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 + TTTT-GAGTCGAAAGGACC--A----------------ACT-TTGCTGGCATTCGGTGGCCAA--------------TAATGCAATTGCATGTC-------------------------------------------------------CTTGTTGCTGTTGCAAT----GTTG-------CAGCTGGAATTGCAATTGCATTTCTAGTTGC------------------CGCTGCTG---------CTGCTCGAGTGGCAATTA--GCTGGGTGTCTC

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

-49.4 -49.4 -49.4 -49.4 -48.9 -48.9

droSim1

-44.8 -44.2 -44.1 -44.0

droSec1

-48.8 -48.6 -48.4 -48.4 -48.2 -48.2

droYak2

-52.9 -52.5 -52.3 -52.3 -52.1 -52.0

droEre2

-46.2 -46.2 -45.5

droAna3

-45.4 -45.3 -45.3 -45.2 -45.2 -45.2

dp4

-42.6 -42.5 -42.1 -42.0

droPer1

-39.9 -39.8 -39.7 -39.6 -39.2 -39.1

droWil1

-32.6 -32.4 -32.3 -32.2 -32.0 -32.0

droVir3

-36.6 -35.7 -35.6 -35.6 -35.6

droMoj3

-40.9 -40.7 -40.6 -40.4

droGri2

-46.4 -45.4

Generated: 01/05/2013 at 05:28 PM