Secondary structure and small RNA-seq evidence for dme-mir-4958

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:15974940-15975104 - GTCCG------------------------------------A------ACCGTACGATCTCT--------------------------------GGCAGCTGCAGTTCCGTTT------CCGGAGCGGGATCTGGAACGGGCTCTGGTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTACCGCTCCAGGTCCCGTTCCCGGAAACGGTGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droSim1 wgm54c09.g1:392-557 + GTCCG------------------------------------A------ACCGCACGATCTCT--------------------------------GGCAGCTGCAGTTCCGTTT------CCGCAGCGGGATCTGGGACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCAGGTCCCGTACCCGGAAGCGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droSec1 super_47:33133-33297 - GTCCG------------------------------------A------ACCGTACGATCTCT--------------------------------GGCAGCTGCAGTTCCGTTT------CCGCAGCGGGATCTGGCACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCATGTCCCGTACCCGGAAACGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droYak2 chrX:10123735-10123899 - GTCCA------------------------------------A------ATCCCACGATCTCT--------------------------------GGCAGCTGCAGTTCCGTTT------CCGCAGCGGGTTCTGGAACGGGCTCTGGTTCTGGATCCGGATCCAATATGGCATCCGGTCCTGGTACCGCTCCAGTTCCCGTACCCGGAAACGGTGCCACCGCCAATGCAGCTGCAGCGGCCTTCA
droEre2 scaffold_4690:11103030-11103194 + GTCCA------------------------------------A------ATCCCACGATCTCT--------------------------------GGCAGCTGCAGTTCTGTTT------CCGGAACGGGTTCTGGAACGGGCTCTGGTTCGGGATCCGGATCCAATCTGGCACCCGGTCCTGGTACTGCTCCAGTTCCCGTACCCGGTAACGGTGGCACCGCCAATGCAGCTGCAGCGGCATTCA
droAna3 scaffold_13165:312527-312640 - GCATA------------------------------------A------GCCACATGGACTCT--------------------------------G---------------------------------------------------------GATCAGGCTCCGTATCTGCGTCAATTTTGGGCACCGGTCCAGGCCCTTTACATGGAAATAGTGCGACCTCGAATGTCTCTTCTGCACCCTTTA
dp4 chrXL_group1e:9575758-9575916 - GCCCC------------------------------------A------ATCCCAATGCCAGC-----------------------------AACGGCAGCTGTGGCTCCGCCTCTGCCTCCGGTTCGTCCAGTGGCTCG-GCACCGGCTCCGGCTCAGGGTCAGACTCAGGCCACGACTCAGGCACCG-----------ACTCACGGCAACACTTCGG---CCGGTGGCACAGCCTCGGCGTACT
droPer1 super_22:633193-633346 + GCCCC------------------------------------A------ATCCCAATGCCAGC-----------------------------AACGGCAGCTGTGGCTCCGCCT------CCGGTTCGTCCAGTGGCTCGGCACCGGTTCCGGGCTCAGGGTCAGACTCAGGCCACGACTCAGGCACC-----------AGCTCACGGCAACACTTCGG---CCGGTGGCACAACCTCGGCGTACT
droWil1 scaffold_181096:10624772-10624892 + CTGCATCATCGGCATCGCCAACTTATCAGAAGGGCAGTCCGAATCCAAATCCCAAT---------------------CTGAATGCAAATGCAACGGC--------------------------------------------------------------------------T------------------------------GGTGGCTCTGGAGCCAGTTCATCTGCTGCCACCGCTGCCTTTA
droVir3 scaffold_12472:523224-523310 + GCCCG------------------------------------A------ATCCCAATGGCGGT--------------------------------GGCTCCAGCGGTGCC------------------------------------------------------------------------------------AGTCTATCTGGCAGTAACAATGTGACTGCCACCGCTACAGCCGCCGCCTTTG
droMoj3 scaffold_6308:2944361-2944510 - GCCCG------------------------------------A------ATCCCAATGGCGGCGGCAGCGGCGCCGGTGG--------------------CGGTGGCGGTGCCGCTGCTGCTGGCTCCAACGGTGGC------------------------GGAAGTCT---------CTCGGGCAGCAGCAGCAGCAATGCAGCCACAGCCAATGCTACAGCCACCGCCGGTGGCGCGGGCTTTG
droGri2 scaffold_15203:4433131-4433217 - GCCCG------------------------------------A------ATCCCAATGGCTGT--------------------------------GTCTCCAGCGGTGCC------------------------------------------------------------------------------------AGTCTCTCTGGCAGCAACACTGTGACTGCCACCGCTACTGCCGCCGCCTTTG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:15974940-15975104 - GTCCGAACCGTACGATCTCTGGCAGCTGCAGTTCCGTTTCCGGAGCGGGATCTGGAACGGGCTCTGGTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTACCGCTCCAGGTCCCGTTCCCGGAAACGGTGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droSim1 wgm54c09.g1:392-557 + GTCCGAACCGCACGATCTCTGGCAGCTGCAGTTCCGTTTCCGCAGCGGGATCTGGGACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCAGGTCCCGTACCCGGAAGCGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droSec1 super_47:33133-33297 - GTCCGAACCGTACGATCTCTGGCAGCTGCAGTTCCGTTTCCGCAGCGGGATCTGGCACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCATGTCCCGTACCCGGAAACGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droYak2 chrX:10123735-10123899 - GTCCAAATCCCACGATCTCTGGCAGCTGCAGTTCCGTTTCCGCAGCGGGTTCTGGAACGGGCTCTGGTTCTGGATCCGGATCCAATATGGCATCCGGTCCTGGTACCGCTCCAGTTCCCGTACCCGGAAACGGTGCCACCGCCAATGCAGCTGCAGCGGCCTTCA
droEre2 scaffold_4690:11103030-11103194 + GTCCAAATCCCACGATCTCTGGCAGCTGCAGTTCTGTTTCCGGAACGGGTTCTGGAACGGGCTCTGGTTCGGGATCCGGATCCAATCTGGCACCCGGTCCTGGTACTGCTCCAGTTCCCGTACCCGGTAACGGTGGCACCGCCAATGCAGCTGCAGCGGCATTCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GTCCGAACCGCACGATC---TCTGGCAGCTGCAGTTCCGTTTCCGCAGCGG-----------GATCTGGGACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCAGGTCCCGTACCCGGAAGCGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GCCCCAATCCCAATGCCAGCAACGGCAGCTGTGGCTCCGCCTCTGCCTCCGGTTCGTCCAGTGGCTCGGCACCGGCTCCGGCTCAGGGTCAGACTCAGGCCAC------GACTCAGGCACCGACTCA-----------CGGCAAC---ACTTCGGCCGGTGGCACAGCCTCGGCGTACTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-42.0,  p-value=0.009901 dG=-41.9,  p-value=0.009901 dG=-41.5,  p-value=0.009901 dG=-41.3,  p-value=0.009901 dG=-41.3,  p-value=0.009901

