Secondary structure and small RNA-seq evidence for dme-mir-87

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:9950403-9950531 - CCAAAGT---------CCTTT--GGCAACACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATTATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGAATTT
droSim1 chr2L:9739846-9739974 - CTTAAGT---------CCTTT--GGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATCATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGGATTT
droSec1 super_3:5397127-5397255 - ACCAAGT---------CCTTT--GGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATCATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGGATTT
droYak2 chr2L:12640967-12641095 - TCCAAGT---------CCTTT--GGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTATGGTCTTCG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTTAGCATTCATC----GGAGGATTT
droEre2 scaffold_4929:10570531-10570659 - CACGAGT---------CCTTT--GGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTGCC-ATTATGGCCTACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTTAGCATTCATC----GGACGATTT
droAna3 scaffold_12916:13789760-13789886 - TG--AAT---------CCTTTCAAGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACC-GATATGGCACAGA-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC----AAAAGAT--
dp4 chr4_group3:220105-220226 + TCCTAC----------CGTGT--GCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCC-ATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC----AC-------
droPer1 super_1:1694906-1695025 + TCCTAC----------CGTGT--GCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCC-ATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC-------------
droWil1 scaffold_180708:12250833-12250971 - CCA--ATCAAAATTAACATTT-GGCCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACCAATTGTGATCTTCATTTCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTGACGGTAACATC----GTTGGAATA
droVir3 scaffold_12723:3996238-3996344 + CTA---T---------CCCTT-GGCCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTGAGACATCTAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGT-------------------------
droMoj3 scaffold_6500:14729857-14729979 - -----AT---------CCTTA--GCCGGCATCTTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTGTCACATCCAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTAGCGGTCTCATC----AAAGCA---
droGri2 scaffold_15252:3661296-3661426 - TT---AT---------CCTTG--ACCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACC-ATTGTGACATCCAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTAGCGGCTTCATCACTTGGTGGATAG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:9950403-9950531 - CCAAAGT---------CCTTT--GGCAACACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATTATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGAATTT
droSim1 chr2L:9739846-9739974 - CTTAAGT---------CCTTT--GGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATCATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGGATTT
droSec1 super_3:5397127-5397255 - ACCAAGT---------CCTTT--GGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCC-ATCATGGCCAACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATC----GGAGGATTT
droYak2 chr2L:12640967-12641095 - TCCAAGT---------CCTTT--GGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTATGGTCTTCG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTTAGCATTCATC----GGAGGATTT
droEre2 scaffold_4929:10570531-10570659 - CACGAGT---------CCTTT--GGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTGCC-ATTATGGCCTACG-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTTAGCATTCATC----GGACGATTT
droAna3 scaffold_12916:13789760-13789886 - TG--AAT---------CCTTTCAAGCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACC-GATATGGCACAGA-ATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC----AAAAGAT--
dp4 chr4_group3:220105-220226 + TCCTAC----------CGTGT--GCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCC-ATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC----AC-------
droPer1 super_1:1694906-1695025 + TCCTAC----------CGTGT--GCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCC-ATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTC-------------
droWil1 scaffold_180708:12250833-12250971 - CCA--ATCAAAATTAACATTT-GGCCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACCAATTGTGATCTTCATTTCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTGACGGTAACATC----GTTGGAATA
droVir3 scaffold_12723:3996238-3996344 + CTA---T---------CCCTT-GGCCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTGAGACATCTAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGT-------------------------
droMoj3 scaffold_6500:14729857-14729979 - -----AT---------CCTTA--GCCGGCATCTTTCATTCGCGCCTGTATCTTGCTGAACCGTTACA-ATTGTCACATCCAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTAGCGGTCTCATC----AAAGCA---
droGri2 scaffold_15252:3661296-3661426 - TT---AT---------CCTTG--ACCGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTTACC-ATTGTGACATCCAAATCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTAGCGGCTTCATCACTTGGTGGATAG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CTTAAGTCCTTTGGCGGCACATTTCATTCGCGCCTGTATCTTGCTGAACCGCTGCCATCATGGCCAACGATC-CGGTTGAGCAAAATTTCAGGTGTGTGAGAAATGTGTTTAGCATTCATCGGAGGATTTSizeHit CountTotal NormTotalGSM343915
Embryo
............................................................................TTGAGCAAAATTTCAGGTGTGTGA..............................2415937.0059375937
............................................................................TTGAGCAAAATTTCAGGTGTGTG...............................2311222.0012221222
.............................................................................TGAGCAAAATTTCAGGTGTGTGA..............................231931.00931931
.............................................................................TGAGCAAAATTTCAGGTGTGTG...............................22192.009292
............................................................................TTGAGCAAAATTTCAGGTGTGT................................22176.007676
............................................................................TTGAGCAAAATTTCAGGTGTG.................................21117.001717
...........................TCGCGCCTGTATCTTGCTGAACC................................................................................23113.001313
...........................TCGCGCCTGTATCTTGCTGAAC.................................................................................2218.0088
..............................................................................GAGCAAAATTTCAGGTGTGTGA..............................2216.0066
............................................................................TTGAGCAAAATTTCAGGTGTGTGAG.............................2513.0033
.............................................................................TGAGCAAAATTTCAGGTGTGTGAG.............................2413.0033
..................................................GCTGCCATCATGGCCAACGATC-CGG......................................................2512.0022
...............................................................................AGCAAAATTTCAGGTGTGTGA..............................2111.0011
........................................................ATCATGGCCAACGATC-CGGT.....................................................2011.0011
.............................GCGCCTGTATCTTGCTGAAC.................................................................................2011.0011
.............................................................................TGAGCAAAATTTCAGGTGTGT................................2111.0011
..................................................................................AAAATTTCAGGTGTGTGA..............................1811.0011
dp4
TCCTAC-CGTGTGCTGGCATATTTCATTCGCGCCTGTATCTTGCTGAACCGTAGCCATAATGGTCTTTCATCCCGGTTGAGCAAAATTTCAGGTGTGTGAGAAATTTGTTAAGCAATCTTCAC-------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
............................................................................TTGAGCAAAATTTCAGGTGTGTGA..............................2413515.0035152998517
............................................................................TTGAGCAAAATTTCAGGTGTGTG...............................231749.00749536213
.............................................................................TGAGCAAAATTTCAGGTGTGTGA..............................231664.0066457193
............................................................................TTGAGCAAAATTTCAGGTGTGT................................221375.00375140235
............................................................................TTGAGCAAAATTTCAGGTGTG.................................211237.00237133104
.............................................................................TGAGCAAAATTTCAGGTGTGTG...............................22179.00794930
.............................................................................TGAGCAAAATTTCAGGTGTGT................................21122.0022220
............................................................................TTGAGCAAAATTTCAGGTGT..................................20121.00211011
...........................TCGCGCCTGTATCTTGCTGAACC................................................................................2318.00871
...........................TCGCGCCTGTATCTTGCTGAAC.................................................................................2216.00633
.............................................................................TGAGCAAAATTTCAGGTGTG.................................2015.00514
.............................................................................TGAGCAAAATTTCAGGTGTGTGAG.............................2415.00541
...........................................................................GTTGAGCAAAATTTCAGGTGTGTG...............................2413.00330
...........................................................................GTTGAGCAAAATTTCAGGTGTGTGA..............................2512.00220
............................................................................TTGAGCAAAATTTCAGGTGTGTGAG.............................2512.00220
.............................................................................TGAGCAAAATTTCAGGTGT..................................1912.00202
...............................................................................AGCAAAATTTCAGGTGTGTGA..............................2111.00110
...........................................................................GTTGAGCAAAATTTCAGGTGTG.................................2211.00110
............................................................................TTGAGCAAAATTTCAGGT....................................1811.00101
...........................TCGCGCCTGTATCTTGCTGAACCG...............................................................................2411.00101

