Secondary structure and small RNA-seq evidence for dme-mir-252

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:9289926-9290048 - GTG-------TGCCG------------CCTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droSim1 chr3R_random:533427-533549 - GTG-------TGCCG------------TCTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droSec1 super_0:12715202-12715324 + GTG-------TGCCG------------TCTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droYak2 chr3R:13598006-13598135 - GTGCTAGATGTACGA------------TGTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droEre2 scaffold_4770:12350666-12350788 + GTG-------CTAGA------------TGTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droAna3 scaffold_13340:1848657-1848824 - GAG--------------------------TACTTAGCCCCAACCATTGGTAAATATTGATTTTATACTTACATTACTTCCTGCGAAG-TCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGTCCAGCAAAATACAAG---GAA
dp4 chr2:16736618-16736739 - T-A-------TCTTG------------TGCATTTTGG-----------------------------------------------CGGTTTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCG-GTGGTCCAACAGTG---------AAA
droPer1 super_0:3659179-3659300 + T-A-------TCTTG------------TGCATTTTGG-----------------------------------------------CGGTTTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCG-GTGGTCCAACAGTG---------AAA
droWil1 scaffold_181130:6363211-6363342 - GAT-------GGATCAATACTTACTTGAAC------------------------------------------------GAAG--CGTATTGCTTTACTAAGTACTAGTGCCGCAGGAGTTTGGTTCGTGTCCGTAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGACGACTTTACCTACTTAA---------AAA
droVir3 scaffold_12855:2861518-2861626 + T----------------------------------------------------------------------------------------TGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATTAAAGCGACTAGTTTTCCACCAGCA-ACAATTAGAAA
droMoj3 scaffold_6540:10349255-10349360 - T----------------------------------------------------------------------------------------TGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGGTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATCAAAGCGACGAGTTTTTCAACAGCA-GCAAT---TAA
droGri2 scaffold_14906:3807816-3807948 - TTG-------TGGCA----CTTACTTGAGC----------------------------------------------TTGATG--CGTATTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATTAAGGCGACGAATTTTCCAACAATGTGC------GAG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:9289926-9290048 - GTG-------TGCCG------------CCTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droSim1 chr3R_random:533427-533549 - GTG-------TGCCG------------TCTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droSec1 super_0:12715202-12715324 + GTG-------TGCCG------------TCTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droYak2 chr3R:13598006-13598135 - GTGCTAGATGTACGA------------TGTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droEre2 scaffold_4770:12350666-12350788 + GTG-------CTAGA------------TGTACTTACC-----------------------------------------------AAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAA---------GAA
droAna3 scaffold_13340:1848657-1848824 - GAG--------------------------TACTTAGCCCCAACCATTGGTAAATATTGATTTTATACTTACATTACTTCCTGCGAAG-TCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGTCCAGCAAAATACAAG---GAA
dp4 chr2:16736618-16736739 - T-A-------TCTTG------------TGCATTTTGG-----------------------------------------------CGGTTTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCG-GTGGTCCAACAGTG---------AAA
droPer1 super_0:3659179-3659300 + T-A-------TCTTG------------TGCATTTTGG-----------------------------------------------CGGTTTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCG-GTGGTCCAACAGTG---------AAA
droWil1 scaffold_181130:6363211-6363342 - GAT-------GGATCAATACTTACTTGAAC------------------------------------------------GAAG--CGTATTGCTTTACTAAGTACTAGTGCCGCAGGAGTTTGGTTCGTGTCCGTAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGACGACTTTACCTACTTAA---------AAA
droVir3 scaffold_12855:2861518-2861626 + T----------------------------------------------------------------------------------------TGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATTAAAGCGACTAGTTTTCCACCAGCA-ACAATTAGAAA
droMoj3 scaffold_6540:10349255-10349360 - T----------------------------------------------------------------------------------------TGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGGTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATCAAAGCGACGAGTTTTTCAACAGCA-GCAAT---TAA
droGri2 scaffold_14906:3807816-3807948 - TTG-------TGGCA----CTTACTTGAGC----------------------------------------------TTGATG--CGTATTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTTGTGTCCGCAATGCCTCCTGCTGCCCAAGTGCTTATTAAGGCGACGAATTTTCCAACAATGTGC------GAG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GTGTGCCGTCTACTTACCAAGTTCGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCGAGTTGCCCAGCAAAAGAASizeHit CountTotal NormTotalGSM343915
Embryo
..............................CTAAGTACTAGTGCCGCAGGAG.......................................................................2214129.0041294129
..............................CTAAGTACTAGTGCCGCAGGAGT......................................................................231324.00324324
..............................CTAAGTACTAGTGCCGCAGGA........................................................................211320.00320320
..............................CTAAGTACTAGTGCCGCAGGAGTT.....................................................................24161.006161
...............................TAAGTACTAGTGCCGCAGGAG.......................................................................21160.006060
...............................TAAGTACTAGTGCCGCAGGAGT......................................................................22153.005353
...........................................................................CCTGCTGCCCAAGTGCTTATTA..........................22116.001616
..............................CTAAGTACTAGTGCCGCAGG.........................................................................20115.001515
