Secondary structure and small RNA-seq evidence for dme-mir-2501

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:8104192-8104292 + GGTGGTAAAAGTGGAGTAAGTTTGGAGTG----CCTGGGCTAAGAACTTCCATT---------------------------------------------------------CTGAAACTTAACTCTTGCAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAG
droSim1 chr3L:7572156-7572239 + GGTGGTAAAAGTGGAGTAAGTTTGGAGTC----CCTGGGCTAAGAACTTCCATT--------------------------------------------------------------------------CAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAG
droSec1 super_0:391632-391715 + GGTGGTAAAAGTGGAGTAAGTTTGGAGTC----CCTGGGCTAAGAACTTCCATT--------------------------------------------------------------------------GAAGCAAACTTTC------------------------------------------------------------------TTTTAGAACCAAGCGTGGTAG
droYak2 chr3L:8691884-8691979 + CGTTGTAAAAGTGGAGTAAGTTTGCGA----------------------------------------------------------------CTTACGTTC-CTTTTATATACCG-ACATACCGTCTTACAACCAAACTTTC------------------------------------------------------------------TTTCAGAACTAAGCGCGGCAG
droEre2 scaffold_4784:3260723-3260819 - GGTGGTAAAAGTGGAGTAAGCTTGCAA----------------------------------------------------------------CTTGAGTTATATCTTTTATCCCG-CTATACTTACTTACAATCAAACTTTC------------------------------------------------------------------TCGCAGAACCAAGCGCGGCAG
droAna3 scaffold_13337:13543116-13543232 - AGTGGTTAAAGTGGAGTAAGTGGCGT----------------------TTAAGGG------AGTGATG----------G---ATAGATGGACCTGAGTCT-TTTTTAGT---TGTTCTCTTTCTCTAACATTCATAATCCG------------------------------------------------------------------TTTCAGAAACAAACGTGGCCG
dp4 chrXR_group3a:1131777-1131868 + GGTGGTCAAAGTAGAGTAAGTGATCC----------------------CCACCGA------ACTATTGTGACTTTACGC------T-------------C-TAATTGGG----------------------TACATTTTTT------------------------------------------------------------------GTGCAGAACCAAGCGTGGCCG
droPer1 super_23:1158678-1158769 + GGTGGTCAAAGTAGAGTAAGTGATCC----------------------CCACCGA------ACTATTGTGGCTTTACGC------T-------------C-TAATTGGG----------------------TACATTTTTT------------------------------------------------------------------GTGCAGAACCAAGCGTGGCCG
droWil1 scaffold_180727:72451-72556 + AGTGGTCAAAGTACAGTAAGTACATGG-----------AATGACCAATCCAATTAACTATA--TA-TGTACATATATGT------T-------------A-AATCCAAC----------------------CATCTCTTTT------------------------------------------------------------------ATCCAGAAATAGACGTGGCCG
droVir3 scaffold_13049:9356761-9356852 - GGTTGTCAAAGTTGAGTAAGTTTCTA----------------------TCAAC----AATAACTA-AGCTTGGTTATGG------TA------------A-TAATTTG------------------------ACACTTTTC------------------------------------------------------------------TGTTAGAAATAAGCGCGGTCG
droMoj3 scaffold_6680:11400964-11401055 + CGTTGTCAAGGTTGAGTAAGTTTGTAGGC----TCTTAACT-----------------------GGCGAAACCAGATGA------T-------------C-TAATTAC-----------------------ACAATTTTCC------------------------------------------------------------------CATTAGAAACAAACGTGGTCG
droGri2 scaffold_15110:6804388-6804550 + CGTTGTCAAAGTCGAGTGAGTAATTTGGCAAAAACTGGCTT-------TTAATG-------------------AGATTACTCC--T-------------C-TTATCAG-----------------------ACAGTTCTCCAAACTCCTCATTTATCTTAGAGCAAATATCAGATTTAAAAATAAAATTATTTTTTCTTCTTTTGATCTTCAGAAATAAGCGCGGTCG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:8104192-8104292 + GGTGGTAAAAGTGGAGTAAGTTTGGAGTGCCTGGGCTAAGAACTTCCATTCTGAAACTTAACTCTTGCAATCAAACTTTCTTTCAGAACCAAGCGTGGCAG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCTGGGCTAAGAACTTCCATT-----------------------------------CAATCAAACTTTCTTTCAGAACCAAGCGTGGCAGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GGTGGTCAAAGTAGAGTAAGTG------------------ATC---C------CCACCGAACTATTGTGACTTTACGCTCTAATTGGGTACATTTTTTGTGCAGAACCAAGCGTGGCCGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-14.6,  p-value=0.009901 dG=-13.9,  p-value=0.009901

droSim1

dG=-8.7,  p-value=0.009901 dG=-8.0,  p-value=0.009901

droSec1

dG=-8.8,  p-value=0.009901 dG=-8.7,  p-value=0.009901 dG=-8.3,  p-value=0.009901 dG=-8.1,  p-value=0.009901 dG=-8.0,  p-value=0.009901

droYak2

dG=-6.3,  p-value=0.009901 dG=-5.4,  p-value=0.009901 dG=-5.4,  p-value=0.009901

droEre2

dG=-4.4,  p-value=0.009901 dG=-4.0,  p-value=0.009901

droAna3

dG=-15.2,  p-value=0.009901 dG=-14.9,  p-value=0.009901 dG=-14.8,  p-value=0.009901 dG=-14.5,  p-value=0.009901 dG=-14.2,  p-value=0.009901

dp4

dG=-5.9,  p-value=0.009901 dG=-5.5,  p-value=0.009901 dG=-5.4,  p-value=0.009901 dG=-5.3,  p-value=0.009901 dG=-5.3,  p-value=0.009901

droPer1

dG=-8.1,  p-value=0.009901 dG=-7.4,  p-value=0.009901 dG=-7.4,  p-value=0.009901 dG=-7.3,  p-value=0.009901

droWil1

dG=-7.8,  p-value=0.009901 dG=-6.9,  p-value=0.009901 dG=-6.1,  p-value=0.009901

droVir3

dG=-7.1,  p-value=0.009901 dG=-6.9,  p-value=0.009901 dG=-6.6,  p-value=0.009901 dG=-6.4,  p-value=0.009901 dG=-6.2,  p-value=0.009901

droMoj3

dG=-8.0,  p-value=0.009901 dG=-7.3,  p-value=0.009901

droGri2

dG=-21.9,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-16.4,  p-value=0.009901

Generated: 03/07/2013 at 04:59 PM