The annotation was based on the pig genome version 10.2.
This release replaces the previous version released Dec 12 2013. The main difference between this and the previous version of the annotation, is that the snoStrip tool was used in a pre-release version in the previous annotation. ChangeLog.
Annotation tracks of structured RNAs. Includes predictions based on homology and prediction of novel miRNAs based on a small RNA library.
| Cutoff-level | # Loci | Comment | ||||
| Curatated | 590 | Hand and machine curated structured RNAs | GTF | BED | Ensembl | UCSC |
| High confident without pseudo-genes | 1,984 | High confident structured RNAs, includes curated, pseudo-genes removed | GTF | BED | Ensembl | UCSC |
| High confident | 3,539 | High confident structured RNAs, includes curated and pseudo-genes | GTF | BED | Ensembl | UCSC |
| Medium confident(nested) | 3,861 | Medium confident structured RNAs, preserved high confident annotation. | GTF | BED | Ensembl | UCSC |
| Medium confident | 3,861 | Medium confident structured RNAs, high confident annotation may change. | GTF | BED | Ensembl | UCSC |
| Low confident(nested) | 36,632 | Low confident structured RNAs, preserved high and medium confident annotation. | GTF | BED | Ensembl | UCSC |
| Low confident | 36,632 | Low confident structured RNAs, high and medium confident annotation may change. | GTF | BED | Ensembl | UCSC |
| De novo predictions | 83,859 | De novo structured RNA loci | GTF | BED | Ensembl | UCSC |
| De novo predictions | 166 | deepBlockAlign de novo predictions | BED | Ensembl | UCSC |
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.
De novo predictions are based on RNAz loci with a cutoff of p=0.9
The structured RNAs were curated by identification of pol-II and pol-III transcripts; by identification of host-genes for snoRNAs; by identification of high confident miRNAs in known clusters; by identification of a complete rRNA cluster; and by identification of close-lying protein coding genes for cis-regulatory elements.
| Data | Download | |
| Alignment of YRNAs in Stockholm format | STK | |
| Pig/human synteny regions | HTML | |
| High confident miRNA sequences and loci | hairpins | BED |
| High confident mature miRNA sequences | mature | |
| Small reads | DATA | UCSC |