Small RNAs annotated to AthaMap
Sequence signatures derived from small RNA transcriptome analyses of different
Arabidopsis thaliana tissues were used for genomic screenings.
The complete lists of screening sequences are available at
Number of sequences
Number of genomic hits
Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ. 2005.
Elucidation of the small RNA component of the transcriptome.
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Axtell MJ, Jan C, Rajagopalan R, Bartel DP. 2006. A two-hit trigger for siRNA biogenesis in plants. Cell. 127:565-77.
Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 20:3407-25.
Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. 2007. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5:e57.
Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. 2007. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One. 2:e219.
Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. 2007. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell. 19:926-42.
Small RNA target genes
5,929 (GSE3008), 4,032 (GSE6682), and 7,696 (GSE5228) genes were predicted
to be post-transcriptionally regulated by small RNAs since their transcribed
regions are targets by at least one smallRNA in antisense orientation.
3,325 genes are common to all three datasets and a total number of 9,166
different genes are predicted targets of small RNAs in antisense orientation.
The complete lists of genes predicted to be down-regulated by small RNAs can be
downloaded as text files: 5929.txt;