Secondary structure and small RNA-seq evidence for dme-mir-968

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:13747733-13747854 - TCAAAGA-AA------------AATTGTTGATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTTCTCAACATG-----CAAATCAACCTTTTGATGTACTACTTTAAGAATCTCCAGTTAAAGTCAACACA--TAAG
droSim1 chr2L:13506671-13506792 - TCAAAGAAAA------------AATTGTTCATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTTCTCAACATG-----CAAATCAACCGTTTGATGTACTACTTTAGGAATCTACAGTCAAAGTCAACAT---TAAA
droSec1 super_3:14598-14719 - TCAAAGAAAA------------AATTGTTCATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTTCTCAACATG-----CAAATCAACCGTTTGATGTACTACTTTAGGAATCTACAGTCAAAGTCAACAT---TAAA
droYak2 chr2L:10160053-10160172 - TCAAGGA-AA------------AGTGTTTGATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTGGTCA-CAAT-----AAGATCAACCTTTTGATTTACTACTTTAGGAATCTCCAGTCAAAGTCAACAT---TAAT
droEre2 scaffold_4929:11718898-11719017 + TCAAAGA-AA------------AGTTGTTGATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTGGTCA-CAAT-----TGAATCGACCGTTTAATGTACTACTTTAAGAATCTCCAGTCAAAGTCAACAA---TAAT
droAna3 scaffold_12943:1815538-1815649 - AAA---------------------T----TATGGCAGTTTCCTTAAGTAGTATCCATTAAAGGGTCGTTAATA-TATT-----CAAAGTGACCGTTTGATGTACTACTTTAGGTAGCTCCATTTAAAGTCGGCTAAAATAAG
dp4 chr4_group1:1722766-1722895 + TTGAATAGTGATTTAGTTCTACAATT----GCTGCAGCTTCCTTAAGTAGTATCCATTAAGAGGTCGTCATCT-AGCT-----AAAATCGACCTTTTGATGTACTACTTTAAAAAAGCACAGTCAAAGTCAACAGAA--CTG
droPer1 super_5:3483598-3483726 - TTGAATAGTGATTTAGTTCCACAATT----GCTGCAGCTTCCTTAAGTAGTATCCATTAAGAGGTCGTCATCT-AGCT-----AAAATCGACCTTTTGATGTACTACTTTAAAAAGC-ACAGTCGAAGTCAACAGAA--CTG
droWil1 scaffold_180772:545302-545417 + CTCGTG------------------------A-TGCAGATTCTTTAAGTAGTAACCTTTAAAGGGTCGTTTGTCCAATTCTTTTAAAGTCGATCCTTTAAGTTACTACTTGCAGAATGTGTTTCTGAAATCAACAAA--TATA
droVir3 scaffold_12723:5044036-5044131 - C---------------------AATT----A-TACATGTGCCTTAAGTAGTAACCATTAAGAGGTTGTTGTTA-GATT-----TAAATCCACCTTTTAATGTACTACTTATGACAAATGCATAG--------------CAAA
droMoj3 scaffold_6500:16664499-16664593 + AAA--------------------ATT----A-TGCAAGTATCATAAGTAGTAACCATTAAAAGGTCGTGATT-----T-----GAACTCAACCTTTTAATTTACTACTTGTGATAAATGCATAGAAATGT------------
droGri2 scaffold_15126:8057347-8057450 - TCTA----------------------------------TGCCTTAAGTAGTAACCATTAAAAGGTTGTTTTTGTAAAT-----TATACCGACCTTTTAGTGTACTACTTAAAGTACATTCATTGCAAGTCGACGAATATATA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:13747733-13747854 - TCAAAGA-AA------------AATTGTTGATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTTCTCAACATG-----CAAATCAACCTTTTGATGTACTACTTTAAGAATCTCCAGTTAAAGTCAACACA--TAAG
droSim1 chr2L:13506671-13506792 - TCAAAGAAAA------------AATTGTTCATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTTCTCAACATG-----CAAATCAACCGTTTGATGTACTACTTTAGGAATCTACAGTCAAAGTCAACAT---TAAA
droSec1 super_3:14598-14719 - TCAAAGAAAA------------AATTGTTCATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTTCTCAACATG-----CAAATCAACCGTTTGATGTACTACTTTAGGAATCTACAGTCAAAGTCAACAT---TAAA
droYak2 chr2L:10160053-10160172 - TCAAGGA-AA------------AGTGTTTGATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTGGTCA-CAAT-----AAGATCAACCTTTTGATTTACTACTTTAGGAATCTCCAGTCAAAGTCAACAT---TAAT
droEre2 scaffold_4929:11718898-11719017 + TCAAAGA-AA------------AGTTGTTGATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTGGTCA-CAAT-----TGAATCGACCGTTTAATGTACTACTTTAAGAATCTCCAGTCAAAGTCAACAA---TAAT
droAna3 scaffold_12943:1815538-1815649 - AAA---------------------T----TATGGCAGTTTCCTTAAGTAGTATCCATTAAAGGGTCGTTAATA-TATT-----CAAAGTGACCGTTTGATGTACTACTTTAGGTAGCTCCATTTAAAGTCGGCTAAAATAAG
dp4 chr4_group1:1722766-1722895 + TTGAATAGTGATTTAGTTCTACAATT----GCTGCAGCTTCCTTAAGTAGTATCCATTAAGAGGTCGTCATCT-AGCT-----AAAATCGACCTTTTGATGTACTACTTTAAAAAAGCACAGTCAAAGTCAACAGAA--CTG
droPer1 super_5:3483598-3483726 - TTGAATAGTGATTTAGTTCCACAATT----GCTGCAGCTTCCTTAAGTAGTATCCATTAAGAGGTCGTCATCT-AGCT-----AAAATCGACCTTTTGATGTACTACTTTAAAAAGC-ACAGTCGAAGTCAACAGAA--CTG
droWil1 scaffold_180772:545302-545417 + CTCGTG------------------------A-TGCAGATTCTTTAAGTAGTAACCTTTAAAGGGTCGTTTGTCCAATTCTTTTAAAGTCGATCCTTTAAGTTACTACTTGCAGAATGTGTTTCTGAAATCAACAAA--TATA
droVir3 scaffold_12723:5044036-5044131 - C---------------------AATT----A-TACATGTGCCTTAAGTAGTAACCATTAAGAGGTTGTTGTTA-GATT-----TAAATCCACCTTTTAATGTACTACTTATGACAAATGCATAG--------------CAAA
droMoj3 scaffold_6500:16664499-16664593 + AAA--------------------ATT----A-TGCAAGTATCATAAGTAGTAACCATTAAAAGGTCGTGATT-----T-----GAACTCAACCTTTTAATTTACTACTTGTGATAAATGCATAGAAATGT------------
droGri2 scaffold_15126:8057347-8057450 - TCTA----------------------------------TGCCTTAAGTAGTAACCATTAAAAGGTTGTTTTTGTAAAT-----TATACCGACCTTTTAGTGTACTACTTAAAGTACATTCATTGCAAGTCGACGAATATATA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TCAAAGAAA------------AAATTGTTCATGGAAGCTTCCTTAAGTAGTATCCATTAAAGGGTTGTTCTCAACATGCAAATCAACCGTTTGATGTACTACTTTAGGAATCTACAGTCAAAGTCAACAT-TAAASizeHit CountTotal NormTotalGSM343915
Embryo
...........................................TAAGTAGTATCCATTAAAGGGTTG....................................................................24125039.002503925039
...........................................TAAGTAGTATCCATTAAAGGGTT.....................................................................231545.00545545
.....................................................................................ACCGTTTGATGTACTACTTTAG............................221307.00307307
..........................................TTAAGTAGTATCCATTAAAGGGTT.....................................................................24184.008484
...........................................TAAGTAGTATCCATTAAAGGGT......................................................................22151.005151
...........................................TAAGTAGTATCCATTAAAGGGTTGT...................................................................25134.003434
............................................AAGTAGTATCCATTAAAGGGTTG....................................................................23125.002525
...........................................TAAGTAGTATCCATTAAAGG........................................................................20118.001818
