Secondary structure and small RNA-seq evidence for dme-mir-3643

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:13653883-13653980 - GAATCCAAGCTGAACGTGAGTTT-A--TCTAAATATG-CCCATTTATCAATAG-TCATAC----------TTATTTA-----T-------GC-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droSim1 chr2R:12393703-12393800 - GAGTCCAAGCTGAACGTGGGTTT-A--TCTAGATACG-CCCATTTATCATTGG-TCATAC----------TTATTTA-----T-------GT-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droSec1 super_1:11152590-11152687 - GAGTCCAAGCTGAACGTGGGTTT-A--TCTATTTACG-CCCATTTATCATTGG-TCATAC----------TTATTTA-----T-------GT-TCCTTTA--ACGCCTTGCAGAGCTTCGAAAAAGAC
droYak2 chr2R:15527673-15527770 + GAATCCAAGCTGAACGTGGGTTC-A--TCTAGATACT-TCCATATATCAAAAG-CCGTAC----------TTATTTA-----T-------GT-TATTTAA--ACTGCTTGCAGAGCTTCGAAAAAGAC
droEre2 scaffold_4845:7883019-7883116 - GAATCCAAGCTGAACGTGGGTTT-T--TCTAGATACG-CCCATTTATCAATGG-CCCTAC----------TTATTTA-----T-------GC-ATTTTAA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droAna3 scaffold_13266:10531972-10532067 + GAATCCAAGCTGAACGTTAGTTACT--TGTGCA-A---CTCGT------------CCAATCGGTTC-AATAACTAGA-----T-------CC-TCCTTTACATCTCCTTGTAGGGCTTCGAGAAGGAC
dp4 chr3:16466931-16467019 - GAATCCAAGCTGAACGTAAGTGC-TTAGCAA---ATG-TTCACTGAACCTTGAAT----------------CATTGCCTTTG------------------TTCTCGGTTCCAGAGCTTCGAAAAGGAC
droPer1 super_4:295271-295359 + GAATCCAAGCTGAACGTAAGTGC-TTAGCAA---ATG-TTCACTGAACCTTGAAT----------------CATTGCCTTTG------------------TTCTCGGTTCCAGAGCTTCGAAAAGGAC
droWil1 scaffold_181141:4609865-4609965 + GAATCAAAATTGAATGTAAGCTG---------A-AAA------------TTTAATTT---ATATTTTGTTTTCTCCTATTTACATACCACGTGTCCTTCA--CTCAATTACAGAGCTTCGAAAAGGAT
droVir3 scaffold_12875:16919908-16919994 - GAATCCAAACTAAATGTGAGTAT-C--TCCTAA-TCGCCTCAT------------CCAAT----------TCATTTT-----T-------GA-CCCTTTG--CCTACTTTTAGAACTTTGAAAAAGAC
droMoj3 scaffold_6496:11084070-11084155 + GAATCTAAACTAAATGTAGGTAT-A--GTAA---TAG-ATGAGTTTTTCTTTTAT----------------TTTAACC-----------------TTTGG--CCCGCTTGCAGAACTTTGAGAAGGAC
droGri2 scaffold_15245:16459236-16459327 - GAATCCAAACTAAATGTGAGATACC--TCTAAA-ACAAATCAT------------AA---AGATTTTGATGTATTGAGATTA------------------TGTACATTTGCAGAACTTTGAGAAAGAC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:13653883-13653980 - GAATCCAAGCTGAACGTGAGTTTATCTAAATATGCCCATTTATCAATAGTCATACTTATTTATGCTCCTTTAACTCCTTGCAGAGCTTCGAAAAAGAC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GAGTCCAAGCTGAACGTGGGT--TTATCTAGATACGCCCATTTATCATTG-GTCATACTTATTTATGTTCCTTTAACTC---CTTGCAGAGCTTCGAAAAAGACSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GAATCCAAGCTGAACGTAAGTGCTTAGC---AAATGTTCACTGAACCTTGAATCAT---T--------GCCTTTG-TTCTCGGTTCCAGAGCTTCGAAAAGGACSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-4.8,  p-value=0.009901 dG=-4.5,  p-value=0.009901 dG=-4.2,  p-value=0.009901 dG=-4.2,  p-value=0.009901 dG=-4.1,  p-value=0.009901

droSim1

dG=-9.6,  p-value=0.009901 dG=-8.6,  p-value=0.009901 dG=-7.8,  p-value=0.009901

droSec1

dG=-9.7,  p-value=0.009901 dG=-7.9,  p-value=0.009901

droYak2

dG=-3.4,  p-value=0.009901 dG=-3.0,  p-value=0.009901 dG=-2.7,  p-value=0.009901 dG=-2.4,  p-value=0.009901 dG=-2.4,  p-value=0.009901

droEre2

dG=-6.1,  p-value=0.009901 dG=-6.1,  p-value=0.009901 dG=-5.9,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.7,  p-value=0.009901

droAna3

dG=-6.2,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.5,  p-value=0.009901

dp4

dG=-6.6,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.8,  p-value=0.009901

droPer1

dG=-6.6,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.8,  p-value=0.009901

droWil1

dG=-4.6,  p-value=0.009901 dG=-4.1,  p-value=0.009901 dG=-4.0,  p-value=0.009901 dG=-4.0,  p-value=0.009901 dG=-3.6,  p-value=0.009901

droVir3

dG=-2.3,  p-value=0.009901 dG=-2.1,  p-value=0.009901 dG=-1.5,  p-value=0.009901 dG=-1.3,  p-value=0.009901 dG=-1.3,  p-value=0.009901

droMoj3

dG=-7.1,  p-value=0.009901 dG=-6.8,  p-value=0.009901 dG=-6.2,  p-value=0.009901 dG=-6.1,  p-value=0.009901

droGri2

dG=-2.7,  p-value=0.009901 dG=-2.7,  p-value=0.009901 dG=-2.6,  p-value=0.009901 dG=-2.6,  p-value=0.009901 dG=-2.5,  p-value=0.009901

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