Secondary Structure

dm3

dG=-29.8,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.6,  p-value=0.009901 dG=-29.4,  p-value=0.009901

droSim1

dG=-29.8,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.6,  p-value=0.009901 dG=-29.4,  p-value=0.009901

droSec1

dG=-29.8,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.6,  p-value=0.009901 dG=-29.4,  p-value=0.009901

droYak2

dG=-27.4,  p-value=0.009901 dG=-27.3,  p-value=0.009901 dG=-27.3,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-26.8,  p-value=0.009901

droEre2

dG=-29.8,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.6,  p-value=0.009901 dG=-29.4,  p-value=0.009901

droAna3

dG=-26.1,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-25.9,  p-value=0.009901

dp4

dG=-28.1,  p-value=0.009901 dG=-28.0,  p-value=0.009901 dG=-28.0,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.7,  p-value=0.009901

droPer1

dG=-28.1,  p-value=0.009901 dG=-28.0,  p-value=0.009901 dG=-28.0,  p-value=0.009901 dG=-27.9,  p-value=0.009901 dG=-27.7,  p-value=0.009901

droWil1

dG=-26.6,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.5,  p-value=0.009901

droVir3

dG=-26.9,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-26.7,  p-value=0.009901 dG=-26.3,  p-value=0.009901

droMoj3

dG=-26.1,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.5,  p-value=0.009901

droGri2

dG=-27.0,  p-value=0.009901 dG=-26.9,  p-value=0.009901 dG=-26.9,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-26.7,  p-value=0.009901

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