Secondary structure and small RNA-seq evidence for dme-mir-1013

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:26617343-26617433 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAAT------------AAAAGTA-----T-GCCGAACTCGC-------AGGCGACGGATGCGCGA
droSim1	chr3R:26257486-26257576 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAAT------------AAAAGTA-----T-GCCGAACTCGC-------AGGCGACGGATGCGCGA
droSec1	super_4:5435200-5435290 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAAT------------AAAAGTT-----T-GCCGAACTCGC-------AGGCGACGGATGCGCGA
droYak2	chr3R:27538983-27539073 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATTGGGACGGCCGTTAAT------------AAAAGTA-----T-GCCGAACTCGC-------AGGCGACGGATGCGCGA
droEre2	scaffold_4820:1381504-1381594 +	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATTGGAGCGGCCGTTAAT------------AAAAGTA-----T-GCCGAACTCGC-------AGGCGACGGATGCGCGA
droAna3	scaffold_12911:4366271-4366356 +	CACTGTGCTGGAGAGGTAATCTTTGAATAATTATCTGTGAGTTGTGGCATCTAAT------------GATTGT-----------TATCTTCC-------AGACGTCGCATGCGTGA
dp4	chr2:577090-577184 +	CACTGTGCTGGAGCGGTAAGT----------CCATGAATTGCATCCCCCTTTGATTATTCTTTAATCTGG---AAATCCC-TGTGATCCCAT-------AGACGACGGATGCGCGA
droPer1	super_7:3361274-3361368 +	CACTGTGCTGGAGCGGTAAGT----------CCATGAATTGCATCCCCCTTTGATTATTCTTTAATCTGG---AAATCCC-TGTGATCCCAT-------AGACGACGGATGCGCGA
droWil1	scaffold_181130:10168431-10168520 -	AACTGTATTAGAAAGGTATAATGAATAAACCAATTTGAATAG-CAAACCATTAAA------------TCAATTT-----C-CTTTTTTGTCT-------AGACGACGTATGCGTGA
droVir3	scaffold_13047:11434928-11435028 -	CACAGTGCTGGAGAGGTGGGT-GCATCCAC---------ATCAGCTGCT--TGATAACCATTTGT--AAATGTAAATCCTCCTTTAACTCG-TTTGAACAGGCGACGCATGCGCGA
droMoj3	scaffold_6540:30312688-30312787 +	CACAGTGCTGGAGAGGTGGGA----------GCATTGATTTCACCACCCATAAG--ACACATTCT--CACAGTTTTTCTTGCT-TAATTCC-TTTGTACAGGCGGCGCATGCGCGA
droGri2	scaffold_14624:1473562-1473665 -	CACAGTGCTGGAAAGGTGATTCAAAT-----CCATAAGCCACAATCTTCTT-AAATATTATTTTCGCTAA---TGCT--A-TTTGTACTCGCTTTGATTAGGCGTCGCATGCGGGA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:26617343-26617433 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAAAAGTATGCCGAACTCGCAGGCGACGGATGCGCGA
droSim1	chr3R:26257486-26257576 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAAAAGTATGCCGAACTCGCAGGCGACGGATGCGCGA
droSec1	super_4:5435200-5435290 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAAAAGTTTGCCGAACTCGCAGGCGACGGATGCGCGA
droYak2	chr3R:27538983-27539073 -	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATTGGGACGGCCGTTAATAAAAGTATGCCGAACTCGCAGGCGACGGATGCGCGA
droEre2	scaffold_4820:1381504-1381594 +	CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATTGGAGCGGCCGTTAATAAAAGTATGCCGAACTCGCAGGCGACGGATGCGCGA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CACCGTGCTGGAGAGGTGAGTTTCGTACACTTAATTAATAGGATCGGCCGTTAATAAAA---------------GTATGCCGAACTCGCAGGCGACGGATGCGCGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.....................................................ATAAAA---------------GTATGCCGAACTCGCAG...............	23	1	48.00	48	48
.....................................................ATAAAA---------------GTATGCCGAACTCGCA................	22	1	11.00	11	11
......................................................TAAAA---------------GTATGCCGAACTCGCAG...............	22	1	8.00	8	8
.....................................................ATAAAA---------------GTATGCCGAACTCGC.................	21	1	4.00	4	4
.....................................................ATAAAA---------------GTATGCCGAACTCG..................	20	1	2.00	2	2
......................................................TAAAA---------------GTATGCCGAACTCGCA................	21	1	1.00	1	1
.......................................................AAAA---------------GTATGCCGAACTCGCAG...............	21	1	1.00	1	1

dp4

CACTGTGCTGGAGCGGTAAGTC----------CATGAATTGCATCCCCCTTTGATTATTCTTTAATCTGGAAATCCCT-GTGATCCCATAGACGACGGATGCGCGA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-17.4, p-value=0.009901	dG=-16.5, p-value=0.009901

droSim1

dG=-17.4, p-value=0.009901	dG=-16.5, p-value=0.009901

droSec1

dG=-17.4, p-value=0.009901	dG=-16.5, p-value=0.009901

droYak2

dG=-18.3, p-value=0.009901	dG=-18.3, p-value=0.009901

droEre2

dG=-17.4, p-value=0.009901	dG=-17.4, p-value=0.009901

droAna3

dG=-6.8, p-value=0.009901	dG=-6.8, p-value=0.009901	dG=-6.7, p-value=0.009901	dG=-6.7, p-value=0.009901	dG=-5.8, p-value=0.009901

dp4

dG=-6.6, p-value=0.009901	dG=-6.4, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-6.0, p-value=0.009901	dG=-5.7, p-value=0.009901	dG=-4.5, p-value=0.009901

droPer1

dG=-6.6, p-value=0.009901	dG=-6.4, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-6.0, p-value=0.009901	dG=-5.7, p-value=0.009901	dG=-4.5, p-value=0.009901

droWil1

dG=-0.5, p-value=0.019802	dG=0.0, p-value=0.009901	dG=0.0, p-value=0.029703	dG=0.1, p-value=0.019802	dG=0.1, p-value=0.009901

droVir3

dG=-5.8, p-value=0.009901	dG=-5.7, p-value=0.009901	dG=-5.7, p-value=0.009901	dG=-5.7, p-value=0.009901	dG=-5.6, p-value=0.009901	dG=-4.8, p-value=0.009901

droMoj3

dG=-5.0, p-value=0.009901	dG=-4.9, p-value=0.009901	dG=-4.7, p-value=0.009901	dG=-4.7, p-value=0.009901	dG=-4.6, p-value=0.009901

droGri2

dG=-6.3, p-value=0.009901

Generated: 03/07/2013 at 04:48 PM