Secondary structure and small RNA-seq evidence for dme-mir-8

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:12718922-12719038 + A-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAC-CAC---
droSim1 chr2R:11454608-11454724 + A-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAC-CAC---
droSec1 super_1:10223793-10223909 + A-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTAAAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAC-CAC---
droYak2 chr2R:16257218-16257334 - A-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAG-CAC---
droEre2 scaffold_4845:13131118-13131232 - G-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAC-C-----
droAna3 scaffold_13266:13876642-13876748 - A-----------------------------------------TCT-----------------------------TGCTTA---------TTTGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TTCTGATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACC---------------
dp4 Unknown_singleton_1898:47537-47693 - AAATAACAAAAGAGGGAAACACAGTGCGGTGACGAAAACACGTTT-----------------------------TGCT-A---------TTCGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-AGATACCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAAT-CC---
droPer1 super_4:6545710-6545866 + AAATAACAAAAGAGGGAAACACAGTGCGGTGACGAAAACACGTTT-----------------------------TGCT-A---------TTCGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-AGATACCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAAT-CC---
droWil1 scaffold_180700:6381462-6381593 + C-----------------------------------------GCT-----------------------------TGCAAAAAGATTCTTCTTGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTTT-GTACTAT-AGATATCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAATCAT---
droVir3 scaffold_12875:10672387-10672513 - A-----------------------------------------TCT----------------GTTTGCTTGCAATTACTTA---------TTTGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTCTTGA--TTT-AAATAATTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATACATCA-----------
droMoj3 scaffold_6496:16285321-16285444 + C-----------------------------------------AAT-----------------------------TGCCTA---------TTTGCTAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTCCTGT--TTT-AAATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTTTCCATCATAAAT-GCAAT
droGri2 scaffold_15245:3783124-3783258 - A-----------------------------------------TTTTTATGTGAAATAATCAATT----------TGCT-------------TGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTCTTGA--TTT-AAATAATTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAAT--C---

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:12718922-12719038 + A-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAC-CAC---
droSim1 chr2R:11454608-11454724 + A-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAC-CAC---
droSec1 super_1:10223793-10223909 + A-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTAAAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAC-CAC---
droYak2 chr2R:16257218-16257334 - A-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAG-CAC---
droEre2 scaffold_4845:13131118-13131232 - G-----------------------------------------TCT-----------------------------TGCTAA---------TTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-TTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTAC-C-----
droAna3 scaffold_13266:13876642-13876748 - A-----------------------------------------TCT-----------------------------TGCTTA---------TTTGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TTCTGATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACC---------------
dp4 Unknown_singleton_1898:47537-47693 - AAATAACAAAAGAGGGAAACACAGTGCGGTGACGAAAACACGTTT-----------------------------TGCT-A---------TTCGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-AGATACCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAAT-CC---
droPer1 super_4:6545710-6545866 + AAATAACAAAAGAGGGAAACACAGTGCGGTGACGAAAACACGTTT-----------------------------TGCT-A---------TTCGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCT------TT-AGATACCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAAT-CC---
droWil1 scaffold_180700:6381462-6381593 + C-----------------------------------------GCT-----------------------------TGCAAAAAGATTCTTCTTGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTTT-GTACTAT-AGATATCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAATCAT---
droVir3 scaffold_12875:10672387-10672513 - A-----------------------------------------TCT----------------GTTTGCTTGCAATTACTTA---------TTTGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTCTTGA--TTT-AAATAATTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATACATCA-----------
droMoj3 scaffold_6496:16285321-16285444 + C-----------------------------------------AAT-----------------------------TGCCTA---------TTTGCTAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTCCTGT--TTT-AAATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTTTCCATCATAAAT-GCAAT
droGri2 scaffold_15245:3783124-3783258 - A-----------------------------------------TTTTTATGTGAAATAATCAATT----------TGCT-------------TGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATTCTTGA--TTT-AAATAATTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAAT--C---

