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
ZFLNCT08367 ZFLNCG05420 ENST00000448389; NONHSAT219723; NONHSAT132767; NONHSAT220913; NONHSAT220912; NONMMUT089975;
ZFLNCT08368 ZFLNCG05420 ENST00000448389; NONHSAT219723; NONHSAT132767; NONHSAT220913; NONHSAT220912; NONMMUT089975;
ZFLNCT08369 ZFLNCG05421 ENST00000448389; NONHSAT220913; NONHSAT220912; NONHSAT219723; NONHSAT132767; NONHSAT163571; NONMMUT089975;
ZFLNCT08410 ZFLNCG05444 NONHSAT131979;
ZFLNCT08532 ZFLNCG05515 ENST00000513533; ENST00000439545; ENST00000481995; ENST00000548801; ENST00000518046; ENST00000518088; ENST00000613383; ENST00000523364; ENST00000429755; ENST00000467897; ENST00000508688; ENST00000613939; ENST00000512427; ENST00000620092; ENST00000616712; ENST00000617934; ENST00000425358; ENST00000521197; ENST00000615604; ENST00000521231; ENST00000464382; ENST00000602610; ENST00000523790; ENST00000518848; ENST00000622675; ENST00000619974; ENST00000434063; ENST00000479766; ENST00000465846; ENST00000611352; ENST00000466037; ENST00000517635; ENST00000455246; ENST00000524304; ENST00000513165; ENST00000492897; ENST00000520395; ENST00000460041; ENST00000426965; ENST00000523331; ENST00000480872; ENST00000509870; ENST00000505700; ENST00000593300; ENST00000521159; ENST00000520360; ENST00000440016; ENST00000619311; ENST00000519935; ENST00000477144; ENST00000518947; ENST00000428939; ENST00000435312; ENST00000512206; ENST00000416928; ENST00000425595; ENST00000521687; ENST00000524048; ENST00000474040; ENST00000517641; ENST00000502764; ENST00000491264; ENST00000429611; ENST00000474324; ENST00000562848; ENST00000498652; ENST00000604081; ENST00000467155; ENST00000514702; ENST00000519694; ENST00000517550; ENST00000476204; ENST00000453875; ENST00000593438; ENST00000522863; ENST00000495032; ENST00000494420; ENST00000522193; ENST00000487849; ENST00000504972; ENST00000620211; ENST00000522674; ENST00000620901; ENST00000567780; ENST00000424518; rna84770; rna84761; rna110524; rna110493; rna110537; rna84762; rna20465; rna20463; rna20461; rna51654; rna110529; rna20470; rna20459; rna110526; rna20469; rna20462; rna110528; rna110538; rna20468; rna84765; rna20467; rna110530; rna51647; rna51632; rna20460; rna51645; rna51633; rna51652; rna110525; rna84763; rna51650; rna20466; rna20444; rna84771; rna20464; NONHSAT054421; NONHSAT028514; NONHSAT075627; NONHSAT211837; NONHSAT028528; NONHSAT119677; NONHSAT119697; NONHSAT183137; NONHSAT119670; NONHSAT175307; NONHSAT119672; NONHSAT119682; NONHSAT075636; NONHSAT054434; NONHSAT119698; NONHSAT028529; NONHSAT163579; NONHSAT175305; NONHSAT119702; NONHSAT119704; NONHSAT054411; NONHSAT028518; NONHSAT119680; NONHSAT119706; NONHSAT054437; NONHSAT054405; NONHSAT185941; NONHSAT028510; NONHSAT211840; NONHSAT119687; NONHSAT119664; NONHSAT211839; NONHSAT211844; NONHSAT054435; NONHSAT054444; NONHSAT028530; NONHSAT054450; NONHSAT054401; NONHSAT119711; NONHSAT119684; NONHSAT119665; NONHSAT211838; NONHSAT028511; NONHSAT185938; NONHSAT119675; NONHSAT054441; NONHSAT185937; NONHSAT119678; NONHSAT054449; NONHSAT119667; NONHSAT175306; NONHSAT119669; NONHSAT163580; NONHSAT119673; NONHSAT054406; NONHSAT054433; NONHSAT211835; NONHSAT054403; NONHSAT211834; NONHSAT213318; NONHSAT175303; NONHSAT119693; NONHSAT028509; NONHSAT119683; NONHSAT119703; NONHSAT054442; NONHSAT075630; NONHSAT054443; NONHSAT119705; NONHSAT054446; NONHSAT028539; NONHSAT075637; NONHSAT028527; NONHSAT075638; NONHSAT119688; NONHSAT119700; NONHSAT119710; NONHSAT175308; NONHSAT028507; NONHSAT211842; NONHSAT119708; NONHSAT211843; NONHSAT211836; NONHSAT028531; NONHSAT185940; NONHSAT163581; NONHSAT054427; NONHSAT054408; NONHSAT054431; NONHSAT163582; NONHSAT028517; NONHSAT119709; NONHSAT028512; NONHSAT175304; NONHSAT119674; NONHSAT028541; NONHSAT119696; NONHSAT054407; NONHSAT213319; NONHSAT054454; NONHSAT119685; NONHSAT119690; NONHSAT119668; NONHSAT119676; NONHSAT028519; NONHSAT054432; NONHSAT211841; NONHSAT119666; NONHSAT028513; NONHSAT028516; NONHSAT119707; ENSMUST00000183562; ENSMUST00000150698; ENSMUST00000185194; ENSMUST00000136302; ENSMUST00000134512; ENSMUST00000185090; ENSMUST00000126966; ENSMUST00000143191; ENSMUST00000152462; ENSMUST00000184301; ENSMUST00000137729; ENSMUST00000131502; ENSMUST00000128562; ENSMUST00000184566; ENSMUST00000190845; ENSMUST00000145799; ENSMUST00000132326; ENSMUST00000152027; ENSMUST00000184104; ENSMUST00000200824; ENSMUST00000100000; ENSMUST00000156515; ENSMUST00000140952; ENSMUST00000156342; ENSMUST00000147174; ENSMUST00000139005; ENSMUST00000141850; ENSMUST00000184302; ENSMUST00000154027; rna35395; rna35407; rna35414; rna10234; rna35403; rna10228; rna10235; NONMMUT085706; NONMMUT037975; NONMMUT037989; NONMMUT056965; NONMMUT037980; NONMMUT056968; NONMMUT037983; NONMMUT037993; NONMMUT056957; NONMMUT056950; NONMMUT056969; NONMMUT085709; NONMMUT037973; NONMMUT037986; NONMMUT037974; NONMMUT122276; NONMMUT037979; NONMMUT037976; NONMMUT037987; NONMMUT037992; NONMMUT056966; NONMMUT056970; NONMMUT011703; NONMMUT056953; NONMMUT056971; NONMMUT037977; NONMMUT056955; NONMMUT085710; NONMMUT085707; NONMMUT011705; NONMMUT107327; NONMMUT037978; NONMMUT056952; NONMMUT011706; NONMMUT056954; NONMMUT056959; NONMMUT109225; NONMMUT107329; NONMMUT085708; NONMMUT037990; NONMMUT107328; NONMMUT109226; NONMMUT037982; NONMMUT011701; NONMMUT056960; NONMMUT056967; NONMMUT037988; NONMMUT056961;
ZFLNCT08533 ZFLNCG05516 ENST00000513533; ENST00000439545; ENST00000481995; ENST00000548801; ENST00000518046; ENST00000518088; ENST00000613383; ENST00000523364; ENST00000429755; ENST00000467897; ENST00000508688; ENST00000613939; ENST00000512427; ENST00000620092; ENST00000616712; ENST00000617934; ENST00000425358; ENST00000521197; ENST00000615604; ENST00000521231; ENST00000464382; ENST00000602610; ENST00000523790; ENST00000518848; ENST00000622675; ENST00000619974; ENST00000434063; ENST00000479766; ENST00000465846; ENST00000611352; ENST00000466037; ENST00000517635; ENST00000455246; ENST00000524304; ENST00000513165; ENST00000520395; ENST00000492897; ENST00000460041; ENST00000426965; ENST00000523331; ENST00000480872; ENST00000509870; ENST00000505700; ENST00000593300; ENST00000521159; ENST00000520360; ENST00000440016; ENST00000619311; ENST00000519935; ENST00000477144; ENST00000518947; ENST00000428939; ENST00000435312; ENST00000512206; ENST00000416928; ENST00000425595; ENST00000521687; ENST00000524048; ENST00000474040; ENST00000517641; ENST00000502764; ENST00000491264; ENST00000429611; ENST00000474324; ENST00000562848; ENST00000498652; ENST00000604081; ENST00000467155; ENST00000514702; ENST00000519694; ENST00000517550; ENST00000476204; ENST00000453875; ENST00000593438; ENST00000522863; ENST00000495032; ENST00000494420; ENST00000522193; ENST00000487849; ENST00000504972; ENST00000620211; ENST00000522674; ENST00000620901; ENST00000567780; ENST00000424518; rna84770; rna84761; rna110524; rna110493; rna110537; rna84762; rna20465; rna20463; rna20461; rna51654; rna110529; rna20470; rna20459; rna110526; rna20469; rna20462; rna110528; rna110538; rna20468; rna84765; rna20467; rna110530; rna51647; rna51632; rna20460; rna51645; rna51633; rna51652; rna110525; rna84763; rna51650; rna20466; rna20444; rna84771; rna20464; NONHSAT054421; NONHSAT028514; NONHSAT075627; NONHSAT211837; NONHSAT028528; NONHSAT119677; NONHSAT119697; NONHSAT183137; NONHSAT119670; NONHSAT175307; NONHSAT119672; NONHSAT119682; NONHSAT075636; NONHSAT054434; NONHSAT119698; NONHSAT028529; NONHSAT163579; NONHSAT175305; NONHSAT119702; NONHSAT119704; NONHSAT054411; NONHSAT028518; NONHSAT119680; NONHSAT119706; NONHSAT054437; NONHSAT054405; NONHSAT185941; NONHSAT028510; NONHSAT211840; NONHSAT119687; NONHSAT119664; NONHSAT211839; NONHSAT211844; NONHSAT054435; NONHSAT054444; NONHSAT028530; NONHSAT054450; NONHSAT054401; NONHSAT119711; NONHSAT119684; NONHSAT119665; NONHSAT211838; NONHSAT028511; NONHSAT185938; NONHSAT119675; NONHSAT054441; NONHSAT185937; NONHSAT119678; NONHSAT054449; NONHSAT119667; NONHSAT175306; NONHSAT119669; NONHSAT163580; NONHSAT119673; NONHSAT054406; NONHSAT054433; NONHSAT211835; NONHSAT054403; NONHSAT211834; NONHSAT213318; NONHSAT175303; NONHSAT119693; NONHSAT028509; NONHSAT119683; NONHSAT119703; NONHSAT054442; NONHSAT075630; NONHSAT054443; NONHSAT119705; NONHSAT054446; NONHSAT028539; NONHSAT075637; NONHSAT028527; NONHSAT075638; NONHSAT119688; NONHSAT119700; NONHSAT119710; NONHSAT175308; NONHSAT028507; NONHSAT211842; NONHSAT119708; NONHSAT211843; NONHSAT211836; NONHSAT028531; NONHSAT185940; NONHSAT163581; NONHSAT054427; NONHSAT054408; NONHSAT054431; NONHSAT163582; NONHSAT028517; NONHSAT119709; NONHSAT028512; NONHSAT175304; NONHSAT119674; NONHSAT028541; NONHSAT119696; NONHSAT054407; NONHSAT213319; NONHSAT054454; NONHSAT119685; NONHSAT119690; NONHSAT119668; NONHSAT119676; NONHSAT028519; NONHSAT054432; NONHSAT211841; NONHSAT119666; NONHSAT028513; NONHSAT028516; NONHSAT119707; ENSMUST00000183562; ENSMUST00000150698; ENSMUST00000185194; ENSMUST00000136302; ENSMUST00000134512; ENSMUST00000185090; ENSMUST00000126966; ENSMUST00000143191; ENSMUST00000152462; ENSMUST00000184301; ENSMUST00000137729; ENSMUST00000131502; ENSMUST00000128562; ENSMUST00000184566; ENSMUST00000190845; ENSMUST00000145799; ENSMUST00000132326; ENSMUST00000152027; ENSMUST00000184104; ENSMUST00000200824; ENSMUST00000100000; ENSMUST00000156515; ENSMUST00000140952; ENSMUST00000156342; ENSMUST00000147174; ENSMUST00000139005; ENSMUST00000141850; ENSMUST00000184302; ENSMUST00000154027; rna35395; rna35407; rna35414; rna10234; rna35403; rna10228; rna10235; NONMMUT