Secondary structure and small RNA-seq evidence for dme-mir-283

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:15401974-15402103 +	AGAGAA-A----------AG-----------------------TGTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droSim1	chrX_random:4022807-4022936 +	AGAGAA-A----------AG-----------------------TGTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droSec1	super_73:136400-136529 +	AGAGAA-A----------AG-----------------------TGTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droYak2	chrX:9587590-9587719 +	AGAGAA-A----------AG-----------------------TGTCACCTTACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droEre2	scaffold_4690:11632475-11632604 -	AGAGAA-A----------AG-----------------------TGTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droAna3	scaffold_12929:2900376-2900509 -	GTGTTA-CAGTGTT------------------------CA-----CCACCTCACCTGATTCTTAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTATGCCTGATTA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTCGAATTGCATTTTATCACCAA
dp4	chrXL_group1a:976013-976147 +	AGAGAA-A-----------G------------CGACGTCACGA-TTCACCTCA--CGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGC-AAGATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACCA-
droPer1	super_26:1090677-1090833 +	AGAGCG--AACGAGAGAGAGTGCCAGAGAAAGCGACGTCACGA-TTCACCTCA--CGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGC-AAGATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACCA-
droWil1	scaffold_180702:1594772-1594907 -	GAGTGC-GAGTGGG------------------------A----GGGAGCCTAACG-AATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTATGCCTAGATATTTGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTAATCACCAA
droVir3	scaffold_12970:2047646-2047770 +	ACA---------------AG----------------------ATGTCACCTCACCCGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACC--
droMoj3	scaffold_6359:3257693-3257822 +	AGTGAACC----------AG----------------------CTGTCACCTCACCCGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCCC-AATA--TGAAACACTCGGAATTTCAGTTGGTATATACTTTTTTGAATTGCATTTTATCACCA-
droGri2	scaffold_14853:6953507-6953633 -	AGAAT--------------G--------------A--------CGTCACCTCACCCGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCC-AAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACCA-

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:15401974-15402103 +	AGAGAA-A----------AG-----------------------TGTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droSim1	chrX_random:4022807-4022936 +	AGAGAA-A----------AG-----------------------TGTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droSec1	super_73:136400-136529 +	AGAGAA-A----------AG-----------------------TGTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droYak2	chrX:9587590-9587719 +	AGAGAA-A----------AG-----------------------TGTCACCTTACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droEre2	scaffold_4690:11632475-11632604 -	AGAGAA-A----------AG-----------------------TGTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT
droAna3	scaffold_12929:2900376-2900509 -	GTGTTA-CAGTGTT------------------------CA-----CCACCTCACCTGATTCTTAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTATGCCTGATTA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTCGAATTGCATTTTATCACCAA
dp4	chrXL_group1a:976013-976147 +	AGAGAA-A-----------G------------CGACGTCACGA-TTCACCTCA--CGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGC-AAGATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACCA-
droPer1	super_26:1090677-1090833 +	AGAGCG--AACGAGAGAGAGTGCCAGAGAAAGCGACGTCACGA-TTCACCTCA--CGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGC-AAGATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACCA-
droWil1	scaffold_180702:1594772-1594907 -	GAGTGC-GAGTGGG------------------------A----GGGAGCCTAACG-AATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTATGCCTAGATATTTGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTAATCACCAA
droVir3	scaffold_12970:2047646-2047770 +	ACA---------------AG----------------------ATGTCACCTCACCCGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCCTAAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACC--
droMoj3	scaffold_6359:3257693-3257822 +	AGTGAACC----------AG----------------------CTGTCACCTCACCCGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCCC-AATA--TGAAACACTCGGAATTTCAGTTGGTATATACTTTTTTGAATTGCATTTTATCACCA-
droGri2	scaffold_14853:6953507-6953633 -	AGAAT--------------G--------------A--------CGTCACCTCACCCGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCAATGCC-AAATA--TGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACCA-

