Identification and characterization of novel conserved RNA structures in Drosophila

BMC Genomics

Table 2 Overlap of CRSs with the Drosophila melanogaster Rfam annotation (v.12.2)

Feature	Total feature number	Filtered feature number	Number of features overlapped	Percentage of filtered features overlapped	Fold enrichment	P-value	Number of CRSs overlapped
tRNA	294	247	32	12.9%	4.53	7·10⁻³⁰	32
miRNA	92	85	18	21.1%	7.57	7·10⁻²⁸	17
rRNA	156	6	1	16.6%	0	0.11	1
C/D-box snoRNA	45	41	2	4.8%	1.76	0.16	2
H/ACA-box snoRNA	27	14	4	28.5%	7.73	1·10⁻⁵	4
scaRNA	6	6	3	50.0%	18.04	6·10⁻⁸	3
snRNA	33	29	20	68.9%	21.15	2·10⁻⁵⁵	20
lncRNA	15	15	2	13.3%	4.81	0.01	2
Cis-regulatory element	20	15	6	40.0%	12.03	8·10⁻¹⁴	7
Signal recognition particle RNA	4	4	0	0%	−	−	0
Histone 3’-UTR stem-loop	71	62	4	6.4%	2.33	0.03	4
Ribozyme	2	2	1	50.0%	18.04	0.04	1
Retroelements	121	1	0	0%	−	−	0
All	886	527	93	17.6%	5.89	2·10⁻¹⁰²	93

Annotations with a base pair content of less than 30% were excluded. Predictions overlap the annotation feature by at least 50% of the prediction or the annotation feature size. Filtered features were filtered for features lying at least 50% of their size within the CMfinder input alignment blocks and overlapping a repeat by less than 50% of their size. The CMfinder input alignments did not contain sisRNAs, hence these are not listed here

ISSN: 1471-2164