Secondary structure and small RNA-seq evidence for dme-mir-4948

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:26876804-26876940 - GCACTCCCAGTCCCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGCGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT----------------
droSim1 chr3R:26523820-26523956 - GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGTT----------------
droSec1 super_4:5701489-5701625 - GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGTGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT----------------
droYak2 chr3R:27815996-27816132 - GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTGGTGGTGACCACTCCAGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTACCTTGCT----------------
droEre2 scaffold_4820:1105506-1105642 + GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTTGTGGTGACCACTCCAGTACGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTGCCCTGCT----------------
droAna3 scaffold_12911:4046748-4046884 + GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCGTGGGTAATCCGAGTGGTGGTCACTATTCCAGTTCGCTTCTTCTCCTTTTGGGCCCACTCCATGACGCTCTGAACGCGTCCTTGCT----------------
dp4 chr2:271882-272018 + GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT----------------
droPer1 super_7:3056347-3056483 + GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT----------------
droWil1 scaffold_181108:531799-531935 - GCATTCCCAGTCCCGATCATATATATGCGCATAGGTTGAGGCAGGCGTGGCATGTGTAATTCTGGTAGTGGTAACAATTCCCGTTCGTTTACCCGCACGCTGGGCCCAATCCATAATGGATTCCACCCGACCCTGTT----------------
droVir3 scaffold_12855:1470098-1470234 + GCACTCCCAGTCCCGATGATAGACACGCGCAAAGGTGGCTGCGGGCGTGGCGTGCGTAATGCGTGTGGTGGTCACCACGCCAGTGCGTTTGCCTTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC----------------
droMoj3 scaffold_6540:27213622-27213758 + GCACTCCCAGTCCCGATGATAGATCCTTGCATAGGTGGCCGCAGGTGTGGCGTGTGTTATACGCGTGGTAGTCACGACGCCGGTCCGCTTGCCCTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC----------------
droGri2 scaffold_15203:6653367-6653519 - GCACTCCCACCGCCGATCGGCGACATGGGCGTAGAGGGCAGCGGGTGTGGCATGGGTTACCCGCGTTGTGGTCACAAATCCAGTGCGCATGCCATCCACCTGCGCCCAGTTGAATATGTTCTGGACGTGATGTTCCTCCTTGAGAGAGGCACT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:26876804-26876940 - GCACTCCCAGTCCCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGCGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT
droSim1 chr3R:26523820-26523956 - GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGTT
droSec1 super_4:5701489-5701625 - GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGTGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT
droYak2 chr3R:27815996-27816132 - GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTGGTGGTGACCACTCCAGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTACCTTGCT
droEre2 scaffold_4820:1105506-1105642 + GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTTGTGGTGACCACTCCAGTACGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTGCCCTGCT
droAna3 scaffold_12911:4046748-4046884 + GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCGTGGGTAATCCGAGTGGTGGTCACTATTCCAGTTCGCTTCTTCTCCTTTTGGGCCCACTCCATGACGCTCTGAACGCGTCCTTGCT
dp4 chr2:271882-272018 + GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT
droPer1 super_7:3056347-3056483 + GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGTTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-33.3,  p-value=0.009901 dG=-33.0,  p-value=0.009901 dG=-32.7,  p-value=0.009901 dG=-32.5,  p-value=0.009901 dG=-32.4,  p-value=0.009901

droSim1

dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.4,  p-value=0.009901 dG=-34.4,  p-value=0.009901 dG=-34.4,  p-value=0.009901

droSec1

dG=-32.5,  p-value=0.009901 dG=-32.2,  p-value=0.009901 dG=-32.2,  p-value=0.009901 dG=-31.9,  p-value=0.009901

droYak2

dG=-26.4,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-25.9,  p-value=0.009901

droEre2

dG=-26.6,  p-value=0.009901 dG=-26.4,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-26.0,  p-value=0.009901

droAna3

dG=-16.4,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-15.7,  p-value=0.009901 dG=-15.4,  p-value=0.009901

dp4

dG=-20.5,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droPer1

dG=-20.5,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droWil1

dG=-11.1,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-10.9,  p-value=0.009901 dG=-10.7,  p-value=0.009901 dG=-10.7,  p-value=0.009901

droVir3

dG=-29.1,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.5,  p-value=0.009901 dG=-28.4,  p-value=0.009901 dG=-28.2,  p-value=0.009901

droMoj3

dG=-26.7,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-25.7,  p-value=0.009901

droGri2

dG=-21.7,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.3,  p-value=0.009901 dG=-21.2,  p-value=0.009901

Generated: 03/07/2013 at 05:46 PM