.....................................................................................ACCGTTTGATGTACTACTTTA.............................21110.001010
...........................................TAAGTAGTATCCATTAAAGGG.......................................................................2118.0088
.............................................AGTAGTATCCATTAAAGGGTTG....................................................................2216.0066
......................................................................................CCGTTTGATGTACTACTTTAGG...........................2215.0055
...........................................TAAGTAGTATCCATTAAAG.........................................................................1915.0055
..........................................TTAAGTAGTATCCATTAAAGGGT......................................................................2314.0044
................................................AGTATCCATTAAAGGGTTG....................................................................1913.0033
....................................................................................AACCGTTTGATGTACTACTTTAG............................2313.0033
......................................................................................CCGTTTGATGTACTACTTTAG............................2113.0033
...............................................TAGTATCCATTAAAGGGTTG....................................................................2012.0022
dp4
TTGAATAGTGATTTAGTTCTACAATTGCT----GCAGCTTCCTTAAGTAGTATCCATTAAGAGGTCGTCATCTAGCTA-AAATCGACCTTTTGATGTACTACTTTAAAAAAGCACAGTCAAAGTCAACAGAACTGSizeHit CountTotal NormTotalGSM343916
Embryo
GSM444067
Head
...........................................TAAGTAGTATCCATTAAGAGGTCG....................................................................24128725.0028725287178
..........................................TTAAGTAGTATCCATTAAGAGGTC.....................................................................241559.005595590
............................................AAGTAGTATCCATTAAGAGGTCG....................................................................231551.005515501
...........................................TAAGTAGTATCCATTAAGAGGTC.....................................................................231280.002802782
............................................AAGTAGTATCCATTAAGAGGTCGT...................................................................241279.002792790
...........................................TAAGTAGTATCCATTAAGAGGTCGT...................................................................25196.0096960
...........................................TAAGTAGTATCCATTAAGAG........................................................................20187.0087870
...........................................TAAGTAGTATCCATTAAGAGGT......................................................................22160.0060600
...........................................TAAGTAGTATCCATTAAGAGG.......................................................................21151.0051510
..........................................TTAAGTAGTATCCATTAAGAGGT......................................................................23144.0044440
...........................................TAAGTAGTATCCATTAAGA.........................................................................19141.0041410
..........................................TTAAGTAGTATCCATTAAGAGGTCG....................................................................25139.0039390
.............................................AGTAGTATCCATTAAGAGGTCG....................................................................22123.0023230
...............................................TAGTATCCATTAAGAGGTCG....................................................................20119.0019190
.....................................................................................ACCTTTTGATGTACTACTTTAA............................22112.0012120
..........................................TTAAGTAGTATCCATTAAGAGG.......................................................................22112.0012120
................................................AGTATCCATTAAGAGGTCG....................................................................19111.0011110
..............................................GTAGTATCCATTAAGAGGTCG....................................................................21110.0010100
............................................AAGTAGTATCCATTAAGAGGT......................................................................21110.0010100
.....................................................................................ACCTTTTGATGTACTACTTTAAA...........................2319.00990
......................................................................................CCTTTTGATGTACTACTTTAAA...........................2216.00660
.....................................................................................ACCTTTTGATGTACTACTTTA.............................2116.00660
..........................................TTAAGTAGTATCCATTAAGA.........................................................................2015.00550
....................................................................................GACCTTTTGATGTACTACTTTA.............................2214.00440
............................................AAGTAGTATCCATTAAGA.........................................................................1814.00440
...........................................TAAGTAGTATCCATTAAG..........................................................................1813.00330
..........................................TTAAGTAGTATCCATTAAGAG........................................................................2113.00330
............................................AAGTAGTATCCATTAAGAG........................................................................1913.00330
............................................AAGTAGTATCCATTAAGAGGTC.....................................................................2213.00330

