Secondary structure and small RNA-seq evidence for dme-mir-987

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:5200513-5200636 - GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAGGAAAA
droSim1 chr2R:3860388-3860511 - GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAGGAAAA
droSec1 super_1:2832514-2832637 - GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAGGAAAA
droYak2 chr2L:17856053-17856176 - GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACGAAATGCAACAGGAAAG
droEre2 scaffold_4929:17456334-17456457 + GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACGAAATGCAACAGGAAAA
droAna3 scaffold_12430:12714-12838 + ACG-GAAAA-ATGT--AC------------AATGTTGGACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGTATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTCGAACGAAATTCAACAGGATAA
dp4 chr3:9267901-9268036 - ATG-CAAC--ACGA--ACACACACAGAAATAATGTTGGACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TATATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGATATGCAACTGGATAA
droPer1 super_4:4590324-4590459 - ATG-CAAC--ACGA--ACACACACAGAAATAATGTTGGACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TATATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGATATGCAACTGGATAA
droWil1 scaffold_180697:853193-853321 + GAGAGAAGGAGAGATCAT------------AATGTTGAACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TATATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAAAAATG
droVir3 scaffold_12875:1241652-1241774 - GCG-TC----GCTC--AC------A-----AATGTTGAACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TTTATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGAAATGCAACAGAAGAA
droMoj3 scaffold_6496:4307034-4307162 - ACG-GATATCGCGAATAA------------ACTGTTGAACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGTTTATATCTAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGAAATGCAACAGAAGCA
droGri2 scaffold_15245:9744744-9744853 + C-------------------------------TGTTGAACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TTTATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGAAATGCAACAAAAGA-

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:5200513-5200636 - GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAGGAAAA
droSim1 chr2R:3860388-3860511 - GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAGGAAAA
droSec1 super_1:2832514-2832637 - GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAGGAAAA
droYak2 chr2L:17856053-17856176 - GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACGAAATGCAACAGGAAAG
droEre2 scaffold_4929:17456334-17456457 + GCG-GAAG--ACGA--AC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACGAAATGCAACAGGAAAA
droAna3 scaffold_12430:12714-12838 + ACG-GAAAA-ATGT--AC------------AATGTTGGACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TGTATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTCGAACGAAATTCAACAGGATAA
dp4 chr3:9267901-9268036 - ATG-CAAC--ACGA--ACACACACAGAAATAATGTTGGACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TATATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGATATGCAACTGGATAA
droPer1 super_4:4590324-4590459 - ATG-CAAC--ACGA--ACACACACAGAAATAATGTTGGACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TATATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGATATGCAACTGGATAA
droWil1 scaffold_180697:853193-853321 + GAGAGAAGGAGAGATCAT------------AATGTTGAACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TATATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAAAAATG
droVir3 scaffold_12875:1241652-1241774 - GCG-TC----GCTC--AC------A-----AATGTTGAACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TTTATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGAAATGCAACAGAAGAA
droMoj3 scaffold_6496:4307034-4307162 - ACG-GATATCGCGAATAA------------ACTGTTGAACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGTTTATATCTAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGAAATGCAACAGAAGCA
droGri2 scaffold_15245:9744744-9744853 + C-------------------------------TGTTGAACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGT-TTTATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGAAATGCAACAAAAGA-

