Secondary structure and small RNA-seq evidence for dme-mir-312

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:16471546-16471641 - AATTAAGTT-TGAAGCGATTTGGTTCGTCACAAGGGCAATTCTGCATT--TTTTAACTAGTATTGCACTTGAGACGGCCTGATTA--CTTTA-----AAACGAATC
droSim1 chr2R:15132834-15132929 - AATTAAGTT-TAAAGCGTTTTGGTTCGTCACAAGGGCAATTCTGCATT--TTTAAACTTGTATTGCACTTGAGACGGCCGAATTA--CTTTA-----AAAAGAATC
droSec1 super_1:14025748-14025843 - AATTAAGTT-TAAAGCGTTTTGGTTCGTCACAAGGGCAATTCTGCATT--TTTAAACTTGTATTGCACTTGAGACGGCCGAATTA--CTTTA-----AAAAGAATC
droYak2 chr2R:12724685-12724781 + AATTGCGTT-TGAAGCGCTTCGGTTCGTCCCAGGAGCAATTCTGCACTA-TTAAAGCTAGTATTGCACTTGAGACGGCCGGATTA--CTTTT-----AAACGAATC
droEre2 scaffold_4845:10618147-10618242 - AATTAAGTT-TGAAGCGCTTCGGTTCGTACCAGGAGCAATTCTGCATT--TTTAAGCTAGTATTGCACTTGAGACGGCCGGATTA--CTTTT-----AAACAAAAC
droAna3 scaffold_13266:4132676-4132765 + TCTACAAT--------TTTCCGGTGCGTCTCTAGTGCAACTCTTGGTTT-TTTATACAAGTATTGCACTTGAGACGGCCGAAATA--TAGTG-----GATCTAAGC
dp4 chr3:8679756-8679828 + G---------------------------------GGCAATACTGTGTTGTATTTCACCAGTATTGCACACCCACTGGCCTGAAAGTGCCTACTGCTGGGTTCAACA
droPer1 gnl|ti|732455623:23-94 + G---------------------------------GGCAATACTGTGTTGTATTTGAACAGTATTGCACACCCACTGGCCTGAAAGTGCCTACTGCTGGGTTCAA--
droWil1 scaffold_180700:3453141-3453235 + CATAAACTCGAAAATTTTTTAGGTTCGTTTAGTCTGCAAATT-GTAAT--ATACGAAAATAATTGCACACTTCACGGCCGGAAAA--GTTCA-----AGTTAAACA
droVir3 scaffold_12875:13669041-13669063 - AGCTATATT-T-----------------------------------------------------------------------------TTCA-----GGCCGTGTC
droMoj3 scaffold_6496:9090603-9090622 - GTCTGCAAT-TTAAGCTTCTT-------------------------------------------------------------------------------------
droGri2 scaffold_15245:17564268-17564358 + AAGCAAATC-TTCAGTTTTTCGGCTGTGGTTAGTGTCAATTCTTTTT---ATTTGACAAGCATTGCACTCTTCACGGCCGGATAA--AT---------GAGGGTCT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:16471546-16471641 - AATTAAGTTT-GAAGCGATTTGGTTCGTCACAAGGGCAATTCTGCATT--TTTTAACTAGTATTGCACTTGAGACGGCCTGATTA--CTTTAAAACGAA-----TC
droSim1 chr2R:15132834-15132929 - AATTAAGTTT-AAAGCGTTTTGGTTCGTCACAAGGGCAATTCTGCATT--TTTAAACTTGTATTGCACTTGAGACGGCCGAATTA--CTTTAAAAAGAA-----TC
droSec1 super_1:14025748-14025843 - AATTAAGTTT-AAAGCGTTTTGGTTCGTCACAAGGGCAATTCTGCATT--TTTAAACTTGTATTGCACTTGAGACGGCCGAATTA--CTTTAAAAAGAA-----TC
droYak2 chr2R:12724685-12724781 + AATTGCGTTT-GAAGCGCTTCGGTTCGTCCCAGGAGCAATTCTGCACTA-TTAAAGCTAGTATTGCACTTGAGACGGCCGGATTA--CTTTTAAACGAA-----TC
droEre2 scaffold_4845:10618147-10618242 - AATTAAGTTT-GAAGCGCTTCGGTTCGTACCAGGAGCAATTCTGCATT--TTTAAGCTAGTATTGCACTTGAGACGGCCGGATTA--CTTTTAAACAAA-----AC
droAna3 scaffold_13266:4132676-4132765 + TCTACA--------ATTTTCCGGTGCGTCTCTAGTGCAACTCTTGGTTT-TTTATACAAGTATTGCACTTGAGACGGCCGAAATA--TAGTGGATCTAA-----GC
dp4 chr3:8679756-8679828 + G---------------------------------GGCAATACTGTGTTGTATTTCACCAGTATTGCACACCCACTGGCCTGAAAGTGCCTACTGCTGGGTTCAACA
droPer1 gnl|ti|732455623:23-94 + G---------------------------------GGCAATACTGTGTTGTATTTGAACAGTATTGCACACCCACTGGCCTGAAAGTGCCTACTGCTGGGTTCA--A
droWil1 scaffold_180700:3453141-3453235 + CATAAACTCGAAAATTTTTTAGGTTCGTTTAGTCTGCAAATT-GTAAT--ATACGAAAATAATTGCACACTTCACGGCCGGAAAA--GTTCAAGTTAAA-----CA
droGri2 scaffold_15245:17564268-17564358 + AAGCAAATCT-TCAGTTTTTCGGCTGTGGTTAGTGTCAATTCTTTTT---ATTTGACAAGCATTGCACTCTTCACGGCCGGATAA--A----TGAGGGT-----CT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AATTAAGTTTAAAGCGTTTTGGTTCGTCACAAGGGCAATTCTGCATT--TTTAAACTTGTATTGCACTTGAGACGGCCGAAT--TACTTTAAAAAGAATC-----SizeHit CountTotal NormTotalGSM343915
Embryo
...........................................................TATTGCACTTGAGACGGCCG..........................20295.00190190
...................TGGTTCGTCACAAGGGCAATTCT...............................................................23225.005050
............................................................ATTGCACTTGAGACGGCCGAA........................2123.5077
............................................................ATTGCACTTGAGACGGCCGA.........................2022.0044
...........................................................TATTGCACTTGAGACGGC............................1820.5011
...................TGGTTCGTCACAAGGGCAATTCTGCA............................................................2620.5011
dp4
--------------------------------GGGCAATACTGTGTTGTATTTCACCAGTATTGCACACCCACTGGCCTGAAAGTGCCTACTGCTGGGTTCAACASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
...........................................................TATTGCACACCCACTGGCCTGA........................222371.007427420
...........................................................TATTGCACACCCACTGGCCTG.........................21250.001001000
...........................................................TATTGCACACCCACTGGCCTGAA.......................23225.0050500
...........................................................TATTGCACACCCACTGGCCT..........................2025.0010100
...........................................................TATTGCACACCCACTGGCCTGAAA......................2423.50770
...............................................................GCACACCCACTGGCCTGAA.......................1920.50110