...............................TAAGTACTAGTGCCGCAGGAGTT.....................................................................2319.0099
............................................................................CTGCTGCCCAAGTGCTTATTA..........................2117.0077
..........................................................................TCCTGCTGCCCAAGTGCTTATTA..........................2314.0044
..........................................................................TCCTGCTGCCCAAGTGCTTATT...........................2213.0033
.........................................................................CTCCTGCTGCCCAAGTGCTTATT...........................2312.0022
....................................................TTAGGTTCGTGTCCGCAATACCT................................................2312.0022
................................AAGTACTAGTGCCGCAGGAGT......................................................................2111.0011
................................AAGTACTAGTGCCGCAGGA........................................................................1911.0011
..........................................................................TCCTGCTGCCCAAGTGCTTATTAA.........................2411.0011
...............................TAAGTACTAGTGCCGCAGGA........................................................................2011.0011
....................................................TTAGGTTCGTGTCCGCAATACC.................................................2211.0011
..............................CTAAGTACTAGTGCCGCAGGAGTTA....................................................................2511.0011
dp4
-TATCTTGTGCATTTTGGCGGTTTGCTTTCCTAAGTACTAGTGCCGCAGGAGTTAGGTTCGTGTCCGCAATACCTCCTGCTGCCCAAGTGCTTATTAAAGCGGCG-GTGGTCCAACAGTGAAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..............................CTAAGTACTAGTGCCGCAGGAG.......................................................................22156918.0056918678050138
..............................CTAAGTACTAGTGCCGCAGGA........................................................................2117724.0077247896935
..............................CTAAGTACTAGTGCCGCAGGAGT......................................................................2311548.0015484371111
..............................CTAAGTACTAGTGCCGCAGG.........................................................................2011383.001383341349
...............................TAAGTACTAGTGCCGCAGGAG.......................................................................2111165.001165951070
...............................TAAGTACTAGTGCCGCAGGAGT......................................................................221247.0024774173
..............................CTAAGTACTAGTGCCGCAGGAGTT.....................................................................241147.001478166
...............................TAAGTACTAGTGCCGCAGGA........................................................................20186.0086779
..............................CTAAGTACTAGTGCCGCAG..........................................................................19135.0035035
...............................TAAGTACTAGTGCCGCAGGAGTT.....................................................................23133.00331914
..........................................................................TCCTGCTGCCCAAGTGCTTATT...........................22132.0032626
..............................CTAAGTACTAGTGCCGCA...........................................................................18118.0018018
...............................TAAGTACTAGTGCCGCAGG.........................................................................19116.0016214
...........................................................................CCTGCTGCCCAAGTGCTTATTA..........................22116.001679
................................AAGTACTAGTGCCGCAGGAG.......................................................................20115.0015114
....................................................TTAGGTTCGTGTCCGCAATACCT................................................23113.0013112
.............................CCTAAGTACTAGTGCCGCAGGAG.......................................................................23112.0012210
..........................................................................TCCTGCTGCCCAAGTGCTTAT............................2119.00909
..........................................................................TCCTGCTGCCCAAGTGCTTA.............................2018.00808
...........................................................................CCTGCTGCCCAAGTGCTTATT...........................2118.00808
..........................................................................TCCTGCTGCCCAAGTGCTT..............................1916.00606
............................................................................CTGCTGCCCAAGTGCTTATTA..........................2115.00550
............................................................................CTGCTGCCCAAGTGCTTATT...........................2015.00523
................................AAGTACTAGTGCCGCAGGAGT......................................................................2114.00404

Secondary Structure

dm3

dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

droSim1

dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

droSec1

dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

droYak2

dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

droEre2

dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

droAna3

dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

dp4

dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

droPer1

dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901

droWil1

dG=-27.4,  p-value=0.009901 dG=-27.3,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-26.5,  p-value=0.009901

droVir3

dG=-26.7,  p-value=0.009901 dG=-26.4,  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

droMoj3

dG=-27.8,  p-value=0.009901

droGri2

dG=-26.4,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-25.7,  p-value=0.009901

Generated: 03/07/2013 at 04:59 PM