Secondary structure and small RNA-seq evidence for dme-mir-4941

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:16024273-16024406 + CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGATTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG
droSim1 chr3L:15362441-15362574 + CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG
droSec1 super_0:8124906-8125039 + CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAATATGGAGCGCACCG
droYak2 chr3L_random:1624866-1624999 - CACGCTCACGAATCCCATGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCGCCTTCGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGCGTCGACATGCACACGCTCAACAACATGGAGCGCACCG
droEre2 scaffold_4784:18269422-18269555 + CACGCTCACGAATCCCATGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCGCCTTCGGCTTGGACATCGAGGCGGTGGCCGCTGCACTGGGCGTCGACATGCACACGCTCAACAACATGGAGCGCACCG
droAna3 scaffold_13337:16593401-16593534 - CACCCTCACGAACCCCCTGACCGGCGAGGAGATGCGCTTTCTGGAGCTGCTCACGTCCTTCGGCATGGACATCGAGACAGTGGCCACCGCCCTGGGCGTGGATATGCACACGCTGAACAACATGGAGCGGACGG
dp4 chrXR_group8:4268508-4268641 + CACACTGACCAATCCGCTGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCTCGTTCGGACTGGACATCGAGGCGGTGGCGGCGGCCCTGGGCGTCGACATGCACACCCTCAACAACATGGAGCGGACGG
droPer1 super_29:501948-502081 + CACACTGACCAATCCGCTGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCTCGTTCGGGCTGGACATCGAGGCGGTGGCGGCGGCCCTGGGCGTCGACATGCACACCCTCAACAACATGGAGCGGACGG
droWil1 scaffold_181024:787133-787266 + CACATTAACCAATCCACTGACAGGTGAAGAGATGCGTTTCCTTGAGCTGCTCACCTCCTTCGGTTTGGATATTGAGGCAGTGGCAGCGGCGCTTGGCGTCGATATGCATACCCTCAACAATATGGAACGTACCG
droVir3 scaffold_13049:9209848-9209981 + CACGCTAACAAATCCGCTGACCGGCGAGGAGATGCGCTTTCTCGAGCTGCTCACCTCCTTCGGCCTGGACATCGAGGCCGTCGCCGCCGCACTCGGCGTCGATATGCACACCCTGAACAACATGGAACGCACCG
droMoj3 scaffold_6680:6136665-6136798 - CACGCTCACGAATCCGCTGACCGGCGAGGAGATGCGCTTCCTCGAACTGCTCACCTCCTTCGGTCTGGACATCGAAGCCGTGGCCGCAGCACTCGGCGTCGATATGCACACGCTGAACAACATGGAACGAACGG
droGri2 scaffold_15110:4981116-4981249 + CACGCTCACGAATCCGCTAACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCTCATTCGGCTTGGACATTGAGGCGGTGGCAGCAGCGCTGGGTGTCGATATGCACACCCTGAATAACATGGAGCGAACGG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:16024273-16024406 + CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGATTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG
droSim1 chr3L:15362441-15362574 + CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCG
droSec1 super_0:8124906-8125039 + CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAATATGGAGCGCACCG
droYak2 chr3L_random:1624866-1624999 - CACGCTCACGAATCCCATGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCGCCTTCGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGCGTCGACATGCACACGCTCAACAACATGGAGCGCACCG
droEre2 scaffold_4784:18269422-18269555 + CACGCTCACGAATCCCATGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCGCCTTCGGCTTGGACATCGAGGCGGTGGCCGCTGCACTGGGCGTCGACATGCACACGCTCAACAACATGGAGCGCACCG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CACGCTCACCAATCCCATGACCGGCGAGGAGATGCGCTTCCTCGAGCTGCTCACCGCCTTTGGCTTGGACATCGAGGCGGTGGCCGCCGCTCTGGGAGTCGATATGCACACGCTCAACAACATGGAGCGCACCGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CACACTGACCAATCCGCTGACCGGCGAGGAGATGCGCTTCCTGGAGCTGCTCACCTCGTTCGGACTGGACATCGAGGCGGTGGCGGCGGCCCTGGGCGTCGACATGCACACCCTCAACAACATGGAGCGGACGGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-39.0,  p-value=0.009901 dG=-38.5,  p-value=0.009901

droSim1

dG=-34.3,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-33.8,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.3,  p-value=0.009901

droSec1

dG=-34.3,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-33.8,  p-value=0.009901 dG=-33.5,  p-value=0.009901 dG=-33.3,  p-value=0.009901

droYak2

dG=-34.2,  p-value=0.009901 dG=-34.2,  p-value=0.009901 dG=-33.7,  p-value=0.009901 dG=-33.7,  p-value=0.009901 dG=-33.5,  p-value=0.009901

droEre2

dG=-34.3,  p-value=0.009901 dG=-34.3,  p-value=0.009901

droAna3

dG=-22.0,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-19.7,  p-value=0.009901

dp4

dG=-25.2,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.6,  p-value=0.009901

droPer1

dG=-26.4,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.8,  p-value=0.009901

droWil1

dG=-23.3,  p-value=0.009901 dG=-23.3,  p-value=0.009901 dG=-22.9,  p-value=0.009901 dG=-22.8,  p-value=0.009901 dG=-22.8,  p-value=0.009901 dG=-21.1,  p-value=0.009901

droVir3

dG=-24.5,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-20.6,  p-value=0.009901

droMoj3

dG=-17.7,  p-value=0.009901 dG=-17.2,  p-value=0.009901 dG=-16.9,  p-value=0.009901 dG=-16.7,  p-value=0.009901

droGri2

dG=-22.0,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.3,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-21.1,  p-value=0.009901

Generated: 03/07/2013 at 05:36 PM