Secondary structure and small RNA-seq evidence for dme-mir-4968

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:11545623-11545808 - AAACTGCATTCAAGT-----------TTTTCC-T-----------------------CAGAGC-----C-GCGACT----GCTGG---CGTGTTA-TTG------------------TTGC----TGTTGCAGCTAGCTGCCACGGT-------TTGTTGCTTCACTGATTACGCGCAATGCAGCAACAGCAGCA---------------GCAGC------A------------------------------------------------------------------GAAGCAACAGCAACT-AACTGCAGAGGAGCAATAGCAGCT-GAGAGTTCAGTTGCGAAAC-CGGCG
droSim1 chr3L:10929570-10929746 - AAACTGCATTCAAGT-----------TTTTCC-T-----------------------CAGAGC-----C-GCGACT----GCTGG---CGTGTTA-TTG------------------TTGC----TGTTGCAGCTAGCTGCCACGGT-------TTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAG------------------------------------------------------------------------------------------------AAGCAACAGCAACT-AACTGCAGAGGAGCAATAGCAGCT-GAGAGTTCAGTTGCGAAAC-CGGCG
droSec1 super_0:3745423-3745605 - AAACTGCATTCGAGT-----------TTTTCC-T-----------------------CAGAGC-----C-GCGACT----GCTGG---CGTGTTA-TTG------------------TTGC----TGTTGCAGCTAGCTGCCACGGT-------TTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGCA---------------GCA---------------------------------------------------------------------------GAAGCAACAGCAACT-AACTGCAGAGGAGCAATAGCAGCT-GAGAGTTCAGTTGCGAAAC-CGGCG
droYak2 chr3L:11579958-11580167 - AAACTGCATTCAAGT-----------TTTTCC-T-----------------------CAGAGC-----C-GCGACT----GCTGG---CGTGTTA-TTG------------------TTGC----TGTTGCAGCTAGCTGCCACGGT-------TTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGAA---------------GCAGC---AGCAGCAGC----------------------------------AGTAGAAA------TAGCAGCA-----GTAGCAACAGCAACT-AACTGCAGAGGAGCAATAGCAGCT-GAGAGTTCAGTTGCGAAAC-CGGCG
droEre2 scaffold_4784:11545792-11545968 - A-ACTGCATTCAAGT-----------TTTTCC-T-----------------------CAGAGC-----C-GCGACT----GCTGG---CGTGTTA-TTG------------------TTGC----TGTTGCAGCTAGCTGCCACGGT-------TTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAG------------------------------------------------------------------------------------------------AAGCAACAGCAACTGAACTGCAGAGGAGCAATAGCAGCT-GAGAGTTCAGTTGCGAAAC-CGGCG
droAna3 scaffold_13337:5830221-5830437 - AAACTGCATTCAAGTTTTGTTTTTGTTATTTTTT-----------------------CTTTGC--TTCT-GCAACTATT-GCTGGTTAGCTGCTAGTTG------------------CTGC----TGCTGCTGCT-GCTGCCACGGT-------TTGTTGCTTCACTGATTACGCGCAATGCAGCAGTAGCAGTA---------------GCAGT---GGCA----------------------------------------------------GAG---GAGACAGAGGAGCCACTGCAAC--AACTGCAACAA---AACAGCAGCT-GAGAGTTCAGTTGCGAAAC-CGGCG
dp4 chrXR_group6:10126891-10127089 + AAACGGCATACAAGT-----------TTTTCC-TCGCCAAACACAAAGCGTTTTAGCCAGAGCTCTTCT-GCAACTATT-GCTGG-------TTG-TAG------------------TTGT----AGTT-------GCTGCCACGGT-------TTGTTGCTTCACTGATTACGCGCAATGCAGCAGCGGTGGCA---------------GCGGT---GGCA----------------------------------------------------GCG---GTGGCAGCGG-----TGGCA------------------GACGGCAGCCCCCGAGTTCAGTTGCAAAAC-CGGCG
droPer1 super_4:4953737-4953917 + TTTC-GTTTTC--GT-----------TTTCATTT--------------------------CGC-----T-GT--AA----ACAAG---C--GATT-TTG------------------TTGC----TCTTTCTGCTCGTAATTGAG-A-------TAAATGCATTTT---AAATGCGCAAC--CGCAGCTGCA------------------GCAGCAGCAGCA----------------------------------------------------GAGGCAGCA-----GTTGCAACAGCAGCT-AGCTTCAACT----GGTTGCAGTT-GCGTATGCAGATGCGATGCAAGGCG
droWil1 scaffold_180698:2057599-2057768 - ACACTGCAGACAAGTTTTAAATGCCTTTTTTT-T-----------------------CGTAGC-------------------TCT---CTTGTTG-TTGTTGTTGCTAA-GT--------C----TTCTGCAACTA-TTGCCACGGT-------TTGTTGCTTCACTGATTACGCGCAATGCAGCAGCAGCAGCG---------------GCAG---------------------------------------------------------------------------------CAGCA------------------AGCGGCAGCT-TCGAGTTCAGTTGCAAAAC-CGGCG