Secondary Structure

dm3

dG=-23.4,  p-value=0.009901 dG=-23.4,  p-value=0.009901 dG=-23.4,  p-value=0.009901 dG=-22.8,  p-value=0.009901 dG=-22.8,  p-value=0.009901

droSim1

dG=-27.2,  p-value=0.009901 dG=-26.9,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.4,  p-value=0.009901

droSec1

dG=-27.2,  p-value=0.009901 dG=-26.9,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.4,  p-value=0.009901

droYak2

dG=-27.5,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-26.8,  p-value=0.009901

droEre2

dG=-23.2,  p-value=0.009901 dG=-23.2,  p-value=0.009901 dG=-23.2,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.6,  p-value=0.009901

droAna3

dG=-24.9,  p-value=0.009901 dG=-24.9,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.2,  p-value=0.009901 dG=-24.2,  p-value=0.009901

dp4

dG=-24.5,  p-value=0.009901 dG=-23.8,  p-value=0.009901 dG=-23.5,  p-value=0.009901

droPer1

dG=-24.5,  p-value=0.009901 dG=-23.8,  p-value=0.009901 dG=-23.7,  p-value=0.009901 dG=-23.5,  p-value=0.009901

droWil1

dG=-27.9,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.3,  p-value=0.009901 dG=-27.1,  p-value=0.009901

droVir3

dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.4,  p-value=0.009901

droMoj3

dG=-27.3,  p-value=0.009901 dG=-27.0,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-26.3,  p-value=0.009901

droGri2

dG=-25.4,  p-value=0.009901 dG=-25.3,  p-value=0.009901 dG=-24.9,  p-value=0.009901 dG=-24.8,  p-value=0.009901 dG=-24.8,  p-value=0.009901

Generated: 03/07/2013 at 07:14 PM