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
ZFLNCT09683 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; NONMMUT104362; NONMMUT032032; NONMMUT032031; NONMMUT032045; NONMMUT032046; NONMMUT104356; NONMMUT032037; NONMMUT032050; NONMMUT104354; NONMMUT032048; NONMMUT032039; NONMMUT032052; NONMMUT032051; NONMMUT104363; NONMMUT104355; NONMMUT104361; NONMMUT032029;
ZFLNCT09684 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; NONMMUT104362; NONMMUT032032; NONMMUT032031; NONMMUT032045; NONMMUT032046; NONMMUT104356; NONMMUT032050; NONMMUT104354; NONMMUT032048; NONMMUT032039; NONMMUT032052; NONMMUT032051; NONMMUT104363; NONMMUT104355; NONMMUT104361; NONMMUT032029;
ZFLNCT09712 ZFLNCG06324 ENST00000544225; ENST00000491732; ENST00000420905; rna82645; rna82615; NONHSAT060835; NONHSAT152519; NONHSAT026856; NONHSAT180143; NONHSAT163297; NONHSAT161846; NONHSAT161841; NONHSAT161845; NONHSAT026860; NONHSAT163295; NONHSAT152520; NONHSAT163296; ENSMUST00000184861; ENSMUST00000160490; rna38271; rna47548; rna47547; rna47545; rna38272; rna47546; NONMMUT123085; NONMMUT064422; NONMMUT059104; NONMMUT123083; NONMMUT127977; NONMMUT064423; NONMMUT123082; NONMMUT123084; NONMMUT124500; NONMMUT059053; NONMMUT059095;
ZFLNCT09713 ZFLNCG06325 ENST00000544225; ENST00000491732; ENST00000420905; rna82645; rna82615; NONHSAT060835; NONHSAT152519; NONHSAT026856; NONHSAT180143; NONHSAT163297; NONHSAT161846; NONHSAT161845; NONHSAT026860; NONHSAT163295; NONHSAT152520; NONHSAT163296; ENSMUST00000160490; rna38271; rna47548; rna47547; rna47545; rna38272; rna47546; NONMMUT123085; NONMMUT064422; NONMMUT059104; NONMMUT123083; NONMMUT127977; NONMMUT064423; NONMMUT123082; NONMMUT123084; NONMMUT059053; NONMMUT059095;
ZFLNCT09836 ZFLNCG06418 rna44248; rna44247;
ZFLNCT09863 ZFLNCG06440 NONMMUT111132;
ZFLNCT09964 ZFLNCG06497 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607;
ZFLNCT09965 ZFLNCG06498 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029605; NONMMUT029606;
ZFLNCT09966 ZFLNCG06499 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607;
ZFLNCT09967 ZFLNCG06500 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117184; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029606; NONMMUT029605; NONMMUT009936;
ZFLNCT09968 ZFLNCG06501 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117184; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029606; NONMMUT029605; NONMMUT009936;
ZFLNCT09969 ZFLNCG06502 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117184; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029606; NONMMUT029605; NONMMUT009936;
ZFLNCT09970 ZFLNCG06503 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117184; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029606; NONMMUT029605; NONMMUT009936;
ZFLNCT09971 ZFLNCG06504 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029605; NONMMUT029606;
ZFLNCT09972 ZFLNCG06505 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607;
ZFLNCT09973 ZFLNCG06506 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117184; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT009936; NONMMUT029607;
ZFLNCT09974 ZFLNCG06507 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607;
ZFLNCT09975 ZFLNCG06508 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607;
ZFLNCT09976 ZFLNCG06509 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607; NONMMUT010657;
ZFLNCT09977 ZFLNCG06510 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029605; NONMMUT029606;
ZFLNCT09978 ZFLNCG06511 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607;
ZFLNCT09979 ZFLNCG06512 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607;
ZFLNCT09980 ZFLNCG06513 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029605; NONMMUT029606;
ZFLNCT09981 ZFLNCG06514 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029605; NONMMUT029606;
ZFLNCT09982 ZFLNCG06515 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029605; NONMMUT029606;