zflncRNApedia is a comprehensive resource for the systematic study of long non-coding lncRNAs in zebrafish.
The resource provides a unified view of the zebrafish lncrnome giving an insight to the genomic context, expression and regulation of each of the lncRNAs.
It currently contains 2,266 lncRNAs derived from three recently published datasets on lncRNAs discovered in zebrafish.
Depending on their genomic location, they have been classified into 4 categories: Intronic (86), Overlapping (485), Promoter associated (309) and linc RNAs (1386).
Expression levels across 15 distinct data-sets encompassing developmental stages and adult tissues has been reported along with the mapping of genomic variations and retroviral insertion lines to lncRNA loci.
References:
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Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP
Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution.
Cell(2011) 147: 1537-1550
PMID:22196729
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Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A, Schier AF
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
Genome Research (2012) 22:577-591
PMID: 22110045
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Kaushik K, Leonard VE, Kv S, Lalwani MK, Jalali S, Patowary A, Joshi A, Scaria V, Sivasubbu S
Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish.
Plos One(2013) 8(12):e83616
PMID: 24391796 -
Varshney GK1, Lu J, Gildea DE, Huang H, Pei W, Yang Z, Huang SC, Schoenfeld D, Pho NH, Casero D, Hirase T, Mosbrook-Davis D, Zhang S, Jao LE, Zhang B, Woods IG, Zimmerman S, Schier AF, Wolfsberg TG, Pellegrini M, Burgess SM, Lin S
A large-scale zebrafish gene knockout resource for the genome-wide study of gene function
Genome Res. (2013) Apr;23(4):727-35
PMID: 23382537
