Secondary structure and small RNA-seq evidence for dme-mir-4982

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:14607658-14607807 + TTTT-GAGTCGAAAGGACC--A----------------ACT-TTGCTGGCATTCGGTGGCCAA--------------TAATGCAATTGCATGTC-------------------------------------------------------CTTGTTGCTGTTGCAAT----GTTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC------------------CGCTGCTG---------CTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droSim1 chr2R:13317686-13317836 + TTTTCGAGTCGAAAGGACC--A----------------ACT-TTGCTGGCATTCGCTGGCCAA--------------TAATGCAATTGCGTGTC-------------------------------------------------------CTTGTTGCTGTTGCAAT----GTTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC------------------CGCTGCTG---------CTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droSec1 super_1:12115359-12115508 + TTTC-GAATCGAAAGGACC--A----------------ACT-TTGCTGGCATTCGCTGGCCAA--------------TAATGCAATTGCATGTC-------------------------------------------------------CTTGTTGCAGTTGCAAT----GTTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC------------------CGCTGCTG---------CTGCTCGAGTGGCAATTA--GCTGGGTGTCTC
droYak2 chr2R:14591968-14592144 - TTTTCGGGTCGAAAGGACC--A----------------ACTTTTGTTGGCATTCGCTGGCCAA--------------TAATGCAATTGCGTGTC-------------------------------------------------------CTTGTTGCTGTTGCAAT----GTTGCAACTTGCAACTGGAATTGCAATTGCATTTCTAGTTGCTTCTCCTCTTTTTCCTGCTGCTCCTA---------CTCCTCGAGTGGCAATTA--GCTGGGTGTCTC
droEre2 scaffold_4845:8798992-8799150 + TTTC-GCGTCGAAAGGACC--A----------------ACT-TTGCTGGCACTCGCTGGCCAA--------------TAATGCAATTGCGTGTC-------------------------------------------------------ATTGTTGCTGTTGCAAT----GTTG-------CAACTGGAATTGCAATTGCATTTCTAGTTGCTCCTCA---------TGCTGCTGCTG---------CTCCTCGAGTGGCAATTA--GCTGGGTGTCTC
droAna3 scaffold_13334:1368045-1368196 + TTTT-GAGCTGCAG-----------------------------------------------------------------------------------------------TTGCAGATAAAGTTACAGTTGTTGTTGCTACTTTCACGTTGTTGTTGTTGTTGT--T----GCGG-------CAGCTGCAGTTGCAGTTGCAGTTGCAATTGT------------------TGCTGCAGCTGTTGGCCTAATGAGAGTGGCCAGCAATGCGGCACGAATC
dp4 chrXL_group3a:862470-862596 - ---------------------A----------------ACT-CTGCTGCCAGTAGTTGGCCAT--------------TGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAAA-------TTGCT-----------------GCTGCTGCTGCTGC----------------------------------TGCTGCTGTTGTTGC------------------TGCTGCTG---------CCGTTGCAGTGGCAATT---------------
droPer1 super_15:2034074-2034206 + ---------------------A----------------ACT-CTGCTGCCAGTAGTTGGCCAT--------------TGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAAA-------T-----------------------TGCTGCTG----------------------CTGCCGCTGCTGCTGTTGTTGTTGTGGTTGC------------------TGCTGCTG---------CCGTTGCAGTGGCAATT---------------
droWil1 scaffold_181096:6674642-6674780 + CTTG-GTGCCGTAT----CAAAGCTGGCATATAGTTCAACT-TCT------T-CATCGG----TGGCATCA------CGTTGCAGTTGT-TGTT-------------------------------------------------------GTTGTTGTTGTTGC-------------------------------TGTTGCAGCTGTTGTTGTTGCTGTTGTTGTTGCTGCAGCTGCTG---------CTGCTCAAGTG---------------------
droVir3 scaffold_12822:1548557-1548661 - TGTT-------------------------------------------------------------------------------------------------------------------------------------------------GCTGCTGCTGTTGCAATTGTTGCTG-------CAGCTGTTGTTGCTGTTGCAGCTGCAGCTGTAACTGT---------TGCTGC---TG------CTGGGCATAGAGCTGCTCCTG--GT--AGTGCTTG
droMoj3 scaffold_6540:8945968-8946087 + AGCC------AGCATCGAC--A----------------ACT-TGGCTGCAATTCAGGT-------------TGCAGCTACTGCTGTTGCCTGTT------------------------------------------------G------CCTGTTGCCGTTGCC------GTTG-------CTGCTGCAGTTGCAGTTGCAGTTGTAGTTAC------------------CGTTGCAA---------TTGC----------------------------
droGri2 scaffold_15245:16288597-16288735 + TGTT-G-----------TC--A----------------GCG-TTGTCGTTG--TGCTTGTTGA--------------TTTTCCAGTTGCT-----------------------------------------------------------GCTGTTGCTGTTGCAGTTGCAGTTG-------CAGCTGTTGCTGCTGTTGCAGTTGCAGTTGTTGCTGC---------TGCTGC---TG------TTGTTGTTGGTGTT---------GTCGGTGGTGTC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:14607658-14607807 + TT-TTGAGTCGAAAGGACCAACT-TTGCTGGCATTCGGTGGCCAATAATGCAATTGCATGTCCTTGTTGCTGTTGCAATGTTGC-------AGCTGGAATTGCAATTGCATTTCTAGTTG------------------CCGCTGCTGCTGCTCGAGTGGCAATTAGCTGGGTGTCTC
droSim1 chr2R:13317686-13317836 + TTTTCGAGTCGAAAGGACCAACT-TTGCTGGCATTCGCTGGCCAATAATGCAATTGCGTGTCCTTGTTGCTGTTGCAATGTTGC-------AGCTGGAATTGCAATTGCATTTCTAGTTG------------------CCGCTGCTGCTGCTCGAGTGGCAATTAGCTGGGTGTCTC
droSec1 super_1:12115359-12115508 + TT-TCGAATCGAAAGGACCAACT-TTGCTGGCATTCGCTGGCCAATAATGCAATTGCATGTCCTTGTTGCAGTTGCAATGTTGC-------AGCTGGAATTGCAATTGCATTTCTAGTTG------------------CCGCTGCTGCTGCTCGAGTGGCAATTAGCTGGGTGTCTC
droYak2 chr2R:14591968-14592144 - TTTTCGGGTCGAAAGGACCAACTTTTGTTGGCATTCGCTGGCCAATAATGCAATTGCGTGTCCTTGTTGCTGTTGCAATGTTGCAACTTGCAACTGGAATTGCAATTGCATTTCTAGTTGCTTCTCCTCTTTTTCCTGCTGCTCCTACTCCTCGAGTGGCAATTAGCTGGGTGTCTC
droEre2 scaffold_4845:8798992-8799150 + TT-TCGCGTCGAAAGGACCAACT-TTGCTGGCACTCGCTGGCCAATAATGCAATTGCGTGTCATTGTTGCTGTTGCAATGTTGC-------AACTGGAATTGCAATTGCATTTCTAGTTGCTCCTC---------ATGCTGCTGCTGCTCCTCGAGTGGCAATTAGCTGGGTGTCTC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTTTCGAGTCGAAAGGACCAACTTTGCTGGCATTCGCTGGCCAATAATGCAATTGCGTGTCCT-------------------------TGTTGCTGTTGCAATGTTGCAGCTGGAATTGCAATTGCATTTCTAGTTGCCGCTGCTGCTGCTCGAGTGGCAATTAGCTGGGTGTCTCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
-------------------AACTCTGCTGCCAGTAGTTGGCCATTGAGAAAATTGTGTGCCCTGGAATTTAATTCATTGCAAACAAATTGCTGCTGCTGC-----------------TGCTGCTGCTGCTGTTGTTGCTGCTGCTGCCGTTGCAGTGGCAATT-------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-27.5,  p-value=0.009901 dG=-26.8,  p-value=0.009901