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GCGGAAGACGAAC------------AATGTTGGACTGTGTTTAAAGTAAATAGTCTGGATTGATGAAAGTTGCATTCGAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTGAACAAAATGCAACAGGAAAASizeHit CountTotal NormTotalGSM343915
Embryo
.........................................TAAAGTAAATAGTCTGGATTGATGA......................................................................251350.00350350
.........................................TAAAGTAAATAGTCTGGATTGATG.......................................................................241258.00258258
..........................................AAAGTAAATAGTCTGGATTGATGA......................................................................24129.002929
..........................................AAAGTAAATAGTCTGGATTGATGAA.....................................................................25126.002626
..........................................AAAGTAAATAGTCTGGATTGATG.......................................................................23119.001919
.........................................TAAAGTAAATAGTCTGGATTGATGAA.....................................................................26118.001818
.........................................TAAAGTAAATAGTCTGGATTGAT........................................................................23110.001010
.........................................TAAAGTAAATAGTCTGGATTGA.........................................................................2215.0055
............................................AGTAAATAGTCTGGATTGATG.......................................................................2112.0022
..........................................AAAGTAAATAGTCTGGATTGATGAAA....................................................................2612.0022
..................................................................AAGTTGCATTCGAGAATTC...................................................1912.0022
....................................................................................CATCAACAGGCATTTACTTCAA..............................2211.0011
..........................................AAAGTAAATAGTCTGGATTGAT........................................................................2211.0011
............................................AGTAAATAGTCTGGATTGATGAA.....................................................................2311.0011
...........................................AAGTAAATAGTCTGGATTGATGA......................................................................2311.0011
dp4
ATGCAACACGAACACACACAGAAATAATGTTGGACTGTGCTTAAAGTAAATAGTCTGGATTGATGAAAGTTATATTCAAGAATTCATCAACAGGCATTTACTTCAACTGCAGTTTAAACGATATGCAACTGGATAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.........................................TAAAGTAAATAGTCTGGATTGAT........................................................................2314166.00416674159
.........................................TAAAGTAAATAGTCTGGATTGATG.......................................................................2413849.0038492833566
.........................................TAAAGTAAATAGTCTGGATTGA.........................................................................2212089.00208922087
.........................................TAAAGTAAATAGTCTGGATTGATGA......................................................................2511482.0014823671115
.........................................TAAAGTAAATAGTCTGGATTG..........................................................................211731.007311730
..........................................AAAGTAAATAGTCTGGATTGAT........................................................................221631.006310631
..........................................AAAGTAAATAGTCTGGATTGATG.......................................................................231567.0056718549
..........................................AAAGTAAATAGTCTGGATTGA.........................................................................211232.002321231
..........................................AAAGTAAATAGTCTGGATTGATGA......................................................................241201.0020127174
..........................................AAAGTAAATAGTCTGGATTGATGAA.....................................................................25187.00872562
.........................................TAAAGTAAATAGTCTGGATTGATGAA.....................................................................26162.0062755
..........................................AAAGTAAATAGTCTGGATTG..........................................................................20158.0058058
.........................................TAAAGTAAATAGTCTGGATT...........................................................................20118.0018018
...........................................AAGTAAATAGTCTGGATTGATG.......................................................................2218.00817
.........................................TAAAGTAAATAGTCTGGATTGATGAAA....................................................................2716.00615
............................................AGTAAATAGTCTGGATTGATGA......................................................................2214.00422
...........................................AAGTAAATAGTCTGGATTGAT........................................................................2114.00404
....................................................................................CATCAACAGGCATTTACTTCA...............................2114.00422
............................................AGTAAATAGTCTGGATTGATG.......................................................................2114.00404
....................................................................................CATCAACAGGCATTTACTTCAA..............................2214.00413
............................................AGTAAATAGTCTGGATTGAT........................................................................2012.00202
..........................................AAAGTAAATAGTCTGGATT...........................................................................1912.00202
............................................AGTAAATAGTCTGGATTGATGAA.....................................................................2312.00211
.........................................TAAAGTAAATAGTCTGGAT............................................................................1912.00202
...........................................AAGTAAATAGTCTGGATTGA.........................................................................2012.00202
.....................................................................................ATCAACAGGCATTTACTTCAA..............................2112.00220
..........................................AAAGTAAATAGTCTGGATTGATGAAA....................................................................2612.00202

Secondary Structure

dm3

dG=-19.4,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.9,  p-value=0.009901

droSim1

dG=-19.4,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.9,  p-value=0.009901

droSec1

dG=-19.4,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.9,  p-value=0.009901

droYak2

dG=-19.4,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.9,  p-value=0.009901

droEre2

dG=-19.4,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.9,  p-value=0.009901

droAna3

dG=-21.7,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-20.8,  p-value=0.009901

dp4

dG=-19.7,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.8,  p-value=0.009901

droPer1

dG=-19.7,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.8,  p-value=0.009901

droWil1

dG=-19.7,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.8,  p-value=0.009901

droVir3

dG=-20.6,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-19.9,  p-value=0.009901

droMoj3

dG=-21.1,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.2,  p-value=0.009901

droGri2

dG=-20.6,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-19.9,  p-value=0.009901

Generated: 03/07/2013 at 07:21 PM