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

-33.6 -33.3 -33.2 -33.0 -32.7 -32.6

droSim1

-29.2 -28.6 -28.4 -28.4

droSec1

-29.2 -28.6 -28.4 -28.4

droYak2

-40.2 -39.6 -39.4 -39.4 -39.3

droEre2

-24.2

droAna3

No secondary structure predictions returned

dp4

-26.5 -25.7 -25.6 -25.6 -25.5 -25.5

droPer1

No secondary structure predictions returned

droWil1

-20.6 -20.1 -20.1 -20.0 -19.9 -19.8

droVir3

No secondary structure predictions returned

droMoj3

-21.5 -21.0 -21.0 -21.0 -20.9 -20.7

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:09 PM