droSim1

dG=-25.4,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.6,  p-value=0.009901

droSec1

dG=-29.4,  p-value=0.009901 dG=-29.0,  p-value=0.009901 dG=-28.7,  p-value=0.009901

droYak2

dG=-34.1,  p-value=0.009901 dG=-33.4,  p-value=0.009901 dG=-33.3,  p-value=0.009901 dG=-33.2,  p-value=0.009901

droEre2

dG=-23.2,  p-value=0.009901 dG=-22.7,  p-value=0.009901 dG=-21.8,  p-value=0.009901

droAna3

dG=-22.8,  p-value=0.009901 dG=-22.8,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-19.9,  p-value=0.009901

dp4

dG=-15.3,  p-value=0.009901 dG=-14.5,  p-value=0.009901 dG=-8.8,  p-value=0.009901

droPer1

dG=-16.5,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-15.8,  p-value=0.009901 dG=-15.6,  p-value=0.009901 dG=-15.6,  p-value=0.009901 dG=-12.2,  p-value=0.009901

droWil1

dG=-10.1,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.4,  p-value=0.009901 dG=-9.2,  p-value=0.009901

droVir3

dG=-23.2,  p-value=0.009901 dG=-23.2,  p-value=0.009901 dG=-23.0,  p-value=0.009901 dG=-22.8,  p-value=0.009901 dG=-22.3,  p-value=0.009901

droMoj3

dG=-22.6,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-21.8,  p-value=0.009901

droGri2

dG=-27.8,  p-value=0.009901 dG=-27.7,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-27.0,  p-value=0.009901 dG=-25.5,  p-value=0.009901

Generated: 03/07/2013 at 06:47 PM