Secondary structure and small RNA-seq evidence for dme-mir-304

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:15402977-15403094 +	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TAAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droSim1	chrX_random:4023795-4023912 +	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droSec1	super_73:137399-137516 +	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droYak2	chrX:9589334-9589451 +	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droEre2	scaffold_4690:11631458-11631575 -	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droAna3	scaffold_12929:2899093-2899202 -	-----------ATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATT-TGAGCCATTTGACGGACTCACTTTGCAACTGGAGATTGCTCGAGACTGCGGCATATGCCACAAAGT
dp4	chrXL_group1a:977383-977495 +	------ACTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATT-TGAGGCATTTGACACACTCACTTTGCAACTGGAGATTGCTCGAAACTGCGGCACATGCCACA--TT
droPer1	Unknown	------ACTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATT-TGAGGCATTTGACACACTCACTTTGCAACTGGAGATTGCTCGAAACTGCGGCACATGCCACA--TT
droWil1	scaffold_180702:1593181-1593292 -	-------TTGTATCTGTAACATTGATTAATCTCAATTTGTAAATGTGAGCGATTTAAATCCATTCGATGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCATATGCCACA--TT
droVir3	scaffold_12970:2048738-2048856 +	TTGTTAAACTTATCTGCAGCATTGATTAATCTCAATTTGTAAATGTGAGCGATTTTAAAGTATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCTTATGCCACA--TA
droMoj3	scaffold_6359:3259146-3259264 +	GTCCAACTCTTATCTGCAGCATTGATTAATCTCAATTTGTAAATGTGAGCGATTTTTAACTATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCAGCATATGCCACA--TT
droGri2	scaffold_14853:6952274-6952391 -	TTGTTAACT-TATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATTATTAAGAATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCATATGCCACA--TT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:15402977-15403094 +	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TAAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droSim1	chrX_random:4023795-4023912 +	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droSec1	super_73:137399-137516 +	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droYak2	chrX:9589334-9589451 +	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droEre2	scaffold_4690:11631458-11631575 -	GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTT-TGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACA--TT
droAna3	scaffold_12929:2899093-2899202 -	-----------ATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATT-TGAGCCATTTGACGGACTCACTTTGCAACTGGAGATTGCTCGAGACTGCGGCATATGCCACAAAGT
dp4	chrXL_group1a:977383-977495 +	------ACTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATT-TGAGGCATTTGACACACTCACTTTGCAACTGGAGATTGCTCGAAACTGCGGCACATGCCACA--TT
droWil1	scaffold_180702:1593181-1593292 -	-------TTGTATCTGTAACATTGATTAATCTCAATTTGTAAATGTGAGCGATTTAAATCCATTCGATGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCATATGCCACA--TT
droVir3	scaffold_12970:2048738-2048856 +	TTGTTAAACTTATCTGCAGCATTGATTAATCTCAATTTGTAAATGTGAGCGATTTTAAAGTATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCTTATGCCACA--TA
droMoj3	scaffold_6359:3259146-3259264 +	GTCCAACTCTTATCTGCAGCATTGATTAATCTCAATTTGTAAATGTGAGCGATTTTTAACTATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCAGCATATGCCACA--TT
droGri2	scaffold_14853:6952274-6952391 -	TTGTTAACT-TATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATTATTAAGAATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGATTGCAGCATATGCCACA--TT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GTACCAATTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGGTTTGAGCCATTTGACGCACTCACTTTGCAATTGGAGATTGCTCGAGACTGCGGCATATGCCACATT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..........................TAATCTCAATTTGTAAATGTGAG.....................................................................	23	1	644.00	644	644
........................................................................CACTTTGCAATTGGAGATTGCT........................	22	1	313.00	313	313
..........................TAATCTCAATTTGTAAATGTGA......................................................................	22	1	38.00	38	38
.......................................................................TCACTTTGCAATTGGAGATTGCT........................	23	1	20.00	20	20
........................................................................CACTTTGCAATTGGAGATTGC.........................	21	1	9.00	9	9
..............................CTCAATTTGTAAATGTGA......................................................................	18	1	3.00	3	3
.......TTGTATCTGCAGCATTGAA............................................................................................	19	1	2.00	2	2
.........................................................................ACTTTGCAATTGGAGATTGCT........................	21	1	2.00	2	2
...............................TCAATTTGTAAATGTGAG.....................................................................	18	1	2.00	2	2
........................................................................CACTTTGCAATTGGAGATTG..........................	20	1	1.00	1	1
..................................................................CGCACTCACTTTGCAATTGGAG..............................	22	1	1.00	1	1
..........................TAATCTCAATTTGTAAATGTGAGC....................................................................	24	1	1.00	1	1
.......................................................................TCACTTTGCAATTGGAGATTGC.........................	22	1	1.00	1	1
...........................AATCTCAATTTGTAAATGTGAG.....................................................................	22	1	1.00	1	1
.......................................................................TCACTTTGCAATTGGAGATTG..........................	21	1	1.00	1	1
............................................................................TTGCAATTGGAGATTGCT........................	18	1	1.00	1	1

