User:M2bioinfo-Orsay/sandbox/team3
Riboswitch s0670[edit]
| Riboswitch s0670 family | |
|---|---|
 Predicted secondary structure using RSCape[1] | |
| Identifiers | |
| Other data | |
| RNA type | Gene; Cis-reg; riboswitch; |
| Domain(s) | Bacteria; Firmicutes |
| PDB structures | PDBe |
The s0670 family was defined with the rfam cloud pipeline from the CD630_s0670 nucleotide sequence which is a non-coding RNA of the pathogenic bacteria Clostridium difficile 630 revealed by RNA-seq and differential 5'-and RNA-seq analyses[2].
RNA of this family were found in the Firmicutes taxa and upstream of some genes which code for enzyme implicated in cellular amino acid metabolic process (GO:0006520) like the O-acetylhomoserine sulfhydrylase of Clostridium difficile (FQTY01000002.1 ⇒ en 5’ d’un gène O-acetylhomoserine sulfhydrylase SHE43394.1), the S-ribosylhomocysteinase LuxS of ?? (DS995361.1 ⇒ en 5’ du gène EEA84185.1), or the cysD gene of ?? (FMDO01000052.1 ⇒ en 5’ du gène SCG84166.1).
The seconday structure was predicted using the locaRNA[3] alignement and with the Rscape prediction software[1].
References[edit]
- ^ a b "Estimating the power of sequence covariation for detecting conserved RNA structure". Bioinformatics. 36 (10): 3072–3076. 2020. doi:10.1093/bioinformatics/btaa080.
{{cite journal}}: Cite uses deprecated parameter|authors=(help) - ^ "Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile". PLoS Genet. 9 (5): e1003493. 2013. doi:10.1371/journal.pgen.1003493. PMID 23675309.
{{cite journal}}: Cite uses deprecated parameter|authors=(help)CS1 maint: unflagged free DOI (link) - ^ "LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs". RNA. 18 (5): 900–914. 2012. doi:10.1261/rna.029041.111.
{{cite journal}}: Cite uses deprecated parameter|authors=(help)
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