Secondary structure and small RNA-seq evidence for dme-mir-3644

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:11018004-11018094 - TTATTGCTGCAGGAGGTGAGTGATTAT----G-GTTTA----AGT-------AATACGAATTACATAAACTATATTTA-------ACCACTATTCTTAGATACAAAACACTGCT
droSim1 chr3R:10448012-10448102 + TTACTGCTGCAGGAGGTGAGTGTTTAT----G-GTTTA----AAT-------TATACGATTTACATAAACTATATTTA-------ACCACTACTCTTAGATCCAAAACACCGCT
droSec1 super_0:10933739-10933828 + TTACTGCTGCAGGAGGTGAGGTTTTAT----G-GT-TA----AGT-------TATACGATTTGCATAAACTATATTTA-------ACCACTACTCTTAGATCCAAAACACCGCT
droYak2 chr3R:15416636-15416724 + TTACTGCTTCAGGAGGTAAGTTTTT------G-GTTCA----GGT-------TTCATGAATTACATAAACTATATTTA-------ACCACATTCCTTAGATCCAAAATACCGCT
droEre2 scaffold_4770:10539530-10539618 - TTACTGCTTCAGGAGGTCAGTTTTT------G-GTTCG----ATT-------TCAACGATTTACATAAACTGTATTTA-------ACCATATTTCGTAGATCCAAAACACCGCT
droAna3 scaffold_13340:6107797-6107878 - TTGTTGCTGCAGGAGGTGGGTAGTG---------------AA---C------TTTTCAAATTACTATACC--------TTCATGAATGTTCTTTTGTAGATTCAAAATACTGCG
dp4 chr2:21002920-21003004 - CTGTTGCTGCAGGAGGTAGGCTACA------GAG------AA---C----ATTTAG---------TAAATAATAGTCGCTCATTC-TTTTCCCTAATAGATCCAAAACACTGCC
droPer1 super_3:3754054-3754138 - CTGTTGCTGCAGGAGGTAGGCTACA------GAG------AA---C----TTTAAG---------TAAATAATAGTCGCTCATTC-TCTTCCCTAATAGATCCAAAACACTGCC
droWil1 scaffold_181130:7245340-7245433 + TTGCTATTGCAAGAGGTCAGTTAGAAT----A-GCAAA----AGACACTCTTGGGATGGTTAATAATA----------TTCATAT-TTGGTTTTTGCAGATTCAAAATACTGCC
droVir3 scaffold_13047:7744104-7744193 - CTGCTGCTTCAAGAGGTGAGCAACTGCTTTTG-GCTTA----TGT----------TCGATTTTCAATGAT--------CTCTCG-AATACTTTTTATAGATACAAAACACAGCG
droMoj3 scaffold_6540:3682572-3682661 - TTGCTGCTGCAAGAGGTAAAATGTT------GAGCTCATAAAAGT----------TTCCTTT---TCAATTACA----TTCACAT-TCATTCGTTTTAGATACAAAATACGGCC
droGri2 scaffold_14830:3558248-3558343 - CTGCTGCTGCAGGAGGTGAGTTGCACCAACTG-ACACA----G-----TGTTTCCATAATTTACATTTTCTCTTTAT--------ATCTTTGTTCTCAGATACAAAACACGGCT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:11018004-11018094 - TTATTGCTGCAGGAGGTGAGTGATTATGGTTTAAGTAATACGAATTACATAAACTATATTTAACCACTATTCTTAGATACAAAACACTGCT
droSim1 chr3R:10448012-10448102 + TTACTGCTGCAGGAGGTGAGTGTTTATGGTTTAAATTATACGATTTACATAAACTATATTTAACCACTACTCTTAGATCCAAAACACCGCT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTACTGCTGCAGGAGGTGAGTGTTTATGGTTTAAATTATACGATTTACA------------TAAACTATATTTAACCACTACTCT------TAGATCCAAAACACCGCTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CTGTTGCTGCAGGAGGTAGGC------------------------TACAGAGAACATTTAGTAAATAATAGTCGCTCATTCTTTTCCCTAATAGATCCAAAACACTGCCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-14.7,  p-value=0.009901 dG=-14.1,  p-value=0.009901 dG=-13.9,  p-value=0.009901

droSim1

dG=-8.3,  p-value=0.009901 dG=-8.3,  p-value=0.009901 dG=-8.2,  p-value=0.009901 dG=-7.9,  p-value=0.009901 dG=-7.4,  p-value=0.009901

droSec1

dG=-6.6,  p-value=0.009901 dG=-6.4,  p-value=0.009901 dG=-6.3,  p-value=0.009901 dG=-6.2,  p-value=0.009901 dG=-6.2,  p-value=0.009901

droYak2

dG=-6.2,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.3,  p-value=0.009901 dG=-5.3,  p-value=0.009901

droEre2

dG=-7.6,  p-value=0.009901 dG=-7.0,  p-value=0.009901

droAna3

dG=-4.8,  p-value=0.009901 dG=-4.3,  p-value=0.009901 dG=-4.0,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.8,  p-value=0.009901

dp4

dG=-2.6,  p-value=0.009901 dG=-2.0,  p-value=0.009901

droPer1

dG=-3.2,  p-value=0.009901 dG=-3.1,  p-value=0.009901 dG=-3.0,  p-value=0.009901 dG=-2.9,  p-value=0.009901 dG=-2.8,  p-value=0.009901

droWil1

dG=-4.9,  p-value=0.009901 dG=-4.1,  p-value=0.009901 dG=-4.1,  p-value=0.009901 dG=-4.1,  p-value=0.009901 dG=-4.0,  p-value=0.009901

droVir3

dG=-7.4,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-7.2,  p-value=0.009901 dG=-7.1,  p-value=0.009901 dG=-7.1,  p-value=0.009901 dG=-6.5,  p-value=0.009901

droMoj3

dG=-2.3,  p-value=0.009901 dG=-2.3,  p-value=0.009901 dG=-1.9,  p-value=0.009901 dG=-1.6,  p-value=0.009901 dG=-1.6,  p-value=0.009901

droGri2

dG=-6.7,  p-value=0.009901 dG=-6.4,  p-value=0.009901 dG=-6.2,  p-value=0.009901 dG=-5.9,  p-value=0.009901

Generated: 03/07/2013 at 05:23 PM