droVir3 scaffold_12855:885802-885977 - AGGATATGGGCGATT-----------GTCTTA-T-----------------------CAGTGG-----TGGTGCCG----GACCA---GCTGTTA-GTG------------------CCGT----TGCTGATGCCAGCGGCAACCTT-------TTGCTCGATCAT-CATCACCATCATC---------ATCAT--CAACAACAGCAGCAGCAGC------A----------------------------------------------------G--------------CAGCAGCAGCAACA-ACAACAACAGCAGCAACAGCAGCA-GCTACTGCAG---------------
droMoj3 scaffold_6496:11355914-11356095 - AAACGAAATGAAACT-----------TTGTGC-G-----------------------CATAG--------GCAACCAACAGC-GG-------CGG-CAG------------------CAGC----AGCAGCAG------------------------------------------------------------------------------CAGC---AGCAGCAGCGCCAGCATCGCTGAGACTTTGACGCGTTGGCAAAAGAAGCAGCAGCAG------CA-----GCAGCAACAGCAAC--AACAGCC--GCAGCAGCAGCAGCA-GCGACGGCAGCAGCAGAAA-CGTCG
droGri2 scaffold_15110:4649694-4649883 + CAAT----------T-----------TTCTCA-T-----------------------CAGTTT-----C-T-------------------TGCCG-ATGATGAAGCAAATGTCATCGCTGCAGAATGTTGCATTTCGC-GCCAAGATGGGTGAGCTGCTGCTGC---------ACACAATGCAACAATCACAAATGCAACAACAGCAGCAACAGC------A----------------------------------------------------GCAGCAGCA-----GCAACAACAACA--------GC--AACAACAACAGGAGCC-G---ATGCAGCAGCA------ACCG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:11545623-11545808 - AAACTGCATTCAAGTTTTTCCTCAGAGCCGCGACTGCTGGCGTGTTATTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAACAGCAGCAGCAGCAGAAGCAACAGCAACTAACTGCAGAGGAGCAATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAACTGCATTCAAGTTTTTCCTC-----------------------AGAGC-----CGCGACT---GCTGGCGTGTTATTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAG---------CAGCAGAAGCAACAGCAACTAACTGCAGAGGAGCAATAGCAGCTG--------AGAGTTCAGTTGCGAAACCGGCGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AAACGGCATACAAGTTTTTCCTCGCCAAACACAAAGCGTTTTAGCCAGAGCTCTTCTGCAACTATTGCTG----GTTGTAGTTGTAGTT-------GCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAGCGGTGGCAGCGGTGGCAGCGGTGGCA---------------GCGGTGGCAGACGGCAGCCCCCGAGTTCAGTTGCAAAACCGGCGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-23.0,  p-value=0.009901 dG=-23.0,  p-value=0.009901 dG=-23.0,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-22.1,  p-value=0.009901

droSim1

dG=-16.0,  p-value=0.009901 dG=-15.8,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.3,  p-value=0.009901

droSec1

dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.1,  p-value=0.009901

droYak2

dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droEre2

dG=-16.0,  p-value=0.009901 dG=-15.8,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.3,  p-value=0.009901

droAna3

dG=-29.1,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.2,  p-value=0.009901 dG=-28.1,  p-value=0.009901 dG=-27.5,  p-value=0.009901

dp4

dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.1,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-34.0,  p-value=0.009901

droPer1

dG=-22.3,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-18.3,  p-value=0.009901

droWil1

dG=-17.0,  p-value=0.009901 dG=-17.0,  p-value=0.009901 dG=-16.8,  p-value=0.009901 dG=-16.8,  p-value=0.009901

droVir3

dG=-10.3,  p-value=0.009901 dG=-10.3,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-9.9,  p-value=0.009901 dG=-8.24,  p-value=0.009901

droMoj3

dG=-19.2,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.8,  p-value=0.009901 dG=-18.7,  p-value=0.009901

droGri2

dG=-30.3,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-29.9,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.5,  p-value=0.009901 dG=-25.7,  p-value=0.009901

Generated: 03/07/2013 at 06:16 PM