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 - AAACTGCATTCAAGTTTTTCCTCAGAGCCGCGACTGCTGGCGTGTTATTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCAACAGCAGCAGCAGCAG---------------------------------AAGCAACAGCAACT-AACTGCAGAGGAGCAATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droSim1 chr3L:10929570-10929746 - AAACTGCATTCAAGTTTTTCCTCAGAGCCGCGACTGCTGGCGTGTTATTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCA---G------CAGCAG---------------------------------AAGCAACAGCAACT-AACTGCAGAGGAGCAATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droSec1 super_0:3745423-3745605 - AAACTGCATTCGAGTTTTTCCTCAGAGCCGCGACTGCTGGCGTGTTATTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCA---GCAGCAGCAGCAG---------------------------------AAGCAACAGCAACT-AACTGCAGAGGAGCAATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droYak2 chr3L:11579958-11580167 - AAACTGCATTCAAGTTTTTCCTCAGAGCCGCGACTGCTGGCGTGTTATTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCA---G------CAGCAGAAGCAGCAGCAGCAGCAGTAGAAATAGCAGCAGTAGCAACAGCAACT-AACTGCAGAGGAGCAATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG
droEre2 scaffold_4784:11545792-11545968 - A-ACTGCATTCAAGTTTTTCCTCAGAGCCGCGACTGCTGGCGTGTTATTGTTGCTGTTGCAGCTAGCTGCCACGGTTTGTTGCTTCACTGATTACGCGCAATGCAGCA---G------CAGCAG---------------------------------AAGCAACAGCAACTGAACTGCAGAGGAGCAATAGCAGCTGAGAGTTCAGTTGCGAAACCGGCG

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

-59.5 -59.5 -58.7 -58.7

droSim1

-53.0 -52.7 -52.6 -52.5 -52.4 -52.3

droSec1

-57.2 -57.2 -56.9 -56.6 -56.4 -56.4

droYak2

-67.6 -67.2 -66.9 -66.7

droEre2

-51.8 -51.1 -50.9 -50.8 -50.8

droAna3

-66.1 -66.0 -65.9 -65.8 -65.6 -65.5

dp4

-62.8 -62.8 -62.4 -62.4 -62.3 -62.3

droPer1

-53.8 -53.5 -53.4 -53.4 -53.1 -53.1

droWil1

-45.0 -44.8 -44.6 -44.6 -44.5 -44.4

droVir3

-44.8 -44.6 -44.5 -44.1 -44.0 -43.9

droMoj3

-45.2 -45.0 -45.0 -44.8 -44.7 -44.7

droGri2

-52.8 -52.7 -52.6 -52.6 -52.5 -52.5

Generated: 01/05/2013 at 05:26 PM