Secondary structure and small RNA-seq evidence for dme-mir-2490

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2LHet:27321-27425 + ACAATCGTACGTTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGCTTTGCTCTT---------------------------------------------------------ACTTTATCGCTTAAACTCGCA-----ACTCGCTTC----------GCTCTCA
droSim1 chr4:281112-281214 + AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGCTTTGCTCTC---------------------------------------------------------GCTATATCGCTTGAGCTCGCA-----ACTCGCTTC----------GCT--CA
droSec1 super_30:85009-85111 + AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGCTTTGCTCTC---------------------------------------------------------GCTATATCGCTTGAGCTCGCA-----ACTCGCTTC----------GCT--CA
droYak2 chrU:9061077-9061181 + ACAATCGTACGCTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGCTTTGCTCTC---------------------------------------------------------GCTTTATCGCTTGAGCTCGCT-----ACTCGCCTC----------GCTCTCA
droEre2 scaffold_4784:23192819-23192904 - ACTATCAGACGCTCTGAGCGAGTTGCAGCGATAATGCAGGTTGCAAACTGTTCTCT----------------------------------------------------------------------------CGCTTGAGCTCGCA-----ACTCGTTTC----------GCTCTCA
droAna3 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4 chr4_group4:3101286-3101457 + AGCAT---GAGC-GTCCACGAGATCAAGCGATAAGACATTTGCAAAGCTACTCTCTTGCTTCGCTTGCACTCGTTGCTGTCTTCGCTATAACTTGTTTCCCGCTCTTCACTGTAAATCGTTTTGCAC-TCTTCGCTCAAACTAGCCGCGCTGCTCTCTTCGCTTATCTTTGCTCTCA
droPer1 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181143:687820-687924 + ACACACGTATAACAGCAGCTGGATGAAGCGATAAAGCGA-TTCAGAATCGCTTTCTCGCAACTCGCTT------------------------------C--------------------------AACTTGTCGCTTTGGCTCTCT-----TCTCGCTTC----------GCTTGCA
droVir3 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6498:432956-433055 + AACAC---ACTTTAT-CATGCGATTAAGCGAGAAAGCGA-TTCAGGAATGCTTTCTCGCAACTCGCTT---------------------------------------------------------AACTTCTCGCTTTGGGTCTCT-----TCTCGCTTC----------GCTTGCA
droGri2 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2LHet:27321-27425 + ACAATCGTACGTTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGCTTTGCTCTTACTTTATCGCTTAAACTCGCAACTCGCTTCGCTCTCA
droSim1 chr4:281112-281214 + AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGCTTTGCTCTCGCTATATCGCTTGAGCTCGCAACTCGCTTCGCT--CA
droSec1 super_30:85009-85111 + AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGCTTTGCTCTCGCTATATCGCTTGAGCTCGCAACTCGCTTCGCT--CA
droYak2 chrU:9061077-9061181 + ACAATCGTACGCTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGCTTTGCTCTCGCTTTATCGCTTGAGCTCGCTACTCGCCTCGCTCTCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGCTTTGCTCTCGC----------------TATA----------------------------------------TCGCTTGAGCTCGCAAC-----TCGCTTCGC------------TCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AGCAT-GAGCGTC---CACGAGATCAAGCGATAAGACATTTGCAAAGCTACTCTCTTGCTTCGCTTGCACTCGTTGCTGTCTTCGCTATAACTTGTTTCCCGCTCTTCACTGTAAATCGTTTTGCACTCTTCGCTCAAACTAGCCGCGCTGCTCTCTTCGCTTATCTTTGCTCTCASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-29.1,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.2,  p-value=0.009901

droSim1

dG=-24.7,  p-value=0.009901 dG=-24.1,  p-value=0.009901 dG=-23.9,  p-value=0.009901 dG=-23.9,  p-value=0.009901

droSec1

dG=-24.7,  p-value=0.009901 dG=-24.1,  p-value=0.009901 dG=-23.9,  p-value=0.009901 dG=-23.9,  p-value=0.009901

droYak2

dG=-34.4,  p-value=0.009901 dG=-33.8,  p-value=0.009901 dG=-33.6,  p-value=0.009901 dG=-33.6,  p-value=0.009901

droEre2

dG=-19.7,  p-value=0.009901

droAna3

No secondary structure predictions returned

dp4

dG=-22.2,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.3,  p-value=0.009901 dG=-21.3,  p-value=0.009901 dG=-18.1,  p-value=0.009901

droPer1

No secondary structure predictions returned

droWil1

dG=-18.6,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-18.2,  p-value=0.009901 dG=-18.2,  p-value=0.009901

droVir3

No secondary structure predictions returned

droMoj3

dG=-21.0,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.6,  p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 04:55 PM