dp4

------ACTGTATCTGCAGCATTGAATAATCTCAATTTGTAAATGTGAGCGATTTGAGGCATTTGACACACTCACTTTGCAACTGGAGATTGCTCGAAACTGCGGCACATGCCACATT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..........................TAATCTCAATTTGTAAATGTGAG.....................................................................	23	1	1680.00	1680	747	933
........................................................................CACTTTGCAACTGGAGATTGCT........................	22	1	544.00	544	391	153
..........................TAATCTCAATTTGTAAATGTGA......................................................................	22	1	109.00	109	42	67
........................................................................CACTTTGCAACTGGAGATTGC.........................	21	1	33.00	33	18	15
.......................................................................TCACTTTGCAACTGGAGATTGCT........................	23	1	20.00	20	16	4
.........................................................................ACTTTGCAACTGGAGATTGCT........................	21	1	9.00	9	4	5
.......................................................................TCACTTTGCAACTGGAGATTGC.........................	22	1	8.00	8	6	2
..........................TAATCTCAATTTGTAAATGT........................................................................	20	1	7.00	7	1	6
.......................................................................TCACTTTGCAACTGGAGATTG..........................	21	1	4.00	4	1	3
..........................TAATCTCAATTTGTAAATGTG.......................................................................	21	1	4.00	4	0	4
..............................CTCAATTTGTAAATGTGAG.....................................................................	19	1	3.00	3	3	0
..........................TAATCTCAATTTGTAAATGTGAGC....................................................................	24	1	3.00	3	1	2
.......CTGTATCTGCAGCATTGAA............................................................................................	19	1	2.00	2	2	0
........................................................................CACTTTGCAACTGGAGATTG..........................	20	1	2.00	2	1	1
.................................................CGATTTGAGGCATTTGACACACT..............................................	23	1	2.00	2	0	2
.........................................................................ACTTTGCAACTGGAGATTGC.........................	20	1	2.00	2	2	0
...........................AATCTCAATTTGTAAATGTGA......................................................................	21	1	1.00	1	0	1
........................................................................CACTTTGCAACTGGAGATT...........................	19	1	1.00	1	0	1
...............................TCAATTTGTAAATGTGAG.....................................................................	18	1	1.00	1	0	1
.....................................................................ACTCACTTTGCAACTGGAGATT...........................	22	1	1.00	1	1	0
............................ATCTCAATTTGTAAATGTGAG.....................................................................	21	1	1.00	1	0	1
...........................AATCTCAATTTGTAAATGTGAG.....................................................................	22	1	1.00	1	1	0
.........................ATAATCTCAATTTGTAAATGT........................................................................	21	1	1.00	1	0	1
...................................................................ACACTCACTTTGCAACTGGAGATTGCT........................	27	1	1.00	1	1	0
.......................................................................TCACTTTGCAACTGGAGATT...........................	20	1	1.00	1	0	1
.............................TCTCAATTTGTAAATGTGAGC....................................................................	21	1	1.00	1	0	1
..........................TAATCTCAATTTGTAAATG.........................................................................	19	1	1.00	1	1	0
..............................CTCAATTTGTAAATGTGA......................................................................	18	1	1.00	1	0	1
.............................TCTCAATTTGTAAATGTGAG.....................................................................	20	1	1.00	1	0	1

Secondary Structure

dm3

dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901

droSim1

dG=-24.0, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901

droSec1

dG=-24.0, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901

droYak2

dG=-24.0, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901

droEre2

dG=-24.0, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901

droAna3

dG=-21.1, p-value=0.009901	dG=-20.9, p-value=0.009901	dG=-20.9, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.6, p-value=0.009901

dp4

dG=-20.9, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.6, p-value=0.009901	dG=-20.2, p-value=0.009901	dG=-20.2, p-value=0.009901

droPer1

dG=-20.9, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.6, p-value=0.009901	dG=-20.2, p-value=0.009901	dG=-20.2, p-value=0.009901

droWil1

dG=-22.8, p-value=0.009901

droVir3

dG=-22.3, p-value=0.009901	dG=-22.1, p-value=0.009901	dG=-21.9, p-value=0.009901	dG=-21.9, p-value=0.009901	dG=-21.8, p-value=0.009901

droMoj3

dG=-21.9, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.5, p-value=0.009901	dG=-21.2, p-value=0.009901	dG=-21.1, p-value=0.009901

droGri2

dG=-23.3, p-value=0.009901	dG=-22.5, p-value=0.009901

Generated: 03/07/2013 at 05:12 PM