Dictyostelium class I RNA
| Class I RNA | |
|---|---|
 Predicted secondary structure of the class I RNA | |
| Identifiers | |
| Rfam | RF01414 |
| Other data | |
| RNA type | Gene |
| Domain(s) | Eukaryota |
| PDB structures | PDBe |
The class I RNA is a non-coding RNA. This family was identified in Shotgun sequencing approach of full-length cDNA libraries from small RNAs from Dictyostelium discoideum. The function of this RNA is unknown, but it bears some resemblance to riboswitches found primarily in bacteria. These RNAs are 42–65 nucleotides (nt) long and they share 5' and 3' sequence elements of 16 and 8 nt respectively. These elements can partially base-pair forming a short hairpin.
There are multiple copies of class I RNA in the D. discoideum genome and the RNA is highly expressed i.e. 14 unique sequences were identified in the small RNA library and it comprised ~12% of all RNA in the small RNA library.[1] Homologs to class I RNA have only been located in D. discoideum to date. Some of the members of this family were also identified in a bioinformatic screen.[2] This family has also been the subject of reviews.[3][4]
See also
[edit]External links
[edit]- Sequence Ontology page for Class I RNA Archived 2011-07-21 at the Wayback Machine
- Rfam entry for class I RNA
References
[edit]- ^ Aspegren A, Hinas A, Larsson P, Larsson A, Söderbom F (2004). "Novel non-coding RNAs in Dictyostelium discoideum and their expression during development". Nucleic Acids Res. 32 (15): 4646–4656. doi:10.1093/nar/gkh804. PMC 516072. PMID 15333696.
- ^ Larsson P, Hinas A, Ardell DH, Kirsebom LA, Virtanen A, Söderbom F (June 2008). "De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring". Genome Res. 18 (6): 888–899. doi:10.1101/gr.069104.107. PMC 2413156. PMID 18347326.
- ^ Hinas A, Söderbom F (March 2007). "Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum". Curr. Genet. 51 (3): 141–159. doi:10.1007/s00294-006-0112-z. PMID 17171561. S2CID 1222832.
- ^ Mosig A, Sameith K, Stadler P (February 2006). "Fragrep: an efficient search tool for fragmented patterns in genomic sequences". Genomics Proteomics Bioinformatics. 4 (1): 56–60. doi:10.1016/S1672-0229(06)60017-X. PMC 5054030. PMID 16689703.
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