Secondary Structure

dm3

dG=-19.9,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.0,  p-value=0.009901

droSim1

dG=-20.4,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-19.7,  p-value=0.009901

droSec1

dG=-20.4,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-19.7,  p-value=0.009901

droYak2

dG=-24.5,  p-value=0.009901 dG=-24.5,  p-value=0.009901 dG=-23.7,  p-value=0.009901 dG=-23.7,  p-value=0.009901

droEre2

dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-21.6,  p-value=0.009901

droAna3

dG=-30.2,  p-value=0.009901 dG=-29.2,  p-value=0.009901 dG=-29.2,  p-value=0.009901

dp4

dG=-16.9,  p-value=0.009901 dG=-16.9,  p-value=0.009901 dG=-16.6,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-13.4,  p-value=0.009901

droPer1

dG=-17.4,  p-value=0.009901 dG=-16.4,  p-value=0.009901 dG=-13.9,  p-value=0.009901

droWil1

dG=-14.6,  p-value=0.009901 dG=-14.6,  p-value=0.009901 dG=-14.6,  p-value=0.009901 dG=-14.6,  p-value=0.009901 dG=-14.6,  p-value=0.009901

droVir3

dG=0.0,  p-value=1.0

droMoj3

dG=0.0,  p-value=1.0

droGri2

dG=-24.4,  p-value=0.009901 dG=-24.0,  p-value=0.009901 dG=-23.9,  p-value=0.009901 dG=-23.9,  p-value=0.009901 dG=-23.5,  p-value=0.009901

Generated: 03/07/2013 at 05:16 PM