Poplar-1 RNA motif

poplar-1
Consensus secondary structure and sequence conservation of poplar-1 RNA
Identifiers
Symbol	poplar-1
Rfam	RF03041
Other data
RNA type	Gene; sRNA
SO	SO:0001263
PDB structures	PDBe

The poplar-1 RNA motif is a conserved RNA structure that was discovered by bioinformatics.^[1] As of 2018, all known examples of the poplar-1 motif are found in metagenomic sequences; no poplar-1 RNA has yet been found in a classified organism. Poplar-1 RNAs were particularly common in a metagenomic sample from decaying yellow poplar tree wood chips.^[2]

Poplar-1 RNAs generally occur in sequencing contigs that are relatively small. Therefore, there is not enough information on surrounding genes to be able to determine whether poplar-1 RNAs are likely to function as cis-regulatory elements or whether they more likely operate in trans as small RNAs.

References

1. Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR (October 2017). "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids Res. 45 (18): 10811–10823. doi:10.1093/nar/gkx699. PMC 5737381. PMID 28977401.
2. van der Lelie D, Taghavi S, McCorkle SM, Li LL, Malfatti SA, Monteleone D, Donohoe BS, Ding SY, Adney WS, Himmel ME, Tringe SG (2012). "The metagenome of an anaerobic microbial community decomposing poplar wood chips". PLOS ONE. 7 (5): e36740. Bibcode:2012PLoSO...736740V. doi:10.1371/journal.pone.0036740. PMC 3357426. PMID 22629327.