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
ZFLNCT16663 ZFLNCG10739 ENST00000416832; NONHSAT088932; ENSMUST00000204125; ENSMUST00000190678; ENSMUST00000203191; rna3588;
ZFLNCT16664 ZFLNCG10740 rna58006;
ZFLNCT16680 ZFLNCG10754 ENST00000435037; ENST00000423329; ENST00000619088; ENST00000596418; ENST00000615681; rna48563; rna91275; rna48562; rna91276; NONHSAT166343; NONHSAT148664; NONHSAT081816; NONHSAT166341; NONHSAT072993; NONHSAT007847; NONHSAT035207; NONHSAT055881; NONHSAT007846; NONHSAT083074; NONHSAT035204; NONHSAT176568; NONHSAT035208; NONHSAT167274; NONHSAT167273;
ZFLNCT16800 ZFLNCG10838 ENSMUST00000188747; NONMMUT133020; NONMMUT070330; NONMMUT070332; NONMMUT133021; NONMMUT070331;
ZFLNCT16815 ZFLNCG10850 ENST00000569214; rna95131; NONHSAT168872; NONHSAT039529; NONMMUT088996;
ZFLNCT16903 ZFLNCG10922 NONMMUT079168; NONMMUT079169;
ZFLNCT17044 ZFLNCG11019 ENST00000626627; ENST00000417586; ENST00000428786; ENST00000589560; ENST00000593183; ENST00000617009; ENST00000623833; ENST00000621190; NONHSAT192431; NONHSAT087030; NONHSAT192945; NONHSAT061526; NONHSAT061503; NONHSAT192434; NONHSAT192433; NONHSAT212784; NONHSAT192432;
ZFLNCT17045 ZFLNCG11020 ENST00000626627; ENST00000417586; ENST00000428786; ENST00000589560; ENST00000593183; ENST00000617009; ENST00000623833; ENST00000621190; NONHSAT192431; NONHSAT087030; NONHSAT192945; NONHSAT061526; NONHSAT061503; NONHSAT192434; NONHSAT192433; NONHSAT212784; NONHSAT192432;
ZFLNCT17046 ZFLNCG11021 ENST00000626627; ENST00000417586; ENST00000428786; ENST00000589560; ENST00000593183; ENST00000617009; ENST00000623833; ENST00000621190; NONHSAT192431; NONHSAT087030; NONHSAT192945; NONHSAT061526; NONHSAT061503; NONHSAT192434; NONHSAT192433; NONHSAT212784; NONHSAT192432;
ZFLNCT17047 ZFLNCG11022 ENST00000626627; ENST00000417586; ENST00000428786; ENST00000589560; ENST00000617009; ENST00000621190; NONHSAT192431; NONHSAT087030; NONHSAT192945; NONHSAT192434; NONHSAT192433; NONHSAT212784; NONHSAT192432;
ZFLNCT17168 ZFLNCG11113 ENST00000442572; NONHSAT152804; NONHSAT152519; NONHSAT009138; NONHSAT152520; NONHSAT007472; rna6648; rna6652; rna6650; rna6649; rna6651; NONMMUT004513; NONMMUT077191; NONMMUT004512; NONMMUT029347;
ZFLNCT17169 ZFLNCG11114 ENST00000442572; NONHSAT152804; NONHSAT152519; NONHSAT009138; NONHSAT152520; NONHSAT007472; rna6648; rna6652; rna6650; rna6649; rna6651; NONMMUT004513; NONMMUT077191; NONMMUT004512; NONMMUT029347;
ZFLNCT17171 ZFLNCG11116 NONMMUT003098; NONMMUT003096; NONMMUT003097;
ZFLNCT17298 ZFLNCG11175 ENST00000542839; NONHSAT175252; NONHSAT002314; rna24923; rna24924; rna24925; rna24922; NONMMUT005647; NONMMUT049549; NONMMUT049550; NONMMUT115617; NONMMUT049548;
ZFLNCT17385 ZFLNCG11230 ENST00000421055; ENST00000486251; ENST00000618350; ENST00000326341; rna129639; NONHSAT024249; NONHSAT084346; NONHSAT152762; NONHSAT108520; NONHSAT104458; NONHSAT125668; NONHSAT125667; NONHSAT008869; NONHSAT108518; NONHSAT084344; ENSMUST00000204790; ENSMUST00000117184; ENSMUST00000121306; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000140414; ENSMUST00000126060; ENSMUST00000134011; NONMMUT127602; NONMMUT010656; NONMMUT010657; NONMMUT105912; NONMMUT063128; NONMMUT009936;
ZFLNCT17386 ZFLNCG11231 ENST00000421055; ENST00000486251; ENST00000618350; ENST00000326341; rna129639; NONHSAT024249; NONHSAT084346; NONHSAT152762; NONHSAT104458; NONHSAT125668; NONHSAT125667; NONHSAT008869; NONHSAT084344; NONHSAT030545; ENSMUST00000120418; ENSMUST00000204141; ENSMUST00000121306; ENSMUST00000117794; ENSMUST00000174677; ENSMUST00000172211; ENSMUST00000126060; ENSMUST00000134011; ENSMUST00000121665; ENSMUST00000203299; ENSMUST00000120109; ENSMUST00000165784; ENSMUST00000190505; ENSMUST00000204790; ENSMUST00000117184; ENSMUST00000122338; ENSMUST00000185802; ENSMUST00000140414; rna94152; rna46815; rna10785; rna81480; rna94151; rna46816; NONMMUT038329; NONMMUT125936; NONMMUT127602; NONMMUT085607; NONMMUT102034; NONMMUT039095; NONMMUT010657; NONMMUT102035; NONMMUT105912; NONMMUT010656; NONMMUT080461; NONMMUT062603; NONMMUT020720; NONMMUT075997; NONMMUT126345; NONMMUT063128; NONMMUT101005; NONMMUT009936; NONMMUT068661;
