Secondary structure and small RNA-seq evidence for dme-mir-278

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:11544556-11544683 +	T--GATACGAG---------------------------ACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCATTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCGT
droSim1	chr2R:10277194-10277321 +	T--GATACGAG---------------------------ACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCGT
droSec1	super_1:9037606-9037733 +	T--GATACGAG---------------------------ACCATAGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCGT
droYak2	chr2R:17445962-17446088 -	T--GATACGAC---------------------------ACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCG-
droEre2	scaffold_4845:14318899-14319025 -	T--GATACGAG---------------------------ACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCG-
droAna3	scaffold_13266:12641317-12641435 -	TATG-----------------------------------TAACGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTCGAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCA----------------------------TCCGG
dp4	chr3:19640883-19641018 -	T--G-----------------------------------CAACGGTAATGGTACGGTGCGACCGGACGATGGTTCACAACGACCGTG---TCTCTTAAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCATCATCGTCGCGCCCCAG---------TGCTCGT
droPer1	super_37:642280-642415 -	T--G-----------------------------------CAACGGTAATGGTACGGTGCGACCGGACGATGGTTCACAACGACCGTG---TCTCTTAAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCATCATCGTCGCGCCCCAG---------TGCTCGT
droWil1	scaffold_181009:1555699-1555856 -	T--GTAACGAGTTAAAAAAAAATAAGGGGAGATCCCCCATAATGGTAATGGTACGGTGCGACCGGATGACGGTTCACAACGACCGTG---TCAATTTTACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCATAATC----------------------TCTAGG
droVir3	scaffold_12875:6427523-6427640 -	T--G---------------------------------------GTTTATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTGCA-TACTTTTAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------A---ATCAG------AT
droMoj3	scaffold_6496:23589388-23589515 +	T--G---------------------------------------GTTTATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTACAGTTTTTTCAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------GCAAATCAGATATCAGC
droGri2	scaffold_15112:1314106-1314223 -	T--GGTC--------------------------------------TGATGGTACGGTGCGACCGGATGACGGTTCACAACGACCGTGCT-TATTTTTAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCA----------------A----------ATCAGT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:11544556-11544683 +	T--GATACGAG---------------------------ACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCATTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCGT
droSim1	chr2R:10277194-10277321 +	T--GATACGAG---------------------------ACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCGT
droSec1	super_1:9037606-9037733 +	T--GATACGAG---------------------------ACCATAGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCGT
droYak2	chr2R:17445962-17446088 -	T--GATACGAC---------------------------ACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCG-
droEre2	scaffold_4845:14318899-14319025 -	T--GATACGAG---------------------------ACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------G---------TGTCCG-
droAna3	scaffold_13266:12641317-12641435 -	TATG-----------------------------------TAACGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTG---TCCTTCGAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCA----------------------------TCCGG
dp4	chr3:19640883-19641018 -	T--G-----------------------------------CAACGGTAATGGTACGGTGCGACCGGACGATGGTTCACAACGACCGTG---TCTCTTAAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCATCATCGTCGCGCCCCAG---------TGCTCGT
droPer1	super_37:642280-642415 -	T--G-----------------------------------CAACGGTAATGGTACGGTGCGACCGGACGATGGTTCACAACGACCGTG---TCTCTTAAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCATCATCGTCGCGCCCCAG---------TGCTCGT
droWil1	scaffold_181009:1555699-1555856 -	T--GTAACGAGTTAAAAAAAAATAAGGGGAGATCCCCCATAATGGTAATGGTACGGTGCGACCGGATGACGGTTCACAACGACCGTG---TCAATTTTACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCATAATC----------------------TCTAGG
droVir3	scaffold_12875:6427523-6427640 -	T--G---------------------------------------GTTTATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTGCA-TACTTTTAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------A---ATCAG------AT
droMoj3	scaffold_6496:23589388-23589515 +	T--G---------------------------------------GTTTATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTACAGTTTTTTCAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATCA----------------GCAAATCAGATATCAGC
droGri2	scaffold_15112:1314106-1314223 -	T--GGTC--------------------------------------TGATGGTACGGTGCGACCGGATGACGGTTCACAACGACCGTGCT-TATTTTTAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCA----------------A----------ATCAGT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGATACGAGACCATGGTAATGGTACGGTGCGACCGGATGATGGTTCACAACGACCGTGTCCTTTAAACGGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAACGATTTATC----------------AGTGTCCGT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................CCGGATGATGGTTCACAACGACC.........................................................................................	23	1	68.00	68	68
.......................................................................TCGGTGGGACTTTCGTCCGTTT...................................................	22	1	4.00	4	4
................................CCGGATGATGGTTCACAACGAC..........................................................................................	22	1	3.00	3	3
.......................................................................TCGGTGGGACTTTCGTCCGTT....................................................	21	1	1.00	1	1

