The annotation was based on the pig genome version 10.2.
Main annotation of structured RNAs in susScrofa 10.2. Includes prediction based on homology and prediction of novel miRNAs based on a small RNA library.
Annotation at different cut-off levels.
| Cutoff-level | Number of structured RNAs | Comment | Download | ||||||
| Curatated | 318 | Hand and machine curated structured RNAs | Curated only version 1 | Ensembl | |||||
| High confident without pseudo-genes | 1,976 | High confident structured RNAs, includes curated, pseudo-genes removed | Curated version 1 | Ensembl | |||||
| High confident | 3,601 | High confident structured RNAs, includes curated and pseudo-genes | High-confident version 1 | Ensembl |
The annotation was the result of an in-house pipe-line and the prediction of novel miRNAs based on a small-RNA library. The RNA classes were found as follows: "cisreg", are cis-regulatory elements from Rfam. "miRNA" are miRNAs obtained by sequence homology from mirBase or from the mirDeep prediction of miRNAs. "rRNA" are ribosomal RNAs mainly found with RNAmmer. "snRNA" and "snoRNA" are small nuclear RNAs and small nucleolar RNAs from sequence and structure homology search. "tRNA" are merged results, but are mainly found with tRNA-scan. "other" are non-coding RNAs from Rfam that do not belong to one of the classes above. "conflicts" are conflicts of annotation.
The structured RNAs were curated by identification of pol-II and pol-III transcripts; by identification of host-genes for snoRNAs; and by identification of close-lying protein coding genes for cis-regulatory elements.
The three tracks presented above is 1) the 318 curated RNAs only, 2) the 1,976 high confident RNAs that remained after the curation procedure 3) The full set of 3,601 high confident RNAs including pseudo-genes and genes that failed the curation procedure.
These results were published as part of the pig genome sequencing and annotation in Nature, 2012. Link to paper. The results also exists as a track in the official Ensembl browser since version 70 and can be found under Genes and Transcripts, Genes, ncRNAs imported. For an example follow this link.