ZFLNCT17387 ZFLNCG11232 ENST00000421055; ENST00000486251; ENST00000618350; NONHSAT024249; NONHSAT152762; NONHSAT104458; NONHSAT125668; NONHSAT125667; NONHSAT008869; NONHSAT030545; ENSMUST00000120418; ENSMUST00000205947; ENSMUST00000204141; ENSMUST00000121306; ENSMUST00000117794; ENSMUST00000174677; ENSMUST00000172211; ENSMUST00000126060; ENSMUST00000134011; ENSMUST00000121665; ENSMUST00000203299; ENSMUST00000120109; ENSMUST00000190505; ENSMUST00000204790; ENSMUST00000117184; ENSMUST00000122338; ENSMUST00000185802; ENSMUST00000140414; ENSMUST00000174025; rna94152; rna46815; rna81480; rna94151; rna46816; NONMMUT038329; NONMMUT039095; NONMMUT010657; NONMMUT126344; NONMMUT062603; NONMMUT085607; NONMMUT075997; NONMMUT009936; NONMMUT068661; NONMMUT102034; NONMMUT010656; NONMMUT063128; NONMMUT101005; NONMMUT127602; NONMMUT125936; NONMMUT080461; NONMMUT102035; NONMMUT105912; NONMMUT064149; NONMMUT020720; NONMMUT126345; NONMMUT029603;
ZFLNCT17388 ZFLNCG11233 ENST00000486251; NONHSAT024249; NONHSAT104458; NONHSAT125668; NONHSAT125667; NONHSAT108518; ENSMUST00000122434; ENSMUST00000126779; ENSMUST00000204141; ENSMUST00000121306; ENSMUST00000117794; ENSMUST00000174677; ENSMUST00000172211; ENSMUST00000126060; ENSMUST00000134011; ENSMUST00000122018; ENSMUST00000203299; ENSMUST00000190505; ENSMUST00000204790; ENSMUST00000117184; ENSMUST00000122338; ENSMUST00000185802; ENSMUST00000140414; NONMMUT085607; NONMMUT010656; NONMMUT102034; NONMMUT010657; NONMMUT102035; NONMMUT105912; NONMMUT038330; NONMMUT038331; NONMMUT062603; NONMMUT036922; NONMMUT075997; NONMMUT009936;
ZFLNCT17539 ZFLNCG11314 rna61714; NONHSAT216644; NONHSAT217788; NONHSAT216645; ENSMUST00000201593; NONMMUT023975; NONMMUT096072; NONMMUT023976;
ZFLNCT17540 ZFLNCG11314 rna61714; NONHSAT216644; NONHSAT217788; NONHSAT216645; ENSMUST00000201593; NONMMUT023975; NONMMUT096072; NONMMUT023976;
ZFLNCT17541 ZFLNCG11314 rna61714; NONHSAT216644; NONHSAT217788; NONHSAT216645; ENSMUST00000201593; NONMMUT023975; NONMMUT096072; NONMMUT023976;
ZFLNCT17542 ZFLNCG11314 rna61714; NONHSAT216644; NONHSAT217788; NONHSAT216645; ENSMUST00000201593; NONMMUT023975; NONMMUT096072; NONMMUT023976;
ZFLNCT17543 ZFLNCG11314 rna61714; NONHSAT216644; NONHSAT217788; NONHSAT216645; ENSMUST00000201593; NONMMUT023975; NONMMUT096072; NONMMUT023976;
ZFLNCT17544 ZFLNCG11315 rna61714; NONHSAT216644; NONHSAT217788; NONHSAT216645; ENSMUST00000201593; NONMMUT023975; NONMMUT096072; NONMMUT023976;
ZFLNCT17589 ZFLNCG11345 ENST00000592319; ENST00000604303; ENST00000555916; ENST00000616184; ENST00000462168; ENST00000474329; ENST00000602874; ENST00000634630; ENST00000634951; ENST00000362602; ENST00000619673; ENST00000600253; ENST00000554009; ENST00000595010; rna122291; rna120635; rna122103; NONHSAT067510; NONHSAT179420; NONHSAT179928; NONHSAT037757; NONHSAT179918; NONHSAT060961; NONHSAT067638; NONHSAT194612; NONHSAT067500; NONHSAT179784; NONHSAT180564; NONHSAT168635; NONHSAT180620; NONHSAT179990; NONHSAT067497; NONHSAT067503; NONHSAT066677; NONHSAT066105; NONHSAT067639; NONHSAT018657; NONHSAT092578; NONHSAT168636; NONHSAT067498; NONHSAT067499; NONHSAT067509; NONHSAT066646; NONHSAT168634; NONHSAT168637; NONHSAT067501; NONHSAT067637; NONHSAT067508; NONHSAT037756; NONHSAT072465; NONHSAT037755; NONHSAT060959; NONHSAT179783; NONHSAT179786; ENSMUST00000180846; ENSMUST00000205272; rna39617; NONMMUT054960; NONMMUT068237; NONMMUT126427; NONMMUT122901; NONMMUT068239; NONMMUT124878; NONMMUT060530; NONMMUT009632; NONMMUT029150; NONMMUT126588; NONMMUT126529; NONMMUT053727; NONMMUT122900; NONMMUT126530; NONMMUT029153; NONMMUT122898; NONMMUT122899; NONMMUT060997; NONMMUT068226; NONMMUT068238; NONMMUT126528;