Small RNA-sequencing read pileup

Species Read pileup
droSim1
A-----------------------------------------TCTTGCTAATTAGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCTTTTTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTAACCTTCAGTACCACSizeHit CountTotal NormTotalGSM343915
Embryo
............................................................................................................TAATACTGTCAGGTAAAGATGTC...........................231175043.00175043175043
.......................................................................CATCTTACCGGGCAGCATTAGA.................................................................2216159.0061596159
............................................................................................................TAATACTGTCAGGTAAAGATGT............................2215347.0053475347
............................................................................................................TAATACTGTCAGGTAAAGATG.............................2111426.0014261426
.......................................................................CATCTTACCGGGCAGCATTAG..................................................................211886.00886886
.............................................................................................................AATACTGTCAGGTAAAGATGTC...........................221190.00190190
...........................................................................................................CTAATACTGTCAGGTAAAGATGTC...........................241128.00128128
..............................................................................................................ATACTGTCAGGTAAAGATGTC...........................21182.008282
........................................................................ATCTTACCGGGCAGCATTAGA.................................................................21156.005656
................................................................................................................ACTGTCAGGTAAAGATGTC...........................19144.004444
.................................................................................................................CTGTCAGGTAAAGATGTC...........................18134.003434
............................................................................................................TAATACTGTCAGGTAAAGATGTCG..........................24126.002626
............................................................................................................TAATACTGTCAGGTAAAGA...............................19122.002222
...............................................................................................................TACTGTCAGGTAAAGATGTC...........................20117.001717
........................................................................ATCTTACCGGGCAGCATTAG..................................................................2019.0099
...........................................................................TTACCGGGCAGCATTAGA.................................................................1818.0088
dp4
AAATAACAAAAGAGGGAAACACAGTGCGGTGACGAAAACACGTTTTGCTA-TTCGCAAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCTTTAGATACCTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTTATCCATCATAAATCCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
............................................................................................................TAATACTGTCAGGTAAAGATGTC...........................231447032.00447032198408248624
............................................................................................................TAATACTGTCAGGTAAAGATGT............................22169948.0069948844861500
............................................................................................................TAATACTGTCAGGTAAAGATG.............................21147189.0047189584441345
.......................................................................CATCTTACCGGGCAGCATTAGA.................................................................22111663.001166356146049
.............................................................................................................AATACTGTCAGGTAAAGATGTC...........................2211371.0013712451126
.......................................................................CATCTTACCGGGCAGCATTAG..................................................................2111277.001277625652
............................................................................................................TAATACTGTCAGGTAAAGAT..............................2011100.001100631037
............................................................................................................TAATACTGTCAGGTAAAGA...............................191432.0043251381
...........................................................................................................CTAATACTGTCAGGTAAAGATGTC...........................241274.00274136138
..............................................................................................................ATACTGTCAGGTAAAGATGTC...........................211247.0024779168
.............................................................................................................AATACTGTCAGGTAAAGATGT............................211166.0016616150
...............................................................................................................TACTGTCAGGTAAAGATGTC...........................201143.0014322121
........................................................................ATCTTACCGGGCAGCATTAGA.................................................................211118.001184573
.......................................................................CATCTTACCGGGCAGCATTA...................................................................201117.0011715102
............................................................................................................TAATACTGTCAGGTAAAGATGTCG..........................241116.001164670
................................................................................................................ACTGTCAGGTAAAGATGTC...........................19196.00963462
.......................................................................CATCTTACCGGGCAGCATT....................................................................19174.00741163
.................................................................................................................CTGTCAGGTAAAGATGTC...........................18168.00683236
...........................................................................................................CTAATACTGTCAGGTAAAGATGT............................23152.0052547
.............................................................................................................AATACTGTCAGGTAAAGATG.............................20146.0046442
..............................................................................................................ATACTGTCAGGTAAAGATGT............................20141.0041239

Secondary Structure

dm3

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901

droSim1

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901

droSec1

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901

droYak2

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901

droEre2

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901

droAna3

dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901

dp4

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901

droPer1

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901

droWil1

dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901

droVir3

dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901

droMoj3

dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901

droGri2

dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901

Generated: 03/07/2013 at 07:02 PM