Secondary structure and small RNA-seq evidence for dme-mir-4975

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:2594652-2594793 - TAGAACTGGAAATCTGGGCAAATAA--AGCACGTTGCTCCCTGTTTACTTGGGTTTTCTG----------------------------TTCATTTCGCCTATCGAACGTTGAACTTAAAAAGCCACGATCAGTTGTTTAACATACAGATATCTCTGTACACAAGAAGATTCA
droSim1 chr2R:1414726-1414867 - TAGAACTGAAAGTCTCGGCAAATAG--AGCACGTTGCTCCCTGTTTACTCAGGTTCCCTG----------------------------TTCATTTCGCCTATCGAACGTTGAACTTCAAGAGCCACGATCAGTTGGTAAAGATACAGATATCTCTGTATACTAGAAGATACA
droSec1 super_1:259050-259190 - TAGAACTGGAAGTCTCGGCAAATAA--AGCACGTTGCTCCCTGTTTACTCAGGTTCCCTG----------------------------TTCAGTTCGCCTATCGAACGTTGAACTTCAAGAGCCACGATCAGTTGGT-AGGATACAGATATCTCTGTATACTAGAAGATACA
droYak2 chr2L:15337545-15337682 - TAGAAATGAAAATCTCGGCAAGTAA--AGCACGTTGCTCCATGTTTACTCAGGTTTGCTG----------------------------TTTATATCGCCTATCAAACGTTGAACTTGA---ATCACGATCAGTTGGTCAACATACATATATTTGT-CACACTAGGTGATCCA
droEre2 scaffold_4929:19950710-19950840 + TAGGACTGCAGATCCCGGCAACTAA--AGCACGTTGCTCCCAGTTTACTCAGGTTCGCTG----------------------------TTTATATCGCCTATCGAGCGTTGAACTTGAGGAGCCACGATCAGTTGGTCAGCATACATATA-----------AAGATGATCCA
droAna3 scaffold_13266:18414789-18414883 + AAGTCTA----ATTTCGGT------------------GCCTTGTTTACTTCGCTCTCCGGCGGAGAGCTGCAGTGCACGAGGTGTCTAATCGGCCAGCCCATAGAGCAATGAACTT--------------------------------------------------------
dp4 chr3:859167-859237 - TAGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTT-TCTGTTTACGTTACTTCTCGT----------------------------CCCGTCCCGTCT------------------------------------------------------------------------
droPer1 super_2:1035040-1035110 - TAGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTT-TCTGTTTACGTTACTTCTCGT----------------------------CCCGTCCCGTCT------------------------------------------------------------------------
droWil1 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:2594652-2594793 - TAGAACTGGAAATCTGGGCAAATAAAGCACGTTGCTCCCTGTTTACTTGGGTTTTCTGTTCATTTCGCCTATCGAACGTTGAACTTAAAAAGCCACGATCAGTTGTTTAACATACAGATATCTCTGTACACAAGAAGATTCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TAGAACTGAAAGTCTCGGCAAATA--GAGCACGTTGCTCCCTGTTTACTCAGGTTCCCTGTTCATTTCGCCTATCGAACGTTGAACTTCAAGAGCCACGATCAGTTGGTAAAGATACAGATATCTCTGTATACTAGAAGATACASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TAGCACAGAAAATCTCGGCAATCAAAAAACACGCCGTTT-CTGTTTACGTTACTTCTCGTCCCGTCCCGTCT------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-12.7,  p-value=0.009901 dG=-12.5,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-12.0,  p-value=0.009901

droSim1

dG=-13.8,  p-value=0.009901 dG=-13.4,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-13.1,  p-value=0.009901

droSec1

dG=-16.5,  p-value=0.009901 dG=-16.5,  p-value=0.009901 dG=-16.4,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-16.1,  p-value=0.009901

droYak2

dG=-11.8,  p-value=0.009901 dG=-11.8,  p-value=0.009901 dG=-11.2,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-10.2,  p-value=0.009901

droEre2

dG=-20.2,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-17.9,  p-value=0.009901

droAna3

dG=-24.3,  p-value=0.009901 dG=-24.1,  p-value=0.009901 dG=-23.9,  p-value=0.009901 dG=-23.7,  p-value=0.009901 dG=-23.7,  p-value=0.009901 dG=-21.9,  p-value=0.009901

dp4

dG=-1.2,  p-value=0.009901 dG=-1.0,  p-value=0.009901 dG=-0.4,  p-value=0.009901 dG=-0.2,  p-value=0.029703

droPer1

dG=-1.2,  p-value=0.009901 dG=-1.0,  p-value=0.009901 dG=-0.4,  p-value=0.009901 dG=-0.2,  p-value=0.009901

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 06:23 PM