085706; NONMMUT037975; NONMMUT037989; NONMMUT056965; NONMMUT037980; NONMMUT056968; NONMMUT037983; NONMMUT037993; NONMMUT056957; NONMMUT056950; NONMMUT056969; NONMMUT085709; NONMMUT037973; NONMMUT037986; NONMMUT037974; NONMMUT122276; NONMMUT037979; NONMMUT037976; NONMMUT037987; NONMMUT037992; NONMMUT056966; NONMMUT056970; NONMMUT011703; NONMMUT056953; NONMMUT056971; NONMMUT037977; NONMMUT056955; NONMMUT085710; NONMMUT085707; NONMMUT011705; NONMMUT107327; NONMMUT037978; NONMMUT056952; NONMMUT011706; NONMMUT056954; NONMMUT056959; NONMMUT109225; NONMMUT107329; NONMMUT085708; NONMMUT037990; NONMMUT107328; NONMMUT109226; NONMMUT037982; NONMMUT011701; NONMMUT056960; NONMMUT056967; NONMMUT037988; NONMMUT056961;
ZFLNCT08669 ZFLNCG05615 NONHSAT186214; NONHSAT186215;
ZFLNCT08670 ZFLNCG05615 NONHSAT186214; NONHSAT186215;
ZFLNCT08671 ZFLNCG05615 NONHSAT186214; NONHSAT186215;
ZFLNCT08672 ZFLNCG05615 NONHSAT186214; NONHSAT186215;
ZFLNCT08673 ZFLNCG05615 NONHSAT186214; NONHSAT186215;
ZFLNCT08790 ZFLNCG05694 ENSMUST00000198638;
ZFLNCT08791 ZFLNCG05695 ENSMUST00000198638;
ZFLNCT08798 ZFLNCG05702 ENSMUST00000198638;
ZFLNCT08803 ZFLNCG05705 ENSMUST00000198638;
ZFLNCT08808 ZFLNCG05710 NONHSAT185675;
ZFLNCT08809 ZFLNCG05711 NONHSAT185675;
ZFLNCT08810 ZFLNCG05711 NONHSAT185675;
ZFLNCT08848 ZFLNCG05739 NONHSAT195578; NONMMUT133554; NONMMUT071099;
ZFLNCT09028 ZFLNCG05849 ENST00000598079; ENST00000485776; ENST00000596286; ENST00000623621; ENST00000596021; ENST00000594939; ENST00000601506; ENST00000594512; ENST00000600104; ENST00000621827; ENST00000399677; ENST00000595979; ENST00000503996; ENST00000597246; ENST00000421271; ENST00000601280; rna121915; rna121914; rna121916; rna121870; rna121871; rna121872; rna121917; rna121874; rna121869; rna121873; rna121913; NONHSAT179903; NONHSAT067399; NONHSAT173775; NONHSAT067378; NONHSAT173776; NONHSAT180537; NONHSAT067407; NONHSAT067380; NONHSAT067401; NONHSAT180535; NONHSAT067381; NONHSAT001450; NONHSAT001452; NONHSAT174023; NONHSAT172532; NONHSAT179901; NONHSAT180532; NONHSAT179902; NONHSAT179900; NONHSAT067392; NONHSAT180533; NONHSAT172877; NONHSAT067398; NONHSAT173530; NONHSAT180536; NONHSAT099651; NONHSAT067383; NONHSAT123825; NONHSAT179904; NONHSAT179905; NONHSAT179899; NONHSAT067404; NONHSAT067379; NONHSAT067400; NONHSAT148503; NONHSAT067393; NONHSAT180534; ENSMUST00000205527; ENSMUST00000161395; NONMMUT028620; NONMMUT028619;
ZFLNCT09126 ZFLNCG05919 rna58006;
ZFLNCT09161 ZFLNCG05945 ENSMUST00000191873; NONMMUT000893;
ZFLNCT09180 ZFLNCG05958 ENST00000488281; ENST00000528407; ENST00000602947; ENST00000597192; ENST00000602529; ENST00000452580; ENST00000578746; ENST00000602517; ENST00000429882; rna54956; rna54955; rna54957; rna22385; NONHSAT180372; NONHSAT153067; NONHSAT030284; NONHSAT215698; NONHSAT186331; NONHSAT075817; NONHSAT195907; NONHSAT126098; NONHSAT008974; NONHSAT036686; NONHSAT065927; NONHSAT091535; NONHSAT008977; NONHSAT077042; NONHSAT077053; NONHSAT179696; NONHSAT179697; NONHSAT212518; ENSMUST00000132100; ENSMUST00000140451; ENSMUST00000101162; ENSMUST00000162526; ENSMUST00000126122; rna48392; rna48389; rna48390; rna48393; NONMMUT083728; NONMMUT107377; NONMMUT009955; NONMMUT109271; NONMMUT064981; NONMMUT130091; NONMMUT064983; NONMMUT064982; NONMMUT130092; NONMMUT107376; NONMMUT002618; NONMMUT038069; NONMMUT002619; NONMMUT078060; NONMMUT001588; NONMMUT047761; NONMMUT009954; NONMMUT064980;