droSim1

dG=-33.0,  p-value=0.009901 dG=-32.9,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.4,  p-value=0.009901 dG=-32.2,  p-value=0.009901

droSec1

dG=-28.9,  p-value=0.009901 dG=-28.9,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.1,  p-value=0.009901 dG=-28.1,  p-value=0.009901

droYak2

dG=-38.3,  p-value=0.009901 dG=-38.2,  p-value=0.009901 dG=-38.1,  p-value=0.009901 dG=-37.9,  p-value=0.009901 dG=-37.8,  p-value=0.009901

droEre2

dG=-41.9,  p-value=0.009901 dG=-41.9,  p-value=0.009901 dG=-41.7,  p-value=0.009901 dG=-41.7,  p-value=0.009901 dG=-41.1,  p-value=0.009901

droAna3

dG=-10.0,  p-value=0.009901 dG=-9.7,  p-value=0.009901 dG=-9.5,  p-value=0.009901 dG=-9.0,  p-value=0.009901

dp4

dG=-19.9,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.4,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.1,  p-value=0.009901

droPer1

dG=-20.9,  p-value=0.009901 dG=-20.6,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.2,  p-value=0.009901 dG=-20.1,  p-value=0.009901

droWil1

dG=0.0,  p-value=1.0

droVir3

dG=-1.5,  p-value=0.009901

droMoj3

dG=-14.2,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-13.4,  p-value=0.009901 dG=-11.0,  p-value=0.009901

droGri2

dG=-1.5,  p-value=0.009901

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