Secondary structure and small RNA-seq evidence for dme-mir-1016

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:10120620-10120707 - CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTGATTGGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droSim1 chr2R:8883298-8883385 - CTCCAAGCTTTTCCAGTAAGTACAGAGATGATGTAATGCGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droSec1 super_1:7628246-7628333 - CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTAATGCGTATAT------TCCAAT----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droYak2 chr2R:10057668-10057755 - CTCCAAGCTGTTCCAGTAAGTATAGAGGGGATGTGATGGGTAAAT------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droEre2 scaffold_4845:15723071-15723158 + CTCCAAGCTGTTTCAGTAAGTATAGAGAGGATGTGATGGGCAAAA------TCCAAA----------GTT-----------------CACCTCTCTCCATAC-TTAGTCGTCGAGGGGTTAT
droAna3 scaffold_13266:5804278-5804360 + CTCTAAACTTTTTCAGTGAGTACTTGTAATATA-AATCCATAAA--------TCAAA----------ACT-----------------CACTT-TTTCCA-AC-TTAGTCGCCGTGGTGTGAT
dp4 chr3:17369366-17369470 - CTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATCGTCTGAAACTAATTTCCCTT-----------------CACTTATCCCTGCCCTGCAGTCGTCGCGGCGTCAT
droPer1 super_31:422912-423016 + TTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATTGTCTGAAACTAATGTCCCTT-----------------CACTTATCCCTGCCCTGCAGTCGGCGCGGCGTCAT
droWil1 scaffold_180700:1839743-1839828 + TTCCAAATTGTTCCAGTAAGTTAAAA-----TGATCTAAAATCAT------TTCAAA----------T-T----------GATT---CAATAATCTCTTCCA-TTAGTCGACGCGGTGTCAT
droVir3 scaffold_12875:17586457-17586541 + TTCCAAACTATTTCAGTAAGTAGCA------GGTGCTGAGTGCAT------G----A----TTGTCTCTA----TATCTT--------GATT-----ATCTTTGCAGTCGACGCGGGGTTAT
droMoj3 scaffold_6496:11208550-11208642 + TTCCAAGCTGTTTCAGTAAGTAGAGCACGCATTTCCAGTACCCAACTA----------------TTCGTTACTATATCTG--------TACA-----ATTTTTGTAGTCGACGCGGGGTTAT
droGri2 scaffold_15245:14096515-14096602 - TTCCAAACTGTTTCAGTAAGTGGTAACACA-ACTACTATGTTTGT------GC-AAC----------ATT----------TAATGGACAG-T-----ATCTTTGCAGTCGACGGGGAGTTAT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:10120620-10120707 - CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTGATTGGTAAATTCCAAAGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT
droSim1 chr2R:8883298-8883385 - CTCCAAGCTTTTCCAGTAAGTACAGAGATGATGTAATGCGTAAATTCCAAAGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT
droSec1 super_1:7628246-7628333 - CTCCAAGCTTTTCCAGTAAGTATAGAGAGGATGTAATGCGTATATTCCAATGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT
droYak2 chr2R:10057668-10057755 - CTCCAAGCTGTTCCAGTAAGTATAGAGGGGATGTGATGGGTAAATTCCAAAGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT
droEre2 scaffold_4845:15723071-15723158 + CTCCAAGCTGTTTCAGTAAGTATAGAGAGGATGTGATGGGCAAAATCCAAAGTTCACCTCTCTCCATACTTAGTCGTCGAGGGGTTAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CTCCAAGCTTTTCCAGTAAGTACAGAGATG---------------ATGTAATGCG----TAAATTCCAAAGTTCACCTCTCTCCATACT-TAGTCGTCGAGGGGTTATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CTCAAAGCTCTTCCAGTGAGTACACAATTCAATTCCTCGGCAAGGCTATCGTCTGAAACTAATTTCC---CTTCACTTATCCCTGCCCTGCAGTCGTCGCGGCGTCATSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-20.9,  p-value=0.009901 dG=-20.4,  p-value=0.009901

droSim1

dG=-9.8,  p-value=0.009901 dG=-9.2,  p-value=0.009901 dG=-8.9,  p-value=0.009901

droSec1

dG=-16.5,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.5,  p-value=0.009901

droYak2

dG=-19.3,  p-value=0.009901 dG=-18.4,  p-value=0.009901

droEre2

dG=-19.3,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.4,  p-value=0.009901

droAna3

dG=-6.1,  p-value=0.009901 dG=-5.4,  p-value=0.009901

dp4

dG=-9.5,  p-value=0.009901 dG=-9.1,  p-value=0.009901 dG=-8.74,  p-value=0.009901 dG=-8.5,  p-value=0.009901 dG=-7.6,  p-value=0.009901

droPer1

dG=-10.2,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-9.7,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-8.2,  p-value=0.009901

droWil1

dG=-3.5,  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=-2.7,  p-value=0.009901

droVir3

dG=-9.5,  p-value=0.009901 dG=-9.1,  p-value=0.009901 dG=-8.9,  p-value=0.009901 dG=-8.8,  p-value=0.009901 dG=-8.6,  p-value=0.009901

droMoj3

dG=-1.7,  p-value=0.009901 dG=-1.6,  p-value=0.019802 dG=-1.6,  p-value=0.009901 dG=-1.6,  p-value=0.009901 dG=-1.5,  p-value=0.009901 dG=-1.4,  p-value=0.009901

droGri2

dG=-8.2,  p-value=0.009901 dG=-8.0,  p-value=0.009901 dG=-8.0,  p-value=0.009901 dG=-7.8,  p-value=0.009901 dG=-7.8,  p-value=0.009901 dG=-7.6,  p-value=0.009901

Generated: 03/07/2013 at 04:48 PM