Secondary structure and small RNA-seq evidence for dme-mir-1011

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:16679012-16679095 - ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droSim1 chr3R:4780974-4781057 + ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droSec1 super_27:54817-54900 + ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droYak2 chr3R:5477803-5477886 - ATTCTGACCGTGCATGTGAGTTTTTGAGCCAGGAATAT--------AATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droEre2 scaffold_4770:4975828-4975911 + ATTCTGACCGTCCACGTGAGTTTTTGAGCCATGAATAT--------AATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droAna3 scaffold_13340:7952070-7952154 - GTGGTGACGGTGCATGTGAGTCTTTGAACCAGGAATAT--------AATTT----G-------TATATATTGGTTCAAATCGCTCGTAGAATCCTCCCTGGCAA
dp4 chr2:12756663-12756757 + ATTGTGACGATGCATGTGAGATTTTGAATCTAATATAT--------AATATAATCCGTACGTGTAT-ATATGGTTCAAATTACTCGTAGAACCCTCCCTGGCAA
droPer1 super_0:7702112-7702205 - ATTGTGACGATGCATGTGAGATTTTGAATCTAATATAT--------AATATAATCT-TACATGTAT-ATATGGTTCAAATAACTCGTAGAATCCTCCCTGGCAA
droWil1 scaffold_181108:2184466-2184552 + ATTCTGACCGTACATGTGAGTCTTTGAATCAGGAATAT--------ATTATCA--T-------TATATATTGGTTCGAAATGCTCGTAGAATCCACCTTGGCAA
droVir3 scaffold_13047:12031331-12031423 + ATTGTCACGGTGCATGTGAGTCATTGAACCAGGAATATATGTATGTAATTC----T-------TATATATTGGTTCAAATTTCTCGCAGAATCCGCCCTGGCAA
droMoj3 scaffold_6540:29750589-29750676 - ATTGTGACAGTGCATGTGAGTCTTTGAGCCAGGAATAT--------ATGTTCATCT-------TAT-TATTGGTTCAAATCTCTCGTAGAATCCTCCCTGGCAA
droGri2 scaffold_14830:1201859-1201943 + ATTGTCACTGAGCATGTGAGTCTTTGAGCCAGGAATAT--------AATTG----T-------TATATATTGGTTCAAACAACTCGTAGAATCCGCCCTGGCAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:16679012-16679095 - ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droSim1 chr3R:4780974-4781057 + ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droSec1 super_27:54817-54900 + ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATAT--------AGTTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droYak2 chr3R:5477803-5477886 - ATTCTGACCGTGCATGTGAGTTTTTGAGCCAGGAATAT--------AATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droEre2 scaffold_4770:4975828-4975911 + ATTCTGACCGTCCACGTGAGTTTTTGAGCCATGAATAT--------AATTC----T-------TAT-TATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAA
droAna3 scaffold_13340:7952070-7952154 - GTGGTGACGGTGCATGTGAGTCTTTGAACCAGGAATAT--------AATTT----G-------TATATATTGGTTCAAATCGCTCGTAGAATCCTCCCTGGCAA
dp4 chr2:12756663-12756757 + ATTGTGACGATGCATGTGAGATTTTGAATCTAATATAT--------AATATAATCCGTACGTGTAT-ATATGGTTCAAATTACTCGTAGAACCCTCCCTGGCAA
droPer1 super_0:7702112-7702205 - ATTGTGACGATGCATGTGAGATTTTGAATCTAATATAT--------AATATAATCT-TACATGTAT-ATATGGTTCAAATAACTCGTAGAATCCTCCCTGGCAA
droWil1 scaffold_181108:2184466-2184552 + ATTCTGACCGTACATGTGAGTCTTTGAATCAGGAATAT--------ATTATCA--T-------TATATATTGGTTCGAAATGCTCGTAGAATCCACCTTGGCAA
droVir3 scaffold_13047:12031331-12031423 + ATTGTCACGGTGCATGTGAGTCATTGAACCAGGAATATATGTATGTAATTC----T-------TATATATTGGTTCAAATTTCTCGCAGAATCCGCCCTGGCAA
droMoj3 scaffold_6540:29750589-29750676 - ATTGTGACAGTGCATGTGAGTCTTTGAGCCAGGAATAT--------ATGTTCATCT-------TAT-TATTGGTTCAAATCTCTCGTAGAATCCTCCCTGGCAA
droGri2 scaffold_14830:1201859-1201943 + ATTGTCACTGAGCATGTGAGTCTTTGAGCCAGGAATAT--------AATTG----T-------TATATATTGGTTCAAACAACTCGTAGAATCCGCCCTGGCAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATTCTGACCGTGCACGTGAGTTTTTGAGCCAGGAATATAGTTCT-----------TATTATTGGTTCAAATCGCTCGCAGAATCCACCCTGGCAASizeHit CountTotal NormTotalGSM343915
Embryo
.........................................................TTATTGGTTCAAATCGCTCGCAG...............2313.0033
.........................................................TTATTGGTTCAAATCGCTCGCA................2211.0011
..........................................................TATTGGTTCAAATCGCTCGCAG...............2211.0011
dp4
ATTGTGACGATGCATGTGAGATTTTGAATCTAATATATAATATAATCCGTACGTGTATATATGGTTCAAATTACTCGTAGAACCCTCCCTGGCAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-21.0,  p-value=0.009901 dG=-20.6,  p-value=0.009901 dG=-20.2,  p-value=0.009901

droSim1

dG=-21.0,  p-value=0.009901 dG=-20.6,  p-value=0.009901 dG=-20.2,  p-value=0.009901

droSec1

dG=-21.0,  p-value=0.009901 dG=-20.6,  p-value=0.009901 dG=-20.2,  p-value=0.009901

droYak2

dG=-21.0,  p-value=0.009901 dG=-20.6,  p-value=0.009901 dG=-20.2,  p-value=0.009901

droEre2

dG=-21.6,  p-value=0.009901

droAna3

dG=-17.2,  p-value=0.009901 dG=-16.6,  p-value=0.009901 dG=-16.4,  p-value=0.009901

dp4

dG=-12.3,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-11.7,  p-value=0.009901 dG=-11.5,  p-value=0.009901

droPer1

dG=-12.2,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-11.7,  p-value=0.009901 dG=-11.7,  p-value=0.009901 dG=-11.6,  p-value=0.009901

droWil1

dG=-14.9,  p-value=0.009901 dG=-14.3,  p-value=0.009901

droVir3

dG=-17.8,  p-value=0.009901 dG=-17.7,  p-value=0.009901 dG=-17.6,  p-value=0.009901 dG=-17.3,  p-value=0.009901 dG=-17.2,  p-value=0.009901

droMoj3

dG=-14.6,  p-value=0.009901 dG=-14.4,  p-value=0.009901 dG=-14.2,  p-value=0.009901 dG=-14.0,  p-value=0.009901 dG=-14.0,  p-value=0.009901

droGri2

dG=-17.3,  p-value=0.009901 dG=-17.1,  p-value=0.009901 dG=-16.7,  p-value=0.009901 dG=-16.5,  p-value=0.009901

Generated: 03/07/2013 at 04:47 PM