Secondary structure and small RNA-seq evidence for dme-mir-2500

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:16991543-16991639 - AAGAACTTTCTGCAGGTAAGGA----------------ACACACATATACAATACCG-------TTTGA-------------ATTTCAAATAATCAGGA------TTTTGTGTGTGGACCTCAGATCATGTTCCAGGCC
droSim1 chr3L:16333274-16333368 - AAGAACTTTCTGCAGGTAAGGA----------------ACACACAT--ACAGTCCCT-------GTTGA-------------ATTTCAAATAATCAGGA------TTTTGTGTGTGGACCTCAGATCATGTTCCAGGCC
droSec1 super_0:9052557-9052651 - AAGAACTTTCTGCAGGTAAGGA----------------ACACACAT--ACAATCCCT-------GTTGA-------------ATATTAAATAATCAGGA------TTTTGTGTGTGGACCTCAGATCATGTTCCAGGCC
droYak2 chr3L:17082640-17082734 + AAGAACTTTCTACAGGTCAGGA----------------TCACACAT--ACATTCCCT-------GTAGA-------------ATTTAATTTAATCAGGA------ATTTATGTGTGAACTTTAGATCATGTTCCAGGCC
droEre2 scaffold_4784:16851458-16851552 + AAGAATTTTCTGCAGGTAAGGA----------------TCGCACAT--ACAATCCCT-------GTCGC-------------ATTTTATGTAATCAGGA------TTTTGCGTGTGAACTTTAGATCATGTTCCAGGCC
droAna3 scaffold_13337:13625775-13625865 + AAAAACTTTCTGCAGGTGAGCA----------------GTTCA----------------AGCTTAGCGAGGTCTGTTCCAGTT-TCCTAACATTC----------TTCCGCTC-----CTTTAGATCATGTTCCAGGCC
dp4 chrXR_group8:4827167-4827262 - AAGAACTTTTTGCAGGTAAGCC----ATCACC------------AGCA-------TTGAAAGCCATTGA-------------AATGCGTCTAAATAGCAGTCT--CTCTCCTC-----CCACAGATCATGTTCCAGGCC
droPer1 gnl|ti|780630171:515-611 - AAGAACTTTTTGCAGGTAAGCC----ATCACC------------AGCA-------TTGAAAGCCATTGA-------------AATGCGTCTAAATAGCAGTCT--CTCTCCTC-----CCACAGATCATGTTCCAGGCC
droWil1 scaffold_180955:197087-197182 - AAAAACTTTTTACAGGTAAGCC----------------ACAACGAT--GAATGGCTCGAGGGAGATTGA-------------ACTCTATGTAATC-------TCTTCACTTTC-----TTGCAGATAATGTTTCAGGCT
droVir3 scaffold_13049:10166522-10166615 + AAGAACTTTCTGCAGGTGCGTT----CCCCCTGGCTGATCACATAT--GTCGTTT---------------------------ATACTATATTTT-CGCC------TTTTGCTC-----CTGCAGATCATGTTCCAGGCC
droMoj3 scaffold_6680:10629193-10629280 - AAGAACTTTCTCCAGGTGAGTT----ACGG-------TTCAC------ATAATTC----------TCGT-------------ATTCCAAATAACGAAAT------CTTTGTCC-----TTGCAGATCATGTTCCAGGCC
droGri2 scaffold_15110:9071735-9071831 - AAGAACTTGCTGCAGGTGAGATTTTGATCG-------ATTAA------TTAAGTC----------TGG--------CTCTCTTTGCTAAATATGCC--A--CT--TTTTGTGT-----TGGCAGATCATGTTCCAGGCC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:16991543-16991639 - AAGAACTTTCTGCAGGTAAGGAACACACATATACAATACCGTTTGAATTTCAAATAATCAGGATTTTGTGTGTGGACCTCAGATCATGTTCCAGGCC
droSim1 chr3L:16333274-16333368 - AAGAACTTTCTGCAGGTAAGGAACACACA--TACAGTCCCTGTTGAATTTCAAATAATCAGGATTTTGTGTGTGGACCTCAGATCATGTTCCAGGCC
droSec1 super_0:9052557-9052651 - AAGAACTTTCTGCAGGTAAGGAACACACA--TACAATCCCTGTTGAATATTAAATAATCAGGATTTTGTGTGTGGACCTCAGATCATGTTCCAGGCC
droYak2 chr3L:17082640-17082734 + AAGAACTTTCTACAGGTCAGGATCACACA--TACATTCCCTGTAGAATTTAATTTAATCAGGAATTTATGTGTGAACTTTAGATCATGTTCCAGGCC
droEre2 scaffold_4784:16851458-16851552 + AAGAATTTTCTGCAGGTAAGGATCGCACA--TACAATCCCTGTCGCATTTTATGTAATCAGGATTTTGCGTGTGAACTTTAGATCATGTTCCAGGCC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAGAACTTTCTGCAGGTAAGGAA-CACACAT--ACAGTCCCTGTTGAATTTCAAATAATCAGGATTTTGTGTGTGGACCTCAGATCATGTTCCAGGCCSizeHit CountTotal NormTotalGSM343915
Embryo
...............GTAAGGAA-CACACAT--ACAGTCCCTG.......................................................2517.0077
...............GTAAGGAA-CACACAT--ACAGTCCC.........................................................2312.0022
............................................................AGGATTTTGTGTGTGGACCTCA................2211.0011
...............GTAAGGAA-CACACAT--ACAGTCCCT........................................................2411.0011
...............................................................ATTTTGTGTGTGGACCTCA................1911.0011
...............GTAAGGAA-CACACAT--ACAGTCC..........................................................2211.0011
..........................................................TCAGGATTTTGTGTGTGGACCT..................2211.0011
...............GTAAGGAA-CACACAT--ACAGTC...........................................................2111.0011
dp4
AAGAACTTTTTGCAGGTAAGCCATCAC-CAGCATTGAAAGCCATTGAAATGCGTCTAAATAGCAGTCTCTCTCC-TCCCACAGATCATGTTCCAGGCCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-17.0,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-16.0,  p-value=0.009901

