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

From: Identification and characterization of novel conserved RNA structures in Drosophila

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
  1. 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