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

-37.0	-36.8	-36.8	-36.8	-36.8	-36.7

droSim1

-37.0	-36.8	-36.8	-36.8	-36.8	-36.7

droSec1

-37.0	-36.8	-36.8	-36.8	-36.8	-36.7

droYak2

-37.0	-36.8	-36.8	-36.8	-36.8	-36.7

droEre2

-37.0	-36.8	-36.8	-36.8	-36.8	-36.7

droAna3

-37.9	-37.7	-37.6	-37.2	-37.0	-37.0

dp4

-38.8	-38.6	-38.6	-38.5	-38.4	-38.3

droPer1

-38.8	-38.6	-38.6	-38.5	-38.4	-38.3

droWil1

-37.4	-37.2	-37.1	-36.7	-36.5	-36.5

droVir3

-35.7	-35.5	-35.4	-34.8

droMoj3

-35.3	-35.1	-35.0	-34.6	-34.6	-34.6

droGri2

-36.5	-36.3	-36.3	-36.2	-36.1	-36.0

Generated: 01/05/2013 at 05:13 PM