ZFLNCT09681 ZFLNCG06298 ENST00000624566; ENST00000507007; ENST00000539533; ENST00000625092; ENST00000624176; ENST00000624712; ENST00000623581; ENST00000624928; ENST00000622826; ENST00000624192; ENST00000623466; ENST00000623995; ENST00000625144; ENST00000623320; ENST00000625195; ENST00000506751; ENST00000625053; ENST00000488078; ENST00000624549; ENST00000625071; ENST00000624089; ENST00000502926; NONHSAT204784; NONHSAT204767; NONHSAT204768; NONHSAT203319; NONHSAT203320; NONHSAT204761; NONHSAT204763; NONHSAT104248; NONHSAT206385; NONHSAT204762; NONHSAT204764; NONHSAT204794; NONHSAT104233; NONHSAT204785; NONHSAT203326; NONHSAT204797; NONHSAT204796; NONHSAT104249; NONHSAT204766; NONHSAT204782; NONHSAT204795; NONHSAT204787; NONHSAT204783; NONHSAT204781; NONHSAT204786; NONHSAT204765; NONHSAT104256; ENSMUST00000194328; ENSMUST00000192178; ENSMUST00000180931; ENSMUST00000193025; ENSMUST00000097612; ENSMUST00000193815; ENSMUST00000193015; ENSMUST00000194575; ENSMUST00000192805; ENSMUST00000194001; ENSMUST00000193299; ENSMUST00000195341; ENSMUST00000194501; ENSMUST00000192501; ENSMUST00000180922; ENSMUST00000192003; ENSMUST00000192440; ENSMUST00000193629; NONMMUT032054; NONMMUT032030; NONMMUT032049; NONMMUT032032; NONMMUT104362; NONMMUT032031; NONMMUT032045; NONMMUT032046; NONMMUT104356; NONMMUT032037; NONMMUT032050; NONMMUT104354; NONMMUT032048; NONMMUT032039; NONMMUT032052; NONMMUT032051; NONMMUT104363; NONMMUT104355; NONMMUT104361; NONMMUT032029;
ZFLNCT09682 ZFLNCG06299 ENST00000624566; ENST00000507007; ENST00000539533; ENST00000625092; ENST00000624176; ENST00000624712; ENST00000623581; ENST00000624928; ENST00000622826; ENST00000624192; ENST00000623466; ENST00000623995; ENST00000625144; ENST00000623320; ENST00000625195; ENST00000506751; ENST00000625053; ENST00000488078; ENST00000624549; ENST00000625071; ENST00000624089; ENST00000502926; rna71003; NONHSAT204784; NONHSAT204767; NONHSAT204768; NONHSAT203319; NONHSAT203320; NONHSAT204761; NONHSAT204763; NONHSAT104248; NONHSAT206385; NONHSAT204762; NONHSAT204764; NONHSAT204794; NONHSAT104233; NONHSAT204785; NONHSAT203326; NONHSAT204797; NONHSAT204796; NONHSAT104249; NONHSAT204766; NONHSAT204782; NONHSAT204795; NONHSAT204787; NONHSAT204783; NONHSAT204781; NONHSAT204786; NONHSAT204765; NONHSAT104256; ENSMUST00000194328; ENSMUST00000192178; ENSMUST00000180931; ENSMUST00000193025; ENSMUST00000097612; ENSMUST00000193815; ENSMUST00000193015; ENSMUST00000194575; ENSMUST00000192805; ENSMUST00000194001; ENSMUST00000193299; ENSMUST00000195341; ENSMUST00000194501; ENSMUST00000192501; ENSMUST00000180922; ENSMUST00000192003; ENSMUST00000192440; ENSMUST00000193629; NONMMUT032054; NONMMUT032030; NONMMUT032049; NONMMUT032032; NONMMUT104362; NONMMUT032031; NONMMUT032045; NONMMUT032046; NONMMUT104356; NONMMUT032037; NONMMUT032050; NONMMUT104354; NONMMUT032048; NONMMUT032039; NONMMUT032052; NONMMUT032051; NONMMUT104363; NONMMUT104355; NONMMUT104361; NONMMUT032029;