Secondary structure and small RNA-seq evidence for dme-mir-4978

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:9893349-9893526 - CGGAAAAG-------------CCAA-GGCGGAC---------------------------------------TTTCCAC------------------------------------TTTT----------CGTTTGG------------C-----TGGCCTGGAAAAGCTCTCTT---------TCTCTAT-TG------------CCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC----CATCGAAAAGCCTGGCAAG----------------------------------------CACACAGCTCGCACAAATTTTC
droSim1 chr2R:8329883-8330063 - CGGAAAAT-------------CCAA-GGCGCAC---------------------------------------TTTCCAC------------------------------------CTTTCCA-------CGTCTGG------------C-----TGGCCTGGAAAAGCTCTCTT---------TCTCTAT-TG------------CCTCTATGGCTCGGCCGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC----CATCGAAAAGCCTGGCAAG----------------------------------------CGCACAGCTCGCACAAATTTTC
droSec1 super_1:7418494-7418674 - CGGAAAAG-------------CCAA-GGCGCAC---------------------------------------TTTCCAC------------------------------------CTTTCCA-------CGTCTGG------------C-----TGGCCTGGAAAAGCTATCTT---------TCTCTAT-TA------------CCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTCCG---AGCCAAAAAC----CATCGAAATGCCTGGCAAG----------------------------------------CACACAGCTCGCACAAATTTTC
droYak2 chr2R:7060227-7060403 + CGGAAAAG-------------CCAA-GGTGGAC---------------------------------------TTTCCAC------------------------------------TTTT----------CGTTTGT------------C-----TGGCCTGGAAAAGCTCTCTT---------TCTCTATT--------------CCTCTATGGCTCGCCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC----CATCGAATAGCCCGGCAAG----------------------------------------CACACAGCTCGCACAAATTTTC
droEre2 scaffold_4845:15928216-15928392 + CTGAAAAG-------------CCAA-GGCGGAC---------------------------------------TTTCCAC------------------------------------TTTT----------CGTCTGG------------C-----TGGCCTGGAAAAGCTCTCTT---------TCTCTATG--------------CCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC----CATCGAATAGCCGTGCAAG----------------------------------------CACACAGCTCGCACAAATTTTC
droAna3 scaffold_13266:6006643-6006792 + -------------------------------AC---------------------------------------TTTCCAC------------------------------------TC---------------------------------------GCTGGAAAAAGCTTTCAT------------CCATTCCGGTTGCAACTTGCCACT------C---GACTCTGGGCTCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAACCGAGCCACCGAAA-CTGGTCAAG----------------------------------------T----AGTACGCACAAATTCAA
dp4 chr3:11241780-11242024 + CGAATGAG-------------AGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTC--------------------------------------------CCCAGTGTTTGTGTGT------------GTGGGGCGAACTGGAAAACCTCTGTT---------TT-CCATCCC------------CCTTTTTGG------CGCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAG----CCACCAAAAGCC---CAAGGAGTTGTCGCA-CTCCGGACTACGCATAAAATCCCCCAAAAGCAGAACTCGC----------
droPer1 super_4:6644552-6644788 + CGAATGAG-------------AGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTC--------------------------------------------CCCAGTGTTTGTGTGTGTGTGTGTGTGTGTGTGACGGACTGGAAAACCTCTGTT---------TT-CCATCCC------------CCTTTTTGG------CGCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAG----CCACCAAAAGCC---CAAGGAGTTGTCGCA-CTC-------------------------CGG--ACTACGCATAAAAT---
droWil1 scaffold_180745:1743803-1743968 + CGGAAAAG-------------CCAA-AGCATAT---------------------------------------AC----------------------------------------------------------TAGA------------T-----TGTACTGGAAAAGCTCTGCAACCAAAAAATT-GCGTCGG------------TCATCTCTG------AGGTCTGTGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTTGGAGAGCC----------CACCACGTTGA-----AAG---------GA-GTA-------------------------CGTACAATGAAAAAAATTGGCC
droVir3 scaffold_12875:2042187-2042370 + CAGGAAAAGCATGCGGAAAAGTGCG-TGTATGGAAAAGCAGCAAT---------------------------CGC--AAACGCCTGGAAAAGCGACCGACTG----------------------------------------------------------------CCGCCGTT---------TG-CCA------CAGCA---C-GCTTTTTCG------ATATCTGTGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTAG---AGCTAG----------TTCAAGGCA----CACGCAGTTCGC--AGC---------------------------TC-------------CACTGTG
droMoj3 scaffold_6496:23220919-23221095 - TGGAAAAG-------------CGCG-TGTGGAGACAAGCAGCGAC---------------------------CGTACGCCCGCCTGGAAAGCCGACTGCCCGCCAGCATTTGTAGCTC---------------------------------------------------------------------------TGTAGCA-----GCTTGTTGG------ATAGCTGAGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTAG---AGCTAG----------TTCAAGGCACACGCAGC----------------------------------------TCCACAGCGGGCACAA------
droGri2 scaffold_15112:4157535-4157620 + CGGAAAAG-------------C-----GCAAAA---------------------------------------TTTGCGA------------------------------------CACT----------CGCTCAA------------C-----TGGC----------------------------------------------------------------AGCTGGGCGCCTAATCCAAACTGCGAGAAAGATCCGCTTTTAG---AGCTA------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:9893349-9893526 - CGGAAAAGCCAAGGCGGACTTTCCACTTTT---CGTTTGGCTGGCCTGGAAAAGCTCTCTTTCTCTATTGCCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAAAAGCCTGGCAAGCACACAGCTCGCACAAATTTTC
droSim1 chr2R:8329883-8330063 - CGGAAAATCCAAGGCGCACTTTCCACCTTTCCACGTCTGGCTGGCCTGGAAAAGCTCTCTTTCTCTATTGCCTCTATGGCTCGGCCGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAAAAGCCTGGCAAGCGCACAGCTCGCACAAATTTTC
droSec1 super_1:7418494-7418674 - CGGAAAAGCCAAGGCGCACTTTCCACCTTTCCACGTCTGGCTGGCCTGGAAAAGCTATCTTTCTCTATTACCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTCCGAGCCAAAAACCATCGAAATGCCTGGCAAGCACACAGCTCGCACAAATTTTC
droYak2 chr2R:7060227-7060403 + CGGAAAAGCCAAGGTGGACTTTCCACTTTT---CGTTTGTCTGGCCTGGAAAAGCTCTCTTTCTCTATT-CCTCTATGGCTCGCCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAATAGCCCGGCAAGCACACAGCTCGCACAAATTTTC
droEre2 scaffold_4845:15928216-15928392 + CTGAAAAGCCAAGGCGGACTTTCCACTTTT---CGTCTGGCTGGCCTGGAAAAGCTCTCTTTCTCTAT-GCCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAATAGCCGTGCAAGCACACAGCTCGCACAAATTTTC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGGAAAATCCAA-GGCGC---------------------------------------ACTTT--CCACCTTTCCACGTCT-----GGCTGGCCTGGAAAAGCTCTCTTTCTCTATTGCCTCTATGGCTCGGCCGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAAAAGCCTGG------------------------------------CAAGCGCACAGCTCGCACAAATTTTCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CGAATGAGAGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTCCCCAGTGTT---TGTGTGTGTGGGGCGAACTGGAAAACCTCTGTTTTCCATCCCCCTTTTTGGC------GCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAAGCCACCAAAAGCCCAAGGAGTTGTCGCACTCCGGACTACGCATAAAATCCCCCAAAAGCAGAACTCGC----------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-35.1,  p-value=0.009901 dG=-34.8,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.2,  p-value=0.009901

