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
ZFLNCT09983 ZFLNCG06516 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117184; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000204790; ENSMUST00000172477; rna24354; rna24353; rna24352; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029606; NONMMUT029605; NONMMUT009936;
ZFLNCT09984 ZFLNCG06517 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117184; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000204790; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029606; NONMMUT029605; NONMMUT009936;
ZFLNCT09985 ZFLNCG06518 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000117794; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000204790; ENSMUST00000172477; NONMMUT010656; NONMMUT029607; NONMMUT010657; NONMMUT029605; NONMMUT029606;
ZFLNCT09986 ZFLNCG06519 ENST00000421055; ENST00000486251; NONHSAT024249; NONHSAT152762; NONHSAT104458; NONHSAT125668; NONHSAT125667; NONHSAT008869; ENSMUST00000172211; ENSMUST00000140414; ENSMUST00000204790; ENSMUST00000134011; ENSMUST00000120418; NONMMUT124900; NONMMUT085607; NONMMUT060621;
ZFLNCT09987 ZFLNCG06520 ENST00000421055; ENST00000486251; NONHSAT024249; NONHSAT152762; NONHSAT104458; NONHSAT125668; NONHSAT125667; NONHSAT008869; ENSMUST00000134011; ENSMUST00000172211; ENSMUST00000120418; NONMMUT124900; NONMMUT085607; NONMMUT060621;
ZFLNCT09988 ZFLNCG06521 ENST00000421055; ENST00000486251; NONHSAT024249; NONHSAT152762; NONHSAT104458; NONHSAT125668; NONHSAT125667; NONHSAT008869; ENSMUST00000117184; ENSMUST00000172211; ENSMUST00000140414; ENSMUST00000204790; ENSMUST00000134011; ENSMUST00000120418; NONMMUT124900; NONMMUT085607; NONMMUT039095; NONMMUT060621; NONMMUT009936;
ZFLNCT09989 ZFLNCG06522 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; ENSMUST00000120418; NONMMUT029605; NONMMUT029606; NONMMUT029607; NONMMUT039095;
ZFLNCT09990 ZFLNCG06523 ENST00000486251; NONHSAT125668; NONHSAT104458; NONHSAT024249; NONHSAT125667; ENSMUST00000172211; ENSMUST00000174168; ENSMUST00000173181; ENSMUST00000172477; NONMMUT029605; NONMMUT029606; NONMMUT029607;
ZFLNCT10250 ZFLNCG06688 ENST00000411759; NONHSAT176187; NONHSAT176254; NONHSAT176198; NONHSAT176955; NONHSAT176191; NONHSAT053996; NONHSAT176199; NONHSAT176193; NONHSAT176189; NONHSAT176188; NONHSAT053631; NONHSAT163560; NONHSAT176196; NONHSAT053995; NONHSAT176190; NONHSAT175207; NONHSAT176195; NONHSAT175206; NONHSAT053988; NONHSAT053990; NONHSAT176194; NONHSAT176255; NONHSAT176192;
ZFLNCT10251 ZFLNCG06689 ENST00000411759; NONHSAT176187; NONHSAT176254; NONHSAT176198; NONHSAT176955; NONHSAT176191; NONHSAT053996; NONHSAT176199; NONHSAT176193; NONHSAT176189; NONHSAT176188; NONHSAT053631; NONHSAT163560; NONHSAT176196; NONHSAT053995; NONHSAT176190; NONHSAT175207; NONHSAT176195; NONHSAT175206; NONHSAT053988; NONHSAT053990; NONHSAT176194; NONHSAT176255; NONHSAT176192;
ZFLNCT10252 ZFLNCG06690 ENST00000411759; NONHSAT176187; NONHSAT176254; NONHSAT176198; NONHSAT176955; NONHSAT176191; NONHSAT053996; NONHSAT176199; NONHSAT176193; NONHSAT176189; NONHSAT176188; NONHSAT053631; NONHSAT163560; NONHSAT176196; NONHSAT053995; NONHSAT176190; NONHSAT175207; NONHSAT176195; NONHSAT175206; NONHSAT053988; NONHSAT053990; NONHSAT176194; NONHSAT176255; NONHSAT176192;
ZFLNCT10287 ZFLNCG06724 NONHSAT136388; NONHSAT222536; NONHSAT222535; NONMMUT074591; NONMMUT074590;
ZFLNCT10375 ZFLNCG06785 NONMMUT040719;
ZFLNCT10376 ZFLNCG06785 NONMMUT040719;
ZFLNCT10377 ZFLNCG06785 NONMMUT040719;
ZFLNCT10661 ZFLNCG06969 NONHSAT175679; NONHSAT056203; NONMMUT012935;
ZFLNCT10662 ZFLNCG06970 NONHSAT175679; NONHSAT056203; NONMMUT012935;
ZFLNCT10902 ZFLNCG07145 ENST00000602711; NONHSAT215431; NONHSAT216786; NONHSAT216785; NONHSAT125094;
ZFLNCT10903 ZFLNCG07146 ENST00000602711; NONHSAT215431; NONHSAT216786; NONHSAT216785; NONHSAT125094;
ZFLNCT10942 ZFLNCG07176 NONHSAT194208; NONHSAT160879;
ZFLNCT11039 ZFLNCG07232 NONHSAT119622; NONHSAT211817;
ZFLNCT11040 ZFLNCG07233 ENST00000623557; NONHSAT141812; NONHSAT141813; ENSMUST00000191038; ENSMUST00000206057; rna46124; NONMMUT063744;
ZFLNCT11041 ZFLNCG07233 ENST00000623557; NONHSAT141812; NONHSAT141813; ENSMUST00000191038; ENSMUST00000206057; rna46124; NONMMUT063744;
ZFLNCT11552 ZFLNCG07553 ENST00000568177; NONHSAT169753; NONHSAT169751; NONHSAT170430; NONHSAT169752; NONHSAT169749; NONHSAT040175; NONHSAT169750; NONHSAT170431; NONHSAT040174;
ZFLNCT11616 ZFLNCG07597 NONMMUT005891; NONMMUT005890;