Secondary structure and small RNA-seq evidence for dme-mir-990

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:12782713-12782828 - TGGGAAAC-----------TGGCGA----ATCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGCTTCGGTGCC-ATTT-----------------------------------------CACCC------------CGAGCACCAAGAGCATCAGACT
droSim1 chr2R:11518341-11518456 - TGGGAAAC-----------TGGCGA----ATCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGCTTCGGTGCC-ATTT-----------------------------------------CACCC------------CGAGCACCAAGAGCATCAGACT
droSec1 super_1:10286785-10286900 - TGGGAAAC-----------TGGCGA----ATCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGCTTCGGTGCC-ATTT-----------------------------------------CACCC------------CGAGCACCAAGAGTATCAGACT
droYak2 chr2R:16191830-16191945 + TGGGAAAC-----------TGGCGA----ATCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGTTTCGGTGCC-ATTT-----------------------------------------CACCC------------CGAACAGCAAGACCATCAGACT
droEre2 scaffold_4845:13064860-13064974 + TGGGTAAC-----------TGGCGA----GTCTG------------CTCTGC-GACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAG--------------CTTTCAGTTTCGGTGCC-ATTT-----------------------------------------CACCC------------CCAGCACCAAGAGCACC-GACT
droAna3 scaffold_13266:13815719-13815830 + TGGGAAAT-----------TGTCGA----AGCCA------------CTTTGC-GACATTCCCCGTTCTGCGTTGGCCCAAGGTGCACGTGGGGCCGACGA----------CTCTCCGCTTCCGGACCCATTG--------------------------------------------------------------CCGAAAATACATTCTTCA
dp4 chr3:6727705-6727891 - TGGGAAAC-----------TGGCGA----GGCG-AGGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGGTTAC--GCCTGAAGCTCCAATTCGGTTACGGT------TTCGGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGACA
droPer1 super_2:6950668-6950854 - TGGGAAAC-----------TGGCGA----GGCG-AGGCGAGGACTCCTCTGC-GACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGGTTAC--GCCTGAAGCTCCAATTCGGTTACGGT------TTCGGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGACA
droWil1 scaffold_180700:6478759-6478837 - TGGGAAATACATCTTCGTTTGGCTTTAGTTTCTC------------TTCTGCGGACATTCAATGTTCTGCGTTTGCCCCAAGCGCACGTGG-------------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_12875:2573949-2574010 + TGGGAAAC-----------TG-CGA----AGCTG------------CTTTGC-GACATTCGACTTGCTGCGTTCGTCGCCGACGCACGTGG-------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6496:22657688-22657749 - TGGGAAAC------------GGCGA----AGCTT------------CTGTGC-GACATTCAACGTTCTGCGTTCGTCGCCGACGCACGTGG-------------------------------------------------------------------------------------------------------------------------
droGri2 scaffold_15112:4702153-4702224 + TGGGAATT-----------TTGCGA----AGCTGCTGCTGTGGCT--GCTGC-GACATTCAACGTTCTGCGTTGGCCGCCGACGCACGTG--------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:12782713-12782828 - TGGGAAACTGGCGAATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGCTTCGGTGCCATTTCACCCCGAGCACCAAGAGCATCAGACT
droSim1 chr2R:11518341-11518456 - TGGGAAACTGGCGAATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGCTTCGGTGCCATTTCACCCCGAGCACCAAGAGCATCAGACT
droSec1 super_1:10286785-10286900 - TGGGAAACTGGCGAATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGCTTCGGTGCCATTTCACCCCGAGCACCAAGAGTATCAGACT
droYak2 chr2R:16191830-16191945 + TGGGAAACTGGCGAATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGTTTCGGTGCCATTTCACCCCGAACAGCAAGACCATCAGACT
droEre2 scaffold_4845:13064860-13064974 + TGGGTAACTGGCGAGTCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCAGCTTTCAGTTTCGGTGCCATTTCACCCCCAGCACCAAGAGCACC-GACT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TGGGAAACTGGCGA-----------ATCTGCTCTGCGACATTCACCGTTCTGAGTTGGCCCCAAGTGCACGTGGGCCA------------------------GCTTTCAGCTTCGG------------------------------TG------CCATTTCACCCCGAGCACCAAGAGCATCAGACTSizeHit CountTotal NormTotalGSM343915
Embryo
.......................................ATTCACCGTTCTGAGTTGGCCC..............................................................................................................................22112.001212
dp4
TGGGAAACTGGCGAGGCGAGGCGAGGACTCCTCTGCGACATTCACCGTTCAGCGTTCGGCCAGCGAGCACGTGGGTTACGCCTGAAGCTCCAATTCGGTTACGGTTTCGGCTACGGCTACGGCTACGGGTACGGCTACGGCTACGGTACATCCTCCACACTAGACGGCGGGTTGAGGGGGTCGGACASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-25.1,  p-value=0.009901 dG=-24.8,  p-value=0.009901

droSim1

dG=-25.1,  p-value=0.009901 dG=-24.8,  p-value=0.009901

droSec1

dG=-25.1,  p-value=0.009901 dG=-24.8,  p-value=0.009901

droYak2

dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901

droEre2

dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901

droAna3

dG=-21.0,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-16.7,  p-value=0.009901

dp4

dG=-36.4,  p-value=0.009901 dG=-36.1,  p-value=0.009901 dG=-35.8,  p-value=0.009901 dG=-35.8,  p-value=0.009901 dG=-35.6,  p-value=0.009901

droPer1

dG=-36.4,  p-value=0.009901 dG=-36.1,  p-value=0.009901 dG=-35.8,  p-value=0.009901 dG=-35.8,  p-value=0.009901 dG=-35.6,  p-value=0.009901

droWil1

dG=-11.5,  p-value=0.009901 dG=-10.7,  p-value=0.009901 dG=-8.7,  p-value=0.009901

droVir3

dG=-9.6,  p-value=0.009901 dG=-9.3,  p-value=0.009901 dG=-9.0,  p-value=0.009901 dG=-8.9,  p-value=0.009901 dG=-8.8,  p-value=0.009901

droMoj3

dG=-9.9,  p-value=0.009901 dG=-9.3,  p-value=0.009901

droGri2

dG=-12.0,  p-value=0.009901 dG=-11.9,  p-value=0.009901 dG=-11.4,  p-value=0.009901 dG=-11.0,  p-value=0.009901

Generated: 03/07/2013 at 07:21 PM