lncRNA loci |
: ID of putative lncRNAs |
Biotype |
: Types of putative lncRNAs based on genomic location including (a) lincRNA, (b) lncNAT and (c) sense/intronic lncRNA |
- lincRNA |
: LncRNA locating at intergenic region without protein coding genes overlapping |
- lncNAT |
: LncRNA locating at intergenic region with protein coding genes overlapping in the opposite strand |
- Sense/intronic lncRNA |
: LncRNA located at untranslated region or intron of protein coding gene |
Genome Location |
: Location of putative lncRNAs in cassava genome version 6.1 (i.e., chromosome, scaffold) based on Phytozome version 12 |
- Chromosome |
: Chromosome in cassava genome version 6.1 based on Phytozome version 12 |
- Strand |
: DNA strand (sense (+) or antisense (-)) in cassava genome version 6.1 based on Phytozome version 12 |
- Start |
: Started position of putative lncRNA in cassava genome version 6.1 based on Phytozome version 12 |
- End |
: End position of putative lncRNA in cassava genome version 6.1 based on Phytozome version 12 |
Nucleotide sequence |
DNA sequences of putative lncRNAs |
Number of publications supporting the expression |
: Number of supporting putative lncRNA expression evidence (maximum is 5) |
Publications |
: Found cassava RNA-seq datasets supporting the expression of cassava lncRNAs
- Li et al., 2017
- Pootakham et al., 2014
- Wilson et al., 2017
- Wang et al., 2014
- Amuge et al., 2017
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Relationship |
: Relationship of putative lncRNA and its target genes based on cis- or trans- regulation |
- Cis-regulation |
: Target prediction based on genomic location of protein coding gene located within 10 Kb. in up or downstream of putative lncRNA |
- Trans-regulation 1 |
: Target prediction based on sequence complementary and normalized binding free energy (ndG) < -0.1 of putative lncRNAs and mRNA of protein coding gene target using LncTar |
- Trans-regulation 2 |
: Target prediction based on the same mature miRNA binding with mismatch ≤ 2 of putative lncRNA and mRNA of protein coding gene target using psRNATarget |
- Target gene ID |
: Target gene ID in cassava genome version 6.1 based on Phytozome version 12 |
- Condition |
: Condition which was found relationship between putative lncRNA and target gene including cold and/or drought stress |
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- miRNA |
: miRNA which was found to share binding region on putative lncRNA sequence and mRNA sequence of target gene |
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