Secondary structure and small RNA-seq evidence for dme-mir-289

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:13613907-13614035 + TAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTT----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSim1 chr3L:12997848-12997976 + TAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTC----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSec1 super_0:5775586-5775714 + TAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTC----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droYak2 chr3L:13706954-13707082 + TAC------------------------GGTTCTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTC----------------------------------------CAGTCCCTCTGACTGACTGGGGTAAGTCTCTCGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEre2 scaffold_4784:13614855-13614983 + AAC------------------------GGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGA---------CTC----------------------------------------CAGTCCCTCTGACGGACTGGGGTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droAna3 scaffold_13337:21827571-21827739 - TTC-CGGCACTCCGGCATTCCAGCTC-GGGTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGACTCTG----CTACTGCC---ACTGCCACTGCCACTGCCACTGCCGCTC------------------------GGGGAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
dp4 chrXR_group8:6818889-6819024 - TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGG---GACTC----------------------------------------CAG-----CTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droPer1 super_36:488140-488275 + TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGG---GACTC----------------------------------------CAG-----CTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droWil1 scaffold_180698:607141-607313 - TTT------------------------TTTTTTTAGGTTGAAGTTTACAGTAAAATAAATATTTAAGTGGAGTC---GACTGTGTCGACTACAGCCCGGACTACC---CGGACTGCTAGAACGACTCGGTTCCGACTCTTTTTCTGTCGGGGTAAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droVir3 scaffold_13049:19817984-19818083 - ---------------------------GTTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG---------------------------------------------------------------------------GCCT-GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droMoj3 scaffold_6680:7513468-7513568 - G--------------------------GCTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGGGCCC----------------------------------------------------------------------------GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droGri2 scaffold_15110:17555344-17555443 + ---------------------------AGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG---------------------------------------------------------------------------GCCT-GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:13613907-13614035 + TACGGTTTTTAGGTTGAGTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGACTTCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TA------CGGTTTTTAGGTTGAGTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC------TCCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TATCCGTCGGGTTTTTAGGTTGAGTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGGACTCCAG-----CTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-27.6,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-27.3,  p-value=0.009901

droSim1

dG=-28.7,  p-value=0.009901 dG=-28.6,  p-value=0.009901 dG=-28.6,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droSec1

dG=-28.7,  p-value=0.009901 dG=-28.6,  p-value=0.009901 dG=-28.6,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droYak2

dG=-26.6,  p-value=0.009901 dG=-26.4,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-22.8,  p-value=0.009901

droEre2

dG=-32.6,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.5,  p-value=0.009901 dG=-32.5,  p-value=0.009901 dG=-32.3,  p-value=0.009901

droAna3

dG=-45.0,  p-value=0.009901 dG=-44.9,  p-value=0.009901 dG=-44.3,  p-value=0.009901 dG=-44.2,  p-value=0.009901 dG=-44.1,  p-value=0.009901

dp4

dG=-30.4,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-29.9,  p-value=0.009901

droPer1

dG=-30.4,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-29.9,  p-value=0.009901

droWil1

dG=-43.7,  p-value=0.009901 dG=-43.7,  p-value=0.009901 dG=-43.7,  p-value=0.009901 dG=-43.6,  p-value=0.009901 dG=-43.6,  p-value=0.009901 dG=-42.4,  p-value=0.009901

droVir3

dG=-17.2,  p-value=0.009901 dG=-16.9,  p-value=0.009901 dG=-16.8,  p-value=0.009901 dG=-16.5,  p-value=0.009901 dG=-16.5,  p-value=0.009901

droMoj3

dG=-22.9,  p-value=0.009901 dG=-22.8,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-22.4,  p-value=0.009901

droGri2

dG=-16.0,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-15.8,  p-value=0.009901 dG=-15.7,  p-value=0.009901

Generated: 03/07/2013 at 06:04 PM