Secondary structure and small RNA-seq evidence for dme-mir-4986

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:9726743-9726895 - AGACTGCCAACTGGGTTC------TGCCGCTT---TTGCTGTGGCTTCTCTGCATGGGATTCCCCATTCTGCATGGCGCCGATCTCTGCCAGCCCATCGGATGGCGGAACTTCCAGTGCAGCGAGGTCGCTTCTCTGCAGGATCTGGTGGACTTGGGCG---------CCG
droSim1 chr3L:9107366-9107518 - CAACTGCCAACTGGGTTC------TGCCGCTT---TTGCTGTGGCTTCTCTGCGTGGGATTCCCCATCCTGCATGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGGTGGATTTGGGCG---------CCG
droSec1 super_0:1960228-1960380 - CAACTGCCAACTGGGTTC------TGTCGCTT---TTGCTGTGCCTTCTCTGCGTGGGATTCCCCATCCTGCATGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGCAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGGTGGACCTGGGCG---------CCG
droYak2 chr3L:9698225-9698377 - CAACTGCCAATTGGGTTC------TGCCGCTT---TTTCTGTGGCTTCTCTGCGCGGGATTCCCCAGCCTGCATGGTGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGAATTGGGCG---------CCG
droEre2 scaffold_4784:9713780-9713932 - CAACTGCCAATTGGGTTC------TGCCGCTC---TTTCTGTGCCTTCTCTGCGCGGGATTCCCCAGCCTGCATGGAGCTGATCTCTGCCAGCCCGTCGGGTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGACCTGGGCG---------CCG
droAna3 scaffold_13337:3652327-3652482 + TGCCAGTCAAATGGACTC------TGTTGCCTTGCTTTTTGTGGCTCTTCTCGAAGGGGCTTCCCTCCACAAGAGCTCAAGATCTTTGCCAGCCCCGAGGTTGGCGCAACTTCGAGTGCCTTGAAGTGGCTTCTCTGCAGGATCTAGTGGATTTGGGGG---------CCG
dp4 chrXR_group6:9932877-9933023 + TGAATGCCAATTGGGTTT------TGTCC------GCTCTGTGGCTCTGCTGCAGGGGCTTCCCCC---AGGTCGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGG---------CCG
droPer1 super_61:212952-213098 + TGAATGCCAATTGGGTTT------TGTCC------GCTCTGTGGCTCTGCTGCAGGGGCTTCCCCC---AGGTCGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGG---------CCG
droWil1 scaffold_180949:1195301-1195459 + CGAATTTCCAGTGGTTTT------GGCCGTTG---GCTTTATGGCTTGTATGTCGGTGCTTCCCGC---GGTGCACAGCTCAAGTCTGTAATCCCCGCGGCTGGCGTAACTACGAATGCAGCGAATTGGCTAGTCTAGAGGATTTAATAAATTCTGAAGGCTTGTCCACTG
droVir3 scaffold_13049:8736379-8736540 + CGAATGCCAAACAGTTCTGGACTTGG---TCA---GTTCTCTGGCTGCTCTGCTGGGCTGTGCCCC---GTGCGTTGGCGCAGTTGTGCGAGGCGCAGGGCTGGCGCAGCTTTGAGTGCCGCGAGCTGGGCAGCCTGCAGGAGCTGATCAATGAGAAGGCCTTGCCCACTG
droMoj3 scaffold_6680:6608267-6608428 - TGAATGCGCAACCTTTGCGCCTAGGT---CCA---GTCCTCTGGCTGCTGTGCTGCGGCCTTTCCC---AGGTGCTGAGTCAGATATGCGAGGCTCAAGGCTGGCGCAGCTTCGAGTGTCGTGAGCTGAGCAGCCTGAAGGAGCTGAAGAACGTTAGGAACTTTCCCAAAG
droGri2 scaffold_15110:4482444-4482593 + TGTTCTACACTTGG---------------CCA---ATTCTTTGCCTGCTCTGCTTTGGGTTTTGC--CCTGGAT-TGGCTGTGGTCTGTGAGGCTCAAGGCTGGCGTAGTTTTGAGTGCCGCGAATTGAGCAGCCTGCAGGAGCTGATCGATGTGAAGGCATTTCCCACCG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:9726743-9726895 - AGACTGCCAACTGGGTTCTGCCGCTTTTGCTGTGGCTTCTCTGCATGGGATTCCCCATTCTGCATGGCGCCGATCTCTGCCAGCCCATCGGATGGCGGAACTTCCAGTGCAGCGAGGTCGCTTCTCTGCAGGATCTGGTGGACTTGGGCGCCG
droSim1 chr3L:9107366-9107518 - CAACTGCCAACTGGGTTCTGCCGCTTTTGCTGTGGCTTCTCTGCGTGGGATTCCCCATCCTGCATGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGGTGGATTTGGGCGCCG
droSec1 super_0:1960228-1960380 - CAACTGCCAACTGGGTTCTGTCGCTTTTGCTGTGCCTTCTCTGCGTGGGATTCCCCATCCTGCATGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGCAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGGTGGACCTGGGCGCCG
droYak2 chr3L:9698225-9698377 - CAACTGCCAATTGGGTTCTGCCGCTTTTTCTGTGGCTTCTCTGCGCGGGATTCCCCAGCCTGCATGGTGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGAATTGGGCGCCG
droEre2 scaffold_4784:9713780-9713932 - CAACTGCCAATTGGGTTCTGCCGCTCTTTCTGTGCCTTCTCTGCGCGGGATTCCCCAGCCTGCATGGAGCTGATCTCTGCCAGCCCGTCGGGTGGCGGAACTTCCAGTGCAACGAGGTCGCTTCTCTGCAGGATCTGGTCGACCTGGGCGCCG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CAACTGCCAACTGGGTTCTGCC-GCTTTTGCTGTGGCTTCTCTGCGTGGGATTCCCCATCCTGCATGGCGCCGATCTCTGCCAGCCCATCGGCTGGCGGAACTTCCAGTGCAACGAAGTCGCCTCGCTGCAGGATCTGGTGGATTTGGGCGCCGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TGAATGCCAATTGGGTTTTGTCCGCT----CTGTGGCTCTGCTGCAGGGGCTTCCCC---CAGGTCGGGGCTCTTCCCTGCCGGACTCTGGCCTGGCGCAGCTTCGAGTGTCGTGAATTAGCCAGTCTGCAGGATCTGTCTGATGTGGGGGCCGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-30.9,  p-value=0.009901 dG=-30.5,  p-value=0.009901 dG=-30.3,  p-value=0.009901 dG=-30.3,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droSim1

