Structured RNAs and synteny regions in the pig genome

BMC Genomics

Table 7 Curated annotation

	# high confident loci	# curated loci	# pseudogenes	# loci,#pseudogenes subtracted
cisreg-elements	139	93	31	108
lncRNA-loci	58	0	0	58
miRNA	369	125	0	369
putative-miRNA	155	0	0	155
ribozyme	8	1	5	3
rRNA	185	3	182	3
snoRNA	638	269	278	360
snRNA	1,030	69	960	70
tRNA	810	0	0	810
Other	153	3	125	28
Conflict	11	8	0	11
Sum	3,556	571	1,581	1,975

The high confident annotation is a combination of the results of the high confident homology pipeline and the miRDeep results. See Table 2 for row labels. Column labels: high confident is the high confident annotation prior to curation; curated are the number of loci curated by methods explained in the text; pseudogenes are the loci expected to be PolII/PolIII transcript, but failing to be so, ribosomal RNAs not part of the cluster on chromosome 6, and cis-regulatory elements without gene context. In the column overlaps to structured RNA loci annotated by homology as well as putative miRNAs are given. Curated annotation contains loci that are a) curated or b) loci not tested in the curation procedure, e.g., miRNA loci. High confident: is the complete high confident annotation (homology + miRDeep). 8 miRNAs detected by miRDeep, but not by high confident BLAST where re-annotated in the section miRNAs in the pig genome. A table with the 3,877 medium confident loci and 36,647 low confident loci are found in Additional file 1: Table S20.

ISSN: 1471-2164