droSim1

dG=-35.1,  p-value=0.009901 dG=-34.8,  p-value=0.009901 dG=-34.2,  p-value=0.009901

droSec1

dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.2,  p-value=0.009901

droYak2

dG=-34.5,  p-value=0.009901 dG=-33.6,  p-value=0.009901 dG=-33.5,  p-value=0.009901

droEre2

dG=-35.1,  p-value=0.009901 dG=-34.8,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-33.1,  p-value=0.009901

droAna3

dG=-21.5,  p-value=0.009901 dG=-21.3,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-16.9,  p-value=0.009901

dp4

dG=-34.6,  p-value=0.009901 dG=-34.6,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901 dG=-34.5,  p-value=0.009901

droPer1

dG=-32.7,  p-value=0.009901 dG=-32.7,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-26.8,  p-value=0.009901

droWil1

dG=-27.8,  p-value=0.009901 dG=-27.5,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-26.8,  p-value=0.009901 dG=-23.7,  p-value=0.009901

droVir3

dG=-13.3,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-12.8,  p-value=0.009901 dG=-12.7,  p-value=0.009901 dG=-12.6,  p-value=0.009901

droMoj3

dG=-14.5,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-13.7,  p-value=0.009901

droGri2

dG=-12.0,  p-value=0.009901 dG=-11.5,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-10.6,  p-value=0.009901

Generated: 03/07/2013 at 06:45 PM