dG=-32.1,  p-value=0.009901 dG=-31.6,  p-value=0.009901 dG=-31.6,  p-value=0.009901 dG=-31.1,  p-value=0.009901 dG=-31.1,  p-value=0.009901 dG=-26.0,  p-value=0.009901

droSec1

dG=-27.5,  p-value=0.009901 dG=-27.0,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.5,  p-value=0.009901 dG=-19.7,  p-value=0.009901

droYak2

dG=-32.6,  p-value=0.009901 dG=-32.0,  p-value=0.009901

droEre2

dG=-36.1,  p-value=0.009901 dG=-35.7,  p-value=0.009901 dG=-35.5,  p-value=0.009901 dG=-35.1,  p-value=0.009901

droAna3

dG=-26.1,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.3,  p-value=0.009901 dG=-23.1,  p-value=0.009901

dp4

dG=-27.5,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.0,  p-value=0.009901

droPer1

dG=-27.5,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.0,  p-value=0.009901

droWil1

dG=-17.7,  p-value=0.009901 dG=-17.0,  p-value=0.009901 dG=-16.8,  p-value=0.009901 dG=-16.7,  p-value=0.009901

droVir3

dG=-36.0,  p-value=0.009901 dG=-35.8,  p-value=0.009901 dG=-35.7,  p-value=0.009901 dG=-35.6,  p-value=0.009901 dG=-35.5,  p-value=0.009901

droMoj3

dG=-25.5,  p-value=0.009901 dG=-25.2,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-24.8,  p-value=0.009901 dG=-24.8,  p-value=0.009901 dG=-20.8,  p-value=0.009901

droGri2

dG=-21.7,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.3,  p-value=0.009901 dG=-18.4,  p-value=0.009901

Generated: 03/07/2013 at 06:55 PM