONHSAT066053; NONHSAT060961; NONHSAT067638; NONHSAT180619; NONHSAT180395; NONHSAT180564; NONHSAT180620; NONHSAT179990; NONHSAT067512; NONHSAT068285; NONHSAT219049; NONHSAT066677; NONHSAT063743; NONHSAT066145; NONHSAT067639; NONHSAT068255; NONHSAT179716; NONHSAT066144; NONHSAT066141; NONHSAT143481; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT066142; NONHSAT012799; NONHSAT068244; NONHSAT179920; NONHSAT067532; NONHSAT180618; NONHSAT173232; NONHSAT155389; NONHSAT180551; NONHSAT068245; NONHSAT068238; NONHSAT180552; NONHSAT068259; NONHSAT032162; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna39617; rna39612; NONMMUT054960; NONMMUT126426; NONMMUT126427; NONMMUT059839; NONMMUT124878; NONMMUT060530; NONMMUT009632; NONMMUT029150; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT090167; NONMMUT068226; NONMMUT126528;
ZFLNCT18460 ZFLNCG11928 ENST00000584410; NONHSAT060562; NONHSAT060560;
ZFLNCT18461 ZFLNCG11928 NONHSAT180095;
ZFLNCT18577 ZFLNCG12021 ENST00000596451; ENST00000592319; ENST00000614138; ENST00000446262; ENST00000597158; ENST00000592296; ENST00000634951; ENST00000619673; ENST00000456718; ENST00000598561; ENST00000591177; ENST00000588040; ENST00000477141; ENST00000616184; ENST00000569091; ENST00000594379; ENST00000383942; ENST00000384113; ENST00000634630; ENST00000594865; ENST00000600253; ENST00000595010; ENST00000412789; rna122103; rna122189; rna119640; rna123184; rna119562; rna120635; rna119534; rna122291; rna118615; rna122192; rna69739; rna122216; rna122190; rna122191; NONHSAT067569; NONHSAT180384; NONHSAT066009; NONHSAT066052; NONHSAT067510; NONHSAT067564; NONHSAT179420; NONHSAT179928; NONHSAT032161; NONHSAT066011; NONHSAT066053; NONHSAT179918; NONHSAT067560; NONHSAT060961; NONHSAT067638; NONHSAT180395; NONHSAT067500; NONHSAT179784; NONHSAT067570; NONHSAT180564; NONHSAT180620; NONHSAT179990; NONHSAT067512; NONHSAT219049; NONHSAT067497; NONHSAT066677; NONHSAT066105; NONHSAT063743; NONHSAT066145; NONHSAT180382; NONHSAT067639; NONHSAT066010; NONHSAT066155; NONHSAT179783; NONHSAT067498; NONHSAT068255; NONHSAT067499; NONHSAT067509; NONHSAT179716; NONHSAT066646; NONHSAT032163; NONHSAT179719; NONHSAT067637; NONHSAT012799; NONHSAT067508; NONHSAT068244; NONHSAT179920; NONHSAT067532; NONHSAT180618; NONHSAT155389; NONHSAT179923; NONHSAT179723; NONHSAT180552; NONHSAT067565; NONHSAT032162; NONHSAT179786; ENSMUST00000143812; ENSMUST00000205272; ENSMUST00000180846; ENSMUST00000049518; rna40907; rna39617; rna39612; rna77966; NONMMUT018127; NONMMUT060396; NONMMUT068237; NONMMUT063768; NONMMUT126426; NONMMUT068232; NONMMUT126427; NONMMUT059839; NONMMUT068239; NONMMUT124878; NONMMUT060530; NONMMUT009632; NONMMUT029150; NONMMUT068235; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT068236; NONMMUT060538; NONMMUT126530; NONMMUT068229; NONMMUT132117; NONMMUT060539; NONMMUT124678; NONMMUT029153; NONMMUT060997; NONMMUT018128; NONMMUT068226; NONMMUT063770; NONMMUT068238; NONMMUT126528;
ZFLNCT18593 ZFLNCG12033 NONHSAT193872; ENSMUST00000180865; ENSMUST00000181099; NONMMUT070901; NONMMUT070899; NONMMUT135347; NONMMUT135346; NONMMUT070900;
ZFLNCT18594 ZFLNCG12034 NONHSAT089823; NONHSAT195756; ENSMUST00000162027; ENSMUST00000192051; ENSMUST00000194628; NONMMUT135349; NONMMUT070903; NONMMUT070902; NONMMUT135348;
ZFLNCT18690 ZFLNCG12103 ENSMUST00000195064; NONMMUT003274;
ZFLNCT18697 ZFLNCG12110 NONHSAT060224; NONHSAT180033; NONHSAT060222;
ZFLNCT18698 ZFLNCG12111 NONHSAT060224; NONHSAT180033; NONHSAT180032; NONHSAT060222;
ZFLNCT18887 ZFLNCG12232 ENST00000622989; NONHSAT175978; NONHSAT172580;
ZFLNCT19008 ZFLNCG12297 ENSMUST00000131221; rna65837; NONMMUT009947; NONMMUT009950; NONMMUT085276; NONMMUT009953; NONMMUT009952; NONMMUT009948; NONMMUT009951;
ZFLNCT19157 ZFLNCG12376 ENST00000593917; ENST00000402419; ENST00000612837; ENST00000586726; NONHSAT207171; NONHSAT112121; NONHSAT207169; NONHSAT207172; NONHSAT112120; NONHSAT207170; NONHSAT112119; NONMMUT100871; NONMMUT100872;
ZFLNCT19169 ZFLNCG12384 NONMMUT136116;
ZFLNCT19170 ZFLNCG12384 NONMMUT136116;
ZFLNCT19289 ZFLNCG12480 ENST00000599320; NONHSAT000905; NONHSAT148388; NONHSAT066267; NONMMUT126577;
ZFLNCT19303 ZFLNCG12492 NONHSAT080950; NONMMUT042059;
ZFLNCT19452 ZFLNCG12599 ENST00000548595; ENST00000549438; ENST00000550947; ENST00000550840; rna85038; NONHSAT162254; NONHSAT162255; NONHSAT028755; NONHSAT028749; NONHSAT028762; NONHSAT028748; NONHSAT028763; NONHSAT028766;
ZFLNCT19453 ZFLNCG12600 ENST00000548595; ENST00000549438; ENST00000550947; ENST00000550840; rna85038; NONHSAT162254; NONHSAT162255; NONHSAT028755; NONHSAT028749; NONHSAT028762; NONHSAT028748; NONHSAT028763; NONHSAT028766;