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

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:15403491-15403594 + AA-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAA
droSim1 chrX_random:4024315-4024418 + AT-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATCGCACTAA
droSec1 super_73:137914-138017 + AT-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATCGCACTAA
droYak2 gnl|ti|371645083:614-718 + AA-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAA
droEre2 scaffold_4690:11630938-11631041 - AA-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAAACCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAA
droAna3 scaffold_12929:2898571-2898667 - -------------------------------GCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCCTTTAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACCGATCGCACTAA
dp4 chrXL_group1a:977995-978098 + AT-----------------CCAG------CAGCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATCGCACTAA
droPer1 super_26:1092636-1092739 + AT-----------------CCAG------CAGCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATCGCACTAA
droWil1 scaffold_180702:1592742-1592841 - ----------------------G------CAGCGCCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTTAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAA
droVir3 scaffold_12970:2049296-2049416 + AACAGCCGCATCAGCATCCGCAT------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCATTTAACTAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAA
droMoj3 scaffold_6359:3259767-3259875 + AG------------CATCAGCAT------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCAATTAACTAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAA
droGri2 scaffold_14853:6951707-6951816 - AA-----------------GCAGCATCACAAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCATTTAACCAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:15403491-15403594 + AA-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAA
droSim1 chrX_random:4024315-4024418 + AT-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATCGCACTAA
droSec1 super_73:137914-138017 + AT-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATCGCACTAA
droYak2 gnl|ti|371645083:614-718 + AA-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAA
droEre2 scaffold_4690:11630938-11631041 - AA-----------------GGAG------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAAACCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAA
droAna3 scaffold_12929:2898571-2898667 - -------------------------------GCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCCTTTAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACCGATCGCACTAA
dp4 chrXL_group1a:977995-978098 + AT-----------------CCAG------CAGCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATCGCACTAA
droPer1 super_26:1092636-1092739 + AT-----------------CCAG------CAGCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATCGCACTAA
droWil1 scaffold_180702:1592742-1592841 - ----------------------G------CAGCGCCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTTAATCCAACAACCAGTACTTATGTCATACTACGCCGTGCACGGATCGCACTAA
droVir3 scaffold_12970:2049296-2049416 + AACAGCCGCATCAGCATCCGCAT------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCATTTAACTAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAA
droMoj3 scaffold_6359:3259767-3259875 + AG------------CATCAGCAT------CAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCAATTAACTAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAA
droGri2 scaffold_14853:6951707-6951816 - AA-----------------GCAGCATCACAAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCATTTAACCAACAACCAGTACTTATGTCATACTACGCCGTGCAGTGGGCGCACTAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATGGAGCAGCGTCTGTACGGTTGAGTATTACATCAGGTACTGGTGTGCCTGAAATCCAACAACCAGTACTTGTGTCATACTACGCCGTGCACGGATCGCACTAASizeHit CountTotal NormTotalGSM343915
Embryo
.....................TGAGTATTACATCAGGTACTGG.............................................................222136.50273273
.....................TGAGTATTACATCAGGTACTG..............................................................21285.50171171
.....................TGAGTATTACATCAGGTACT...............................................................20254.50109109
...............................................................CAGTACTTGTGTCATACTACG....................21210.502121
......................GAGTATTACATCAGGTACTGGT............................................................2223.5077
.....................TGAGTATTACATCAGGTACTGGTG...........................................................2422.5055
.......................AGTATTACATCAGGTACTGGT............................................................2122.0044
.....................TGAGTATTACATCAGGTAC................................................................1921.5033
......................GAGTATTACATCAGGTACTGG.............................................................2121.5033
.....................TGAGTATTACATCAGGTA.................................................................1821.0022
................................................................AGTACTTGTGTCATACTACGC...................2120.5011
...GAGCAGCGTCTGTACGGT...................................................................................1820.5011
dp4
ATCCAGCAGCGTCTGTACGGCTGAGTATTACATCAGGTACTGGTGTGCTTTAAATCCAACAACCAGTACTTATGTTATACTACGCCGTGCACTGATCGCACTAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.....................TGAGTATTACATCAGGTACTGGT............................................................2323228.00645664560
.....................TGAGTATTACATCAGGTACTG..............................................................212375.00750214536
.....................TGAGTATTACATCAGGTACT...............................................................20248.50977720
.....................TGAGTATTACATCAGGTACTGGTG...........................................................24236.0072720
......................GAGTATTACATCAGGTACTGGT............................................................22225.5051510
.....................TGAGTATTACATCAGGTAC................................................................1925.501129
.TCCAGCAGCGTCTGTACGGC...................................................................................2023.50770
......................GAGTATTACATCAGGTACTGG.............................................................2122.50505
..CCAGCAGCGTCTGTACGGC...................................................................................1922.00404
ATCCAGCAGCGTCTGTACGGC...................................................................................2122.00431
.....................TGAGTATTACATCAGGTA.................................................................1821.50321
....................CTGAGTATTACATCAGGTACTGGT............................................................2421.00202
...CAGCAGCGTCTGTACGGC...................................................................................1821.00220
.......................AGTATTACATCAGGTACTGGT............................................................2120.50101
......................GAGTATTACATCAGGTACTGGTGT..........................................................2420.50101
........................GTATTACATCAGGTACTGGT............................................................2020.50101
.........................TATTACATCAGGTACTGGT............................................................1920.50101
......................GAGTATTACATCAGGTACTG..............................................................2020.50101
.........................TATTACATCAGGTACTGG.............................................................1820.50110

Secondary Structure

dm3

dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droSim1

dG=-31.3,  p-value=0.009901 dG=-31.3,  p-value=0.009901 dG=-30.4,  p-value=0.009901 dG=-30.3,  p-value=0.009901 dG=-30.3,  p-value=0.009901

droSec1

dG=-31.3,  p-value=0.009901 dG=-31.3,  p-value=0.009901 dG=-30.4,  p-value=0.009901 dG=-30.3,  p-value=0.009901 dG=-30.3,  p-value=0.009901

droYak2

dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droEre2

dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droAna3

dG=-31.0,  p-value=0.009901 dG=-31.0,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-30.0,  p-value=0.009901 dG=-30.0,  p-value=0.009901

dp4

dG=-31.2,  p-value=0.009901 dG=-31.2,  p-value=0.009901 dG=-30.3,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droPer1

dG=-31.2,  p-value=0.009901 dG=-31.2,  p-value=0.009901 dG=-30.3,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droWil1

dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droVir3

dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droMoj3

dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droGri2

dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.4,  p-value=0.009901

Generated: 03/07/2013 at 04:50 PM