Secondary structure and small RNA-seq evidence for dme-mir-974

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19445696-19445826 + AG----GTCC-AGGTAAGCTCAA-TTGTCACCGGTCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTTCCAA-GAGCAAATATAACTTCATTGGAA-GCTAAGTGGATTTGCCCA-AAT-------CAGCTTGGTATTTAT
droSim1 chrX:15011423-15011546 + GT----A---------AACTCAA-TTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTGGTATTTGCG--TTTCCAA-GAACAAATATAACTTCTTTGAAA-GCTAGGTGGATTTGCCCA-AGT-------CACCTTGGTATTTAT
droSec1 super_8:1728102-1728227 + AG----G-------TAAACTCGA-TTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGCG--TTTCCAA-GAACAAATATAACTTCTTTGAAA-GCTAGGTGGATTTGCCCA-AGT-------CTCCTTGGTATTTAT
droYak2 Unknown GA----AAAC-AGAACCACTGAC-TTAGCACTGGTCATGGCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTCCAAA-AGTCAAATATAACTTTTTTGGAA-GCTACGGGGACTTGTCCA-AGA-------CAGC-----------
droEre2 scaffold_4690:9682437-9682562 + GA----AAAC-AGAACCACTAAC-TCAGCACTGGGCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTCCAAA-AGTCAAATATAACTTTTTTGGAA-GCTACGGGGATTTGCCCA-AGC-------CAACTTGCTG-----
droAna3 scaffold_13417:2478487-2478598 - GG----TTGC-A---ATCCTGGC-TTGGGGTAGGTCATCTCCTCTAAGCGAGCAAAGAAGTAGTATTTGTTTGCTTTTAATGGTCAAATATAACTTTTTTGGAA-GCTACGAGGAGTTGTCC---------------------------
dp4 Unknown -----------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown -----------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181096:7946609-7946719 + AT-----------------TCATTTTTCCAATGGCCATATCCTCTAAGCGAGCAAGAAAGTGGTATTTGTC--TTTGGAA-ATTCAAATATAACTTTTTTGGAA-GCTACAAGGCAATGTCCACAAT-------CAAC-----------
droVir3 scaffold_13042:917533-917679 - ATCCGAATATGAGATTTACCA-ATTATTAACTGGGCATTCCCTCTGAGCGAGCAGAGAAGTATTATTTGCGTGAATCTGA-TATCAAATAAGACTTTTTTGGTTCGCTATGAGGTATTGTTCA-TAAATAAACACGTCTGCCTATATAC
droMoj3 scaffold_6328:2908489-2908614 - TC----A---------------ATCAGACGCTGGGCATTCCCTCTGAGCGAGCAGAGAAGTATTTT-TGCGTGCATCTGA-TATCAAATAAAACTTTTTTGGTT-GCTGCGAGGTATTGTTGA-AATGTAAACGTTGCTCGCTCTCTAC
droGri2 scaffold_15081:2051206-2051247 - CA----------------------------AAGGACATCTTCTGTAAGCGAGCAAAAATATAATATTTGT-------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19445696-19445826 + AG----GTCC-AGGTAAGCTCAA-TTGTCACCGGTCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTTCCAA-GAGCAAATATAACTTCATTGGAA-GCTAAGTGGATTTGCCCA-AAT-------CAGCTTGGTATTTAT
droSim1 chrX:15011423-15011546 + GT----A---------AACTCAA-TTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTGGTATTTGCG--TTTCCAA-GAACAAATATAACTTCTTTGAAA-GCTAGGTGGATTTGCCCA-AGT-------CACCTTGGTATTTAT
droSec1 super_8:1728102-1728227 + AG----G-------TAAACTCGA-TTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGCG--TTTCCAA-GAACAAATATAACTTCTTTGAAA-GCTAGGTGGATTTGCCCA-AGT-------CTCCTTGGTATTTAT
droYak2 Unknown GA----AAAC-AGAACCACTGAC-TTAGCACTGGTCATGGCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTCCAAA-AGTCAAATATAACTTTTTTGGAA-GCTACGGGGACTTGTCCA-AGA-------CAGC-----------
droEre2 scaffold_4690:9682437-9682562 + GA----AAAC-AGAACCACTAAC-TCAGCACTGGGCATGTCCTCCAAGCGAGCAAAGAAGTAGTATTTGTG--TTCCAAA-AGTCAAATATAACTTTTTTGGAA-GCTACGGGGATTTGCCCA-AGC-------CAACTTGCTG-----
droAna3 scaffold_13417:2478487-2478598 - GG----TTGC-A---ATCCTGGC-TTGGGGTAGGTCATCTCCTCTAAGCGAGCAAAGAAGTAGTATTTGTTTGCTTTTAATGGTCAAATATAACTTTTTTGGAA-GCTACGAGGAGTTGTCC---------------------------
droWil1 scaffold_181096:7946609-7946719 + AT-----------------TCATTTTTCCAATGGCCATATCCTCTAAGCGAGCAAGAAAGTGGTATTTGTC--TTTGGAA-ATTCAAATATAACTTTTTTGGAA-GCTACAAGGCAATGTCCACAAT-------CAAC-----------
droVir3 scaffold_13042:917533-917679 - ATCCGAATATGAGATTTACCA-ATTATTAACTGGGCATTCCCTCTGAGCGAGCAGAGAAGTATTATTTGCGTGAATCTGA-TATCAAATAAGACTTTTTTGGTTCGCTATGAGGTATTGTTCA-TAAATAAACACGTCTGCCTATATAC
droMoj3 scaffold_6328:2908489-2908614 - TC----A---------------ATCAGACGCTGGGCATTCCCTCTGAGCGAGCAGAGAAGTATTTT-TGCGTGCATCTGA-TATCAAATAAAACTTTTTTGGTT-GCTGCGAGGTATTGTTGA-AATGTAAACGTTGCTCGCTCTCTAC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
--------GTAAACTCAATTGTCACTGGTCGTGTCCTCCAAGCGAGCAAAGAAGTGGTATTTGCGTTTCCAAGAACAAATATAACTTCTTTGAAAGCTAGGTGGATTTGCCCAAGTCACCTTGGTATTTATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
-----------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-21.2,  p-value=0.009901 dG=-20.2,  p-value=0.009901

droSim1

dG=-26.3,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-25.5,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.3,  p-value=0.009901

droSec1

dG=-26.3,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-25.5,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.3,  p-value=0.009901

droYak2

dG=-23.6,  p-value=0.009901 dG=-23.5,  p-value=0.009901

droEre2

dG=-23.6,  p-value=0.009901 dG=-23.5,  p-value=0.009901

droAna3

dG=-26.1,  p-value=0.009901

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

dG=-20.0,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.0,  p-value=0.009901

droVir3

dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.7,  p-value=0.009901 dG=-28.4,  p-value=0.009901

droMoj3

dG=-23.8,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.4,  p-value=0.009901 dG=-23.2,  p-value=0.009901 dG=-23.1,  p-value=0.009901

droGri2

dG=-0.1,  p-value=0.019802 dG=0.0,  p-value=0.019802 dG=0.1,  p-value=0.009901 dG=0.5,  p-value=0.019802 dG=0.7,  p-value=0.009901

Generated: 03/07/2013 at 07:17 PM