droSim1

dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.7,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.3,  p-value=0.009901

droSec1

dG=-20.3,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.1,  p-value=0.009901

droYak2

dG=-18.8,  p-value=0.009901 dG=-18.8,  p-value=0.009901 dG=-18.8,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.5,  p-value=0.009901

droEre2

dG=-18.2,  p-value=0.009901 dG=-18.0,  p-value=0.009901 dG=-18.0,  p-value=0.009901 dG=-18.0,  p-value=0.009901 dG=-17.4,  p-value=0.009901

droAna3

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

dp4

dG=-5.1,  p-value=0.009901 dG=-4.8,  p-value=0.009901 dG=-4.6,  p-value=0.009901 dG=-4.1,  p-value=0.009901

droPer1

dG=-5.1,  p-value=0.009901 dG=-4.8,  p-value=0.009901 dG=-4.6,  p-value=0.009901 dG=-4.1,  p-value=0.009901

droWil1

dG=-12.0,  p-value=0.009901 dG=-12.0,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-8.4,  p-value=0.009901

droVir3

dG=-5.9,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.6,  p-value=0.009901 dG=-5.5,  p-value=0.009901 dG=-5.4,  p-value=0.009901

droMoj3

dG=-3.0,  p-value=0.009901 dG=-3.0,  p-value=0.009901 dG=-2.8,  p-value=0.009901 dG=-2.8,  p-value=0.009901 dG=-2.6,  p-value=0.009901 dG=-2.6,  p-value=0.009901

droGri2

dG=-10.0,  p-value=0.009901 dG=-10.0,  p-value=0.009901 dG=-10.0,  p-value=0.009901 dG=-10.0,  p-value=0.009901 dG=-9.8,  p-value=0.009901 dG=-7.7,  p-value=0.009901

Generated: 03/07/2013 at 04:58 PM