Secondary structure and small RNA-seq evidence for dme-mir-288

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:20618351-20618477 - TGGAATTCCGGGT-------------------GCC------GGCCATGTCGTAATTAGCGGAGCACGGCATC-GCCGGCGATAATTAATGACGGTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-ACCTCCCAAT
droSim1 chr2L:20181621-20181747 - TGGAATTCCGGGT-------------------GCC------GGTCATGTCGTAATTAGCGGAGCACGGCATT-GCCGGCGATAATTAATGACGGTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-ACCTCCCAGT
droSec1 super_18:498537-498663 - TGGAATTCCGGGT-------------------GCC------GGTCATGTCGTAATTAGCGGAGCACGGCATT-GCCGGCGATAATTAATGACGGTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-ACCTCCCAGT
droYak2 chr2R:6966481-6966606 - TGGAATTCCGGGT-------------------GCC------GGTCATGTCGTAATTAGCGGAGCACGGCGTT-GCCGGCGATAATTAATGACGGTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCACAGGC-ACCTCCA-GT
droEre2 scaffold_4845:3835093-3835218 + TGGAATTCCGGGT-------------------GCC------GGTCATGTCGTAATTAGCGGAGCTCGGCGTT-GCCGGCGATAATTAATGACGGTGGTCACGTTGGTTTCATGTCGATTTCATTTCAGGACACGGCCGCAGGC-GCCTCCA-CT
droAna3 scaffold_12916:7118734-7118858 - AAAAGTCCGGGGT-------------------CCA------GGTCATGTCGTAATTAGCAGGGCACAGAATT-GCCGGCGATAATTAATGACGTTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-TCCACCCA--
dp4 chr4_group3:7696584-7696728 + GGGAGGTCAGAGAGCTAGAGGGGGGGCCAGGCGCC-----TGGCCATGTCGTAATTAGCAGGGTACAGCGTT-GCCGGCGATAATTAATGACGTTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-AGG--CAGAC
droPer1 super_1:9142351-9142488 + CAGAAAGCTA-------GAGGGGGGGCCAGGCGCC-----TGGCCATGTCGTAATTAGCAGGGTACAGCGTT-GCCGGCGAAAATTAATGACGTTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-AGG--CAGAC
droWil1 scaffold_180708:2031441-2031569 - TGGCCGGCTGACT-------------------CCC------CCTCAGGTCGTAATTAGCAGCGCACAACATTCGTCGGCGATAATTAATGACGTTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGCCAGCTCTGATG
droVir3 scaffold_12963:13472850-13472962 + C----------------------------------------AGCCGCGTCGTAATTAGCTGTGCACAACGTT-GCTGGCGATAATTAATGACTTTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-AGTTCCTGTG
droMoj3 scaffold_6500:24709786-24709910 - G-----TCCAG---------------------GCAGGACATGGACGCGTCGTAATTAGCTGTGCACAGCGTT-GCTGGCGATAATTAATGACGTTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-AGTTCCT-GT
droGri2 scaffold_15126:6391659-6391788 - TTGTGTCCTGG----------------------CAGGACATGGCCGTGTCGTAATTAGCTGTGCAGAACGTA-GCTGGCGATAATTAATGACGTTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGC-AGTTCCTGTG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:20618351-20618477 - TGGAATTCCGGGTGCCGGCCATGTCGTAATTAGCGGAGCACGGCATCGCCGGCGATAATTAATGACGGTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGCACCTCCCAAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TGGAATTCCGGGTGC--------------------CGGTCATGTCGTAATTAGCGGAGCACGGCATTGCCGGCGATAATTAATGACGGTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGCACCTCCCAGTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GGGAGGTCAGAGAGCTAGAGGGGGGGCCAGGCGCCTGGCCATGTCGTAATTAGCAGGGTACAGCGTTGCCGGCGATAATTAATGACGTTGGTCACGTTGGTTTCATGTCGATTTCATTTCATGACACGGCCGCAGGCA--GGCAGACSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-45.3,  p-value=0.009901 dG=-45.0,  p-value=0.009901 dG=-45.0,  p-value=0.009901 dG=-44.9,  p-value=0.009901 dG=-44.6,  p-value=0.009901

droSim1

dG=-42.6,  p-value=0.009901 dG=-42.3,  p-value=0.009901 dG=-42.3,  p-value=0.009901 dG=-42.2,  p-value=0.009901 dG=-41.9,  p-value=0.009901

droSec1

dG=-42.6,  p-value=0.009901 dG=-42.3,  p-value=0.009901 dG=-42.3,  p-value=0.009901 dG=-42.2,  p-value=0.009901 dG=-41.9,  p-value=0.009901

droYak2

dG=-43.3,  p-value=0.009901 dG=-43.0,  p-value=0.009901 dG=-42.8,  p-value=0.009901 dG=-42.7,  p-value=0.009901 dG=-42.5,  p-value=0.009901

droEre2

dG=-43.2,  p-value=0.009901 dG=-43.1,  p-value=0.009901 dG=-42.9,  p-value=0.009901 dG=-42.9,  p-value=0.009901 dG=-42.9,  p-value=0.009901

droAna3

dG=-35.4,  p-value=0.009901 dG=-35.4,  p-value=0.009901 dG=-35.4,  p-value=0.009901 dG=-34.8,  p-value=0.009901 dG=-34.7,  p-value=0.009901

dp4

dG=-44.7,  p-value=0.009901 dG=-44.4,  p-value=0.009901 dG=-44.1,  p-value=0.009901 dG=-43.9,  p-value=0.009901 dG=-43.9,  p-value=0.009901 dG=-43.9,  p-value=0.009901

droPer1

dG=-43.9,  p-value=0.009901 dG=-43.8,  p-value=0.009901 dG=-43.6,  p-value=0.009901 dG=-43.4,  p-value=0.009901 dG=-43.1,  p-value=0.009901

droWil1

dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droVir3

dG=-29.8,  p-value=0.009901 dG=-29.5,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-29.3,  p-value=0.009901 dG=-29.3,  p-value=0.009901 dG=-23.3,  p-value=0.009901

droMoj3

dG=-34.6,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.1,  p-value=0.009901 dG=-32.0,  p-value=0.009901

droGri2

dG=-44.9,  p-value=0.009901 dG=-44.9,  p-value=0.009901 dG=-44.7,  p-value=0.009901 dG=-44.6,  p-value=0.009901 dG=-44.5,  p-value=0.009901 dG=-38.4,  p-value=0.009901

Generated: 03/07/2013 at 05:20 PM