Secondary structure and small RNA-seq evidence for dme-mir-4952

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:18306519-18306675 + CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droSim1 chr3R:18115675-18115831 + CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droSec1 super_0:18660821-18660977 + CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATATTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGATTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCAGTCTACGTGCCGCCCACCAAGCA
droYak2 chr3R:19151970-19152126 + CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGAAGCGGAGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droEre2 scaffold_4820:9770831-9770987 - CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGAAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droAna3 scaffold_12911:5347592-5347748 + CTCCGGCGAGTGGCTATCCGGGTGCCCTGGACGATCTGATCTTCTCGGGAGCGGGATCCGGGTGCCGGGGCGATGACGAGGACGAGTGCACGCCACCCTTCGAGTCGGGCAGCGGGGACGACCTGATCACTCCGGTGTATGTACCGCCCACCAAGCA
dp4 chr2:13773155-13773311 - CGCCGGCCAGCGGCTATCCCGGCACCATTGACGATCTGATCTTCTCCGGGGCCGGGTCCGGGTGCCGCGGCGACGACGAGGACGAGTGCACACCGCCCTTCGAGTCGGGCAGCGGCGATGACCTCATCACGCCCGTGTATGTGCCACCCACCAAGCA
droPer1 super_0:6673715-6673871 + CGCCGGCCAGCGGCTATCCCGGCACCATTGACGATCTGATCTTCTCCGGGGCCGGGTCCGGGTGCCGCGGCGACGACGAGGACGAGTGCACACCGCCCTTCGAGTCGGGCAGCGGCGATGACCTCATCACGCCCGTGTATGTGCCACCCACCAAGCA
droWil1 scaffold_181089:2782020-2782176 + CGCCGGCCAGTGGCTATCCTGGGGCCATAGATGATCTTATATTCTCCGGTGCCGGATCCGGTTGTCGCGGCGACGATGAAGACGAATGTACGCCGCCCTTCGAGTCGGGCAGTGGAGATGATCTAATCACACCTGTCTATGTGCCTCCGACAAAACA
droVir3 scaffold_12822:645540-645696 - CGCCTGCGAGCGGCTATCCGGGCGCCATAGACGATCTGATCTTCTCCGGGGCCGGGTCCGGTTGTCGCGGCGACGACGAGGACGAATGCACGCCCCCCTTCGAGTCGGGCAGCGGGGATGACCTAATAACGCCCGTCTATGTGCCGCCCACCAAGCA
droMoj3 scaffold_6540:33300209-33300365 - CGCCGGCTAGTGGCTATCCGGGCGCCATAGACGACCTGATCTTCTCCGGAGCCGGATCTGGGTGTCGCGGCGACGACGAGGATGAATGCACGCCGCCCTTCGAGTCGGGCAGTGGGGATGACCTGATCACACCCGTCTATGTGCCGCCCACCAAACA
droGri2 scaffold_15074:3142694-3142850 + CGCCGGCGAGTGGTTATCCGGGTGCGATAGACGATCTGATCTTCTCCGGTGCGGGATCCGGGTGTCGCGGCGACGATGAGGACGAATGCACGCCGCCCTTCGAGTCGGGCAGCGGGGATGATCTAATTACGCCCGTCTATGTGCCACCCACCAAACA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:18306519-18306675 + CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droSim1 chr3R:18115675-18115831 + CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droSec1 super_0:18660821-18660977 + CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATATTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGATTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCAGTCTACGTGCCGCCCACCAAGCA
droYak2 chr3R:19151970-19152126 + CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGAAGCGGAGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA
droEre2 scaffold_4820:9770831-9770987 - CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGAAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGCCGGCGAGTGGTTATCCGGGTGCGCTGGACGATCTGATCTTCTCGGGAGCCGGATCCGGATGTCGCGGCGACGACGAGGACGAGTGCACGCCGCCATTCGAATCGGGTAGCGGGGATGATCTCATAACACCGGTCTACGTGCCGCCCACCAAGCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CGCCGGCCAGCGGCTATCCCGGCACCATTGACGATCTGATCTTCTCCGGGGCCGGGTCCGGGTGCCGCGGCGACGACGAGGACGAGTGCACACCGCCCTTCGAGTCGGGCAGCGGCGATGACCTCATCACGCCCGTGTATGTGCCACCCACCAAGCASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-28.8,  p-value=0.009901

droSim1

dG=-28.8,  p-value=0.009901

droSec1

dG=-28.2,  p-value=0.009901

droYak2

dG=-28.0,  p-value=0.009901

droEre2

dG=-28.0,  p-value=0.009901

droAna3

dG=-20.5,  p-value=0.009901 dG=-19.8,  p-value=0.009901 dG=-19.8,  p-value=0.009901 dG=-19.8,  p-value=0.009901 dG=-19.7,  p-value=0.009901

dp4

dG=-31.8,  p-value=0.009901 dG=-31.7,  p-value=0.009901 dG=-31.6,  p-value=0.009901 dG=-31.5,  p-value=0.009901 dG=-31.0,  p-value=0.009901 dG=-23.9,  p-value=0.009901

droPer1

dG=-31.8,  p-value=0.009901 dG=-31.7,  p-value=0.009901 dG=-31.6,  p-value=0.009901 dG=-31.5,  p-value=0.009901 dG=-31.0,  p-value=0.009901 dG=-23.9,  p-value=0.009901

droWil1

dG=-31.3,  p-value=0.009901 dG=-30.6,  p-value=0.009901 dG=-30.5,  p-value=0.009901 dG=-30.5,  p-value=0.009901 dG=-30.5,  p-value=0.009901

droVir3

dG=-26.7,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-22.9,  p-value=0.009901

droMoj3

dG=-25.4,  p-value=0.009901

droGri2

dG=-26.9,  p-value=0.009901 dG=-26.1,  p-value=0.009901

Generated: 03/07/2013 at 05:52 PM