Secondary structure and small RNA-seq evidence for dme-mir-4979

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:19621540-19621679 - GG-AT----GGGAA--A-------TTATACATAGGTG------TTATATCT-AGGCCAAATATATATACTTG--TTCTATGTA---TTAGTTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droSim1 chr2R:18187644-18187778 - GG-AT----GGGAA--A-------CT----ATAGGTA------TTATATCT-AGGCCAAATATATATACTTG--T-CTATGTA---TTAGTTATTTGCAAAGGAATACATGTG-CGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droSec1 super_9:2901906-2902041 - GG-AT----GGGAA--A-------CT----ATAGGTA------TTATATCT-AGGCCAAATATATATACTTG--TTCTATGTA---TTAGTTATTTGCAAAGGAATACATGTG-CGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droYak2 chr2R:19599592-19599718 - TA-AG----GGGAA--A--------------------------TTATACCT-AGGCCAAATATATATACTTG--TTCTGTGTA---TCAATTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droEre2 scaffold_4845:20984379-20984510 - CT-GTAGAAGGAAA--A------------------------G-TTACACCT-AGGCCAAATATATATACTTG--TTCTATGTA---TTAATTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droAna3 scaffold_13266:8260384-8260523 - GG-TT----CAATG--A-------TTAT---TAGA------GCTAACAACTAATGCCAAATATATATACTCA--ATCGATGTA--CTTGGTTATTTGCAAAGGAATACACTGCGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCAAAGCTTGTTAGT
dp4 chr3:9376521-9376668 + AC-------GAGAA--A-------TGCCATATAGGCAATAAACTATTAGCT-ATCGCAAATATATATACTCA--TTTCATGTA--CTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTAATCACATCTTTGAATCTTT-CCATAGCTCGTTAGA
droPer1 super_4:4699742-4699885 + GAGAT----GCCA----------------TATAGGCAATAAGCTATTAGCT-ATCGCAAATATATATACTCA--TTTCATGTA--CTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTGATCACATCTTTGAATCTCT-CCATAGCTCGTTAGA
droWil1 scaffold_181141:2403442-2403586 + GT-GT----AGGTATAAGTGTTGCCT----TTTTGTG------TTATTTCT-AGTTCAAATATATATACGCA--TTTTCTGTA--TATGACTATATGCAAAGGTATACATTTA---TGTATATATATTTGGTAAAATCACATCTTTGAAT--AATCCATAGCTCGTCAGA
droVir3 scaffold_12823:519093-519222 + GT-AT----TAT------------CT----AC-----------ATATATCT-ATGTCAAATATATATATCCCCATTTTGTATA--ACTATTTATATGCAAGGGTATACGTTTA---CGTATATATATTTGTTAAAATCACATCTTTGAAT--GCTATATAGCTCGTTAGC
droMoj3 scaffold_6496:318093-318227 + AG-TT----GCAGA--A-------GTATTCATATGTA------CAAAATCTTATATCAAATATATATATATG--TCCCA----------TTTGTATGCAAGGGTATGCGTTTC-TCTATATATATATTTGTTAAAATCACATCTTTGAAT--GGTATTTAGCTCGTTAGC
droGri2 scaffold_15245:6158007-6158151 - TT-GC----CAGGA--G-------TC-T-TACAACTAACTAC-TTATATCT-ATATCAAATATATATACTCA--CTTTGTGTATAGCTACGTATAAGCAAAGGTATACGCTTG---CGTATATATATTTGTTAAAATCACATCTTTGAAT--GGTATATAGCTCGTCAGC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:19621540-19621679 - G----GATGGGAAATTATACATAGGTGTTATATCTAGGCCAAATATATATACTTGTTCTATGTATTAGTTATTTGCAAAGGAATACATGTGCCTGTATATATATTCGGTAAAATCACATCTTTGAATTGCCACAGCTCGCTAGT
droSim1 chr2R:18187644-18187778 - G----GATGGGAAACTA----TAGGTATTATATCTAGGCCAAATATATATACTTGT-CTATGTATTAGTTATTTGCAAAGGAATACATGTGCGTGTATATATATTCGGTAAAATCACATCTTTGAATTGCCACAGCTCGCTAGT
droSec1 super_9:2901906-2902041 - G----GATGGGAAACTA----TAGGTATTATATCTAGGCCAAATATATATACTTGTTCTATGTATTAGTTATTTGCAAAGGAATACATGTGCGTGTATATATATTCGGTAAAATCACATCTTTGAATTGCCACAGCTCGCTAGT
droYak2 chr2R:19599592-19599718 - T----AAGGGGAAA-------------TTATACCTAGGCCAAATATATATACTTGTTCTGTGTATCAATTATTTGCAAAGGAATACATGTGCCTGTATATATATTCGGTAAAATCACATCTTTGAATTGCCACAGCTCGCTAGT
droEre2 scaffold_4845:20984379-20984510 - CTGTAGAAGGAAAA------------GTTACACCTAGGCCAAATATATATACTTGTTCTATGTATTAATTATTTGCAAAGGAATACATGTGCCTGTATATATATTCGGTAAAATCACATCTTTGAATTGCCACAGCTCGCTAGT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGATGGGAAACT----ATAGGTATTA------TATCTAGGCCAAATATATATACTTGT-CTATGTATTAGT-TATTTGCAAAGGAATACATGTGCG-TGTATATATATTCGGTAAAATCACATCTTTGAAT--TGCCACAGCTCGCTAGTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
--ACGAGAAATGCCATATAGGCAATAAACTATTAGCTATCGCAAATATATATACTCATTTCATGTACTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTAATCACATCTTTGAATCTTTCCATAGCTCGTTAGASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-15.9,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.0,  p-value=0.009901 dG=-14.9,  p-value=0.009901

droSim1

dG=-17.8,  p-value=0.009901 dG=-17.4,  p-value=0.009901 dG=-16.9,  p-value=0.009901 dG=-16.8,  p-value=0.009901

droSec1

dG=-16.7,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-15.8,  p-value=0.009901 dG=-15.7,  p-value=0.009901

droYak2

dG=-13.5,  p-value=0.009901 dG=-13.4,  p-value=0.009901 dG=-13.1,  p-value=0.009901 dG=-13.1,  p-value=0.009901 dG=-13.1,  p-value=0.009901

droEre2

dG=-16.7,  p-value=0.009901 dG=-15.8,  p-value=0.009901

droAna3

dG=-13.2,  p-value=0.009901 dG=-12.4,  p-value=0.009901 dG=-12.3,  p-value=0.009901 dG=-12.2,  p-value=0.009901

dp4

dG=-14.7,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-13.4,  p-value=0.009901

droPer1

dG=-14.7,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-13.4,  p-value=0.009901

droWil1

dG=-16.6,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-15.7,  p-value=0.009901

droVir3

dG=-16.8,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-15.8,  p-value=0.009901

droMoj3

dG=-16.9,  p-value=0.009901

droGri2

dG=-22.8,  p-value=0.009901

Generated: 03/07/2013 at 06:44 PM