dp4

TG--------CAACGGTAATGGTACGGTGCGACCGGACGATGGTTCACAACGACCGTGTCTCTTAAACTGGTCGGTGGGACTTTCGTCCGTTTGTAACGCCATTTGTCAGCGATTTATCATCATCGTCGCGCCCCAGTGCTCGT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................................................................TCGGTGGGACTTTCGTCCGTTT...................................................	22	1	1009.00	1009	13	996
.......................................................................TCGGTGGGACTTTCGTCCGTT....................................................	21	1	534.00	534	0	534
................................CCGGACGATGGTTCACAACGACC.........................................................................................	23	1	103.00	103	58	45
.......................................................................TCGGTGGGACTTTCGTCCGT.....................................................	20	1	17.00	17	0	17
.........................................................................GGTGGGACTTTCGTCCGTTT...................................................	20	1	8.00	8	0	8
.........................................................................GGTGGGACTTTCGTCCGTT....................................................	19	1	5.00	5	0	5
.......................................................................TCGGTGGGACTTTCGTCCGTTTG..................................................	23	1	2.00	2	0	2
................................CCGGACGATGGTTCACAACGA...........................................................................................	21	1	2.00	2	0	2
........................................................................CGGTGGGACTTTCGTCCGTTT...................................................	21	1	2.00	2	0	2
..................................GGACGATGGTTCACAACGACC.........................................................................................	21	1	1.00	1	0	1
...................................................................CTGGTCGGTGGGACTTTCGTCCGT.....................................................	24	1	1.00	1	0	1
.........................................................................GGTGGGACTTTCGTCCGT.....................................................	18	1	1.00	1	0	1
................................CCGGACGATGGTTCACAACG............................................................................................	20	1	1.00	1	0	1
................................CCGGACGATGGTTCACAA..............................................................................................	18	1	1.00	1	0	1
........................................................................CGGTGGGACTTTCGTCCGTT....................................................	20	1	1.00	1	0	1
................................CCGGACGATGGTTCACAACGAC..........................................................................................	22	1	1.00	1	0	1

Secondary Structure

dm3

dG=-30.8, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.2, p-value=0.009901

droSim1

dG=-30.8, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.2, p-value=0.009901

droSec1

dG=-30.8, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.2, p-value=0.009901

droYak2

dG=-30.8, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.2, p-value=0.009901

droEre2

dG=-30.8, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.2, p-value=0.009901

droAna3

dG=-31.7, p-value=0.009901	dG=-30.8, p-value=0.009901	dG=-30.7, p-value=0.009901

dp4

dG=-32.6, p-value=0.009901	dG=-32.4, p-value=0.009901

droPer1

dG=-32.6, p-value=0.009901	dG=-32.4, p-value=0.009901

droWil1

dG=-31.2, p-value=0.009901	dG=-30.3, p-value=0.009901

droVir3

dG=-30.4, p-value=0.009901	dG=-29.5, p-value=0.009901

droMoj3

dG=-30.0, p-value=0.009901	dG=-29.3, p-value=0.009901	dG=-29.3, p-value=0.009901	dG=-29.3, p-value=0.009901

droGri2

dG=-30.1, p-value=0.009901	dG=-29.9, p-value=0.009901	dG=-29.2, p-value=0.009901

Generated: 03/07/2013 at 05:02 PM