Secondary structure and small RNA-seq evidence for dme-mir-12-as

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:15403491-15403594 - TTAGTGCGATCCGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGATTTAAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------TT
droSim1 chrX_random:4024315-4024418 - TTAGTGCGATCCGTGCACGGCGTAGTATGACACAAGTACTGGTTGTTGGATTTCAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------AT
droSec1 super_73:137914-138017 - TTAGTGCGATCCGTGCACGGCGTAGTATGACACAAGTACTGGTTGTTGGATTTCAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------AT
droYak2 gnl|ti|369397274:327-428 - ---GTGCGATCCGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGATTTAAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------TT
droEre2 scaffold_4690:11630938-11631041 + TTAGTGCGATCCGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGTTTTAAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------TT
droAna3 scaffold_12929:2898571-2898666 + TTAGTGCGATCGGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGATTAAAGGCACACCAGTACCTGATGTAATACTCAGCCGTACAGACGC-------------------------------
dp4 chrXL_group1a:977995-978098 - TTAGTGCGATCAGTGCACGGCGTAGTATAACATAAGTACTGGTTGTTGGATTTAAAGCACACCAGTACCTGATGTAATACTCAGCCGTACAGACGCT------GCTGG-----------------AT
droPer1 super_26:1092636-1092739 - TTAGTGCGATCAGTGCACGGCGTAGTATAACATAAGTACTGGTTGTTGGATTTAAAGCACACCAGTACCTGATGTAATACTCAGCCGTACAGACGCT------GCTGG-----------------AT
droWil1 scaffold_180702:1592742-1592840 + TTAGTGCGATCCGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGATTAAAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGGCGCT------GC----------------------
droVir3 scaffold_12970:2049296-2049416 - TTAGTGCGCCCACTGCACGGCGTAGTATGACATAAGTACTGGTTGTTAGTTAAATGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GATGCGGATGCTGATGCGGCTGTT
droMoj3 scaffold_6359:3259767-3259875 - TTAGTGCGCCCACTGCACGGCGTAGTATGACATAAGTACTGGTTGTTAGTTAATTGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GATGCTGATG------------CT
droGri2 scaffold_14853:6951707-6951816 + TTAGTGCGCCCACTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGTTAAATGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCTTGTGATGCTGC-----------------TT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:15403491-15403594 - TTAGTGCGATCCGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGATTTAAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------TT
droSim1 chrX_random:4024315-4024418 - TTAGTGCGATCCGTGCACGGCGTAGTATGACACAAGTACTGGTTGTTGGATTTCAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------AT
droSec1 super_73:137914-138017 - TTAGTGCGATCCGTGCACGGCGTAGTATGACACAAGTACTGGTTGTTGGATTTCAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------AT
droYak2 gnl|ti|369397274:327-428 - ---GTGCGATCCGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGATTTAAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------TT
droEre2 scaffold_4690:11630938-11631041 + TTAGTGCGATCCGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGTTTTAAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GCTCC-----------------TT
droAna3 scaffold_12929:2898571-2898666 + TTAGTGCGATCGGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGATTAAAGGCACACCAGTACCTGATGTAATACTCAGCCGTACAGACGC-------------------------------
dp4 chrXL_group1a:977995-978098 - TTAGTGCGATCAGTGCACGGCGTAGTATAACATAAGTACTGGTTGTTGGATTTAAAGCACACCAGTACCTGATGTAATACTCAGCCGTACAGACGCT------GCTGG-----------------AT
droPer1 super_26:1092636-1092739 - TTAGTGCGATCAGTGCACGGCGTAGTATAACATAAGTACTGGTTGTTGGATTTAAAGCACACCAGTACCTGATGTAATACTCAGCCGTACAGACGCT------GCTGG-----------------AT
droWil1 scaffold_180702:1592742-1592840 + TTAGTGCGATCCGTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGATTAAAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGGCGCT------GC----------------------
droVir3 scaffold_12970:2049296-2049416 - TTAGTGCGCCCACTGCACGGCGTAGTATGACATAAGTACTGGTTGTTAGTTAAATGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GATGCGGATGCTGATGCGGCTGTT
droMoj3 scaffold_6359:3259767-3259875 - TTAGTGCGCCCACTGCACGGCGTAGTATGACATAAGTACTGGTTGTTAGTTAATTGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCT------GATGCTGATG------------CT
droGri2 scaffold_14853:6951707-6951816 + TTAGTGCGCCCACTGCACGGCGTAGTATGACATAAGTACTGGTTGTTGGTTAAATGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCTTGTGATGCTGC-----------------TT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTAGTGCGATCCGTGCACGGCGTAGTATGACACAAGTACTGGTTGTTGGATTTCAGGCACACCAGTACCTGATGTAATACTCAACCGTACAGACGCTGCTCCATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TTAGTGCGATCAGTGCACGGCGTAGTATAACATAAGTACTGGTTGTTGGATTTAAAGCACACCAGTACCTGATGTAATACTCAGCCGTACAGACGCTGCTGGATSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-25.7 -24.9 -24.9 -24.9 -24.8

droSim1

-26.7 -25.9 -25.9

droSec1

-26.7 -25.9 -25.9

droYak2

-25.7 -24.9 -24.9 -24.9 -24.8

droEre2

-25.7 -24.9 -24.9 -24.9 -24.8

droAna3

-30.5 -29.7 -29.7 -29.7 -29.6

dp4

-31.2 -30.4 -30.4 -30.3

droPer1

-31.2 -30.4 -30.4 -30.3

droWil1

-25.7 -24.9 -24.9 -24.9 -24.8

droVir3

-27.1 -26.3 -26.3 -26.3 -26.2

droMoj3

-26.4 -26.4 -25.6 -25.6 -25.6 -25.6

droGri2

-25.6 -25.1 -24.8 -24.8 -24.8 -24.7

Generated: 01/05/2013 at 05:07 PM