Secondary structure and small RNA-seq evidence for dme-mir-4910

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:4817801-4817896 - GGGTGAAACAGGCAGGTTTGTATGGAAT---TCCATGAGCTT--------------------------CAAAGTAATGCTTCTAACTCTGTGGTTTTTC-ATA-----TTTCCCAGTGGCAAGAGCACCCA
droSim1 chr2L:4687585-4687681 - GGGTGAAACAGGCAGGTTTGTATGGAAT---TCCAGAAGCTC--------------------------CAAAGTAATCTTTCTAACTCTGCGGGTTTTCTATC-----TTTCCCAGTGGCAAGAGCACCCA
droSec1 super_5:2913658-2913754 - GGGTGAAACAGGCAGGTTTGTATGGAAT---TCCAGGTGTTC--------------------------CAAAGTAATCTTTCTAGCTCTGTGGTTTTTTCATA-----TTTCCCAGTGGCAAGAGCACCCA
droYak2 chr2L:4827662-4827759 - GGGTGAAACAGGCAGGTTTGTTTGGAAC---TCCACAAGAT-------------------------TTCAAGGTATTCCTTCTAACTCTGTGGTTTTTCCACA-----TTTTCCAGTGGGAAAAGCACCCA
droEre2 scaffold_4929:4898740-4898837 - GGGTGAAACAGGCAGGTGTGTATGCAAT---TCCAAAAGGT-------------------------CTCAATGTATTCCTTCTAACTCTGTGGTTTTTCTATA-----TTTCCCAGTGGCAAGAGCACCCA
droAna3 scaffold_12916:9386286-9386375 - GGGCGAGACCGGCAGGTGAGAATACAAT---TCTACAACCCA--------------------------TACCCTTGTTTTCA------TATCATTTTTT-CAA-----TTTTTCAGTGGCAAGAGCACCCA
dp4 chr4_group3:3567830-3567920 - GGGCGAAACAGGAAGGTGAGTGAGAAGCAAAT----------------ATGTATGCCCCAAGAAATCCTAACGA----------------TC--------ATATTTTCCCCTTCAGCGGCAAGAGCACACA
droPer1 super_1:5048029-5048119 - GGGCGAAACAGGAAGGTGAGTGAGAAGCAAAT----------------ATGTATGCCCCAAGAAATCCTAACGA----------------TC--------ATATTTTCCCCTTCAGCGGCAAGAGCACACA
droWil1 scaffold_180772:7924021-7924113 + CGGAGAGACGGGCAGGTAATT----AAA---ACCATAAGGTTACCTTAATGTATATTTAAAGTATTTAT-----------------------G---TACGATA-----TTTTGCAGTGGAAAGAGCACTCA
droVir3 scaffold_13246:521378-521407 + GGGCGAGACGGGC-----------------------------------------------------------------------------------------------------AGCGGGAAGAGCACGCA
droMoj3 scaffold_6500:7585086-7585115 - GGGCGAGACGGGG-----------------------------------------------------------------------------------------------------TCTGGCAAAACGACGCA
droGri2 scaffold_15252:16729554-16729583 - GGGTGAAACTGGC-----------------------------------------------------------------------------------------------------AGTGGGAAGAGCACACA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:4817801-4817896 - GGGTGAAACAGGCAGGTTTGTATGGAATTCCATGAGCT-TCAAAGTAATGCTTCTAACTCTGTGGTTTTTC-ATATTTCCCAGTGGCAAGAGCACCCA
droSim1 chr2L:4687585-4687681 - GGGTGAAACAGGCAGGTTTGTATGGAATTCCAGAAGCT-CCAAAGTAATCTTTCTAACTCTGCGGGTTTTCTATCTTTCCCAGTGGCAAGAGCACCCA
droSec1 super_5:2913658-2913754 - GGGTGAAACAGGCAGGTTTGTATGGAATTCCAGGTGTT-CCAAAGTAATCTTTCTAGCTCTGTGGTTTTTTCATATTTCCCAGTGGCAAGAGCACCCA
droYak2 chr2L:4827662-4827759 - GGGTGAAACAGGCAGGTTTGTTTGGAACTCCACAAGATTTCAAGGTATTCCTTCTAACTCTGTGGTTTTTCCACATTTTCCAGTGGGAAAAGCACCCA
droEre2 scaffold_4929:4898740-4898837 - GGGTGAAACAGGCAGGTGTGTATGCAATTCCAAAAGGTCTCAATGTATTCCTTCTAACTCTGTGGTTTTTCTATATTTCCCAGTGGCAAGAGCACCCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGGTGAAACAGGCAGGTTTGTATGGA---ATTCCAGAAGCTCCAAAGTAATCTTTCTAACTCTGCGGGTTTTCTATC-----TTTCCCAGTGGCAAGAGCACCCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GGGCGAAACAGGAAGGTGAGTGAGAAGCAAATATGTATGCCCCA-AGAAATCCTAACGA------------TC-ATATTTTCCCCTTCAGCGGCAAGAGCACACASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-15.5,  p-value=0.009901 dG=-14.5,  p-value=0.009901

droSim1

dG=-10.8,  p-value=0.009901 dG=-10.8,  p-value=0.009901 dG=-10.8,  p-value=0.009901 dG=-10.8,  p-value=0.009901 dG=-10.5,  p-value=0.009901

droSec1

dG=-11.9,  p-value=0.009901 dG=-11.5,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-10.9,  p-value=0.009901

droYak2

dG=-14.8,  p-value=0.009901 dG=-14.8,  p-value=0.009901 dG=-14.4,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-14.3,  p-value=0.009901

droEre2

dG=-3.7,  p-value=0.019802 dG=-3.5,  p-value=0.019802 dG=-3.4,  p-value=0.009901 dG=-3.3,  p-value=0.009901 dG=-3.1,  p-value=0.009901 dG=-2.3,  p-value=0.009901

droAna3

dG=-4.3,  p-value=0.009901 dG=-3.3,  p-value=0.009901

dp4

dG=-3.6,  p-value=0.009901 dG=-3.4,  p-value=0.009901 dG=-3.2,  p-value=0.009901 dG=-3.0,  p-value=0.009901 dG=-2.9,  p-value=0.009901

droPer1

dG=-3.6,  p-value=0.009901 dG=-3.4,  p-value=0.009901 dG=-3.2,  p-value=0.009901 dG=-3.0,  p-value=0.009901 dG=-2.9,  p-value=0.009901

droWil1

dG=-6.4,  p-value=0.009901 dG=-6.4,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-5.7,  p-value=0.009901 dG=-4.7,  p-value=0.009901

droVir3

dG=0.0,  p-value=1.0

droMoj3

dG=0.0,  p-value=1.0

droGri2

dG=0.0,  p-value=1.0

Generated: 03/07/2013 at 05:30 PM