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

-17.4	-16.5

droSim1

-17.4	-16.5

droSec1

-17.4	-16.5

droYak2

-18.3	-18.3

droEre2

-17.4	-17.4

droAna3

-6.8	-6.8	-6.7	-6.7	-5.8	-5.8

dp4

-6.6	-6.4	-6.3	-6.0	-5.7

droPer1

-6.6	-6.4	-6.3	-6.0	-5.7

droWil1

-0.5	0.0	0.0	0.1	0.1	0.2

droVir3

-5.8	-5.7	-5.7	-5.7	-5.6	-5.6

droMoj3

-5.0	-4.9	-4.7	-4.7	-4.6	-4.5

droGri2

-6.3

Generated: 01/05/2013 at 05:06 PM