Annotation of structured RNAs in pig

Genome version 10.2, Annotation version 1.03, Version date June 02 2014

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.

Latest version

The current version is 1.03, click here to view. For previous versions see Release History below.

Annotation tracks

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

Notes on the annotation

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.

Additional data

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 DATAUCSC

Download all annotation and additional data

Download all data by following this link.

References

Release history

The current version is 1.03, click here to view. For previous versions see below.
Annotation version Genome version Release date Comments
Version 1.03 version 10.2 June 02 2014 Updated version for the pig genome companion paper. ChangeLog. Current version.
Version 1.02 version 10.2 Dec 12 2013 Version for the pig genome companion paper.
Version 1.0 version 10.2 June 21 2012 Version for the pig genome sequencing paper and Ensembl version 70.