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AGAGAAAAGT----------GTCACCTCACACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGCCTAAATATGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTGATCACCAT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.............................................AAATATCAGCTGGTAATTCTGGG........................................................................	23	1	7202.00	7202	7202
.............................................AAATATCAGCTGGTAATTCTGGGA.......................................................................	24	1	191.00	191	191
.............................................AAATATCAGCTGGTAATTCTGG.........................................................................	22	1	176.00	176	176
.............................................AAATATCAGCTGGTAATTCTG..........................................................................	21	1	102.00	102	102
..........................TCACACGATTCTCAAAGGT...............................................................................................	19	1	48.00	48	48
.............................................AAATATCAGCTGGTAATTCT...........................................................................	20	1	41.00	41	41
.................................................ATCAGCTGGTAATTCTGGG........................................................................	19	1	36.00	36	36
............................................TAAATATCAGCTGGTAATTCTGGG........................................................................	24	1	23.00	23	23
..............................................AATATCAGCTGGTAATTCTGGG........................................................................	22	1	16.00	16	16
............................................................................................CGGAATTTCAGTTGGTATCGAC..........................	22	1	15.00	15	15
...............................................ATATCAGCTGGTAATTCTGGG........................................................................	21	1	10.00	10	10
................................................TATCAGCTGGTAATTCTGGG........................................................................	20	1	9.00	9	9
................................................TATCAGCTGGTAATTCTGGGAGC.....................................................................	23	1	9.00	9	9
.............................................AAATATCAGCTGGTAATT.............................................................................	18	1	7.00	7	7
............................................TAAATATCAGCTGGTAATTCTGG.........................................................................	23	1	5.00	5	5
.........................CTCACACGATTCTCAAAGGT...............................................................................................	20	1	4.00	4	4
............................................................................................CGGAATTTCAGTTGGTATCGA...........................	21	1	3.00	3	3
............................................TAAATATCAGCTGGTAATTCTGGGA.......................................................................	25	1	2.00	2	2
............................................TAAATATCAGCTGGTAATTCTG..........................................................................	22	1	2.00	2	2
.............................................AAATATCAGCTGGTAATTC............................................................................	19	1	1.00	1	1
......................CACCTCACACGATTCTCAAAGGT...............................................................................................	23	1	1.00	1	1
..................................................TCAGCTGGTAATTCTGGG........................................................................	18	1	1.00	1	1
...............................................ATATCAGCTGGTAATTCTGG.........................................................................	20	1	1.00	1	1
..............................................AATATCAGCTGGTAATTCTG..........................................................................	20	1	1.00	1	1
.............................................AAATATCAGCTGGTAATTCTGGGAG......................................................................	25	1	1.00	1	1

dp4

AGAGAAA-GCGACGTCACGATTCACCTC--ACGATTCTCAAAGGTAAATATCAGCTGGTAATTCTGGGAGCTAAGC-AAGATATGAAACACTCGGAATTTCAGTTGGTATCGACTTTTTTGAATTGCATTTTATCACCA-	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.............................................AAATATCAGCTGGTAATTCTGGG........................................................................	23	1	3690.00	3690	3601	89
.............................................AAATATCAGCTGGTAATTCTG..........................................................................	21	1	277.00	277	265	12
.............................................AAATATCAGCTGGTAATTCTGG.........................................................................	22	1	159.00	159	149	10
.............................................AAATATCAGCTGGTAATTCT...........................................................................	20	1	126.00	126	63	63
........................CCTC--ACGATTCTCAAAGGT...............................................................................................	19	1	113.00	113	113	0
.............................................AAATATCAGCTGGTAATTCTGGGA.......................................................................	24	1	69.00	69	54	15
.................................................ATCAGCTGGTAATTCTGGG........................................................................	19	1	28.00	28	28	0
..............................................AATATCAGCTGGTAATTCTGGG........................................................................	22	1	15.00	15	14	1
.............................................AAATATCAGCTGGTAATTC............................................................................	19	1	8.00	8	5	3
.............................................AAATATCAGCTGGTAATT.............................................................................	18	1	6.00	6	3	3
................................................TATCAGCTGGTAATTCTGGG........................................................................	20	1	6.00	6	6	0
............................................................................................CGGAATTTCAGTTGGTATCGAC..........................	22	1	5.00	5	4	1
...............................................ATATCAGCTGGTAATTCTGGG........................................................................	21	1	5.00	5	5	0
............................................................................................CGGAATTTCAGTTGGTATCGA...........................	21	1	3.00	3	3	0
.......................ACCTC--ACGATTCTCAAAGGT...............................................................................................	20	1	2.00	2	2	0
..............................................AATATCAGCTGGTAATTCTGGGA.......................................................................	23	1	2.00	2	2	0
.........................CTC--ACGATTCTCAAAGGT...............................................................................................	18	1	1.00	1	0	1
..............................................AATATCAGCTGGTAATTCTGG.........................................................................	21	1	1.00	1	1	0
.................................................ATCAGCTGGTAATTCTGG.........................................................................	18	1	1.00	1	1	0

Secondary Structure

dm3

dG=-24.4, p-value=0.009901	dG=-23.9, p-value=0.009901

droSim1

dG=-24.4, p-value=0.009901	dG=-23.9, p-value=0.009901

droSec1

dG=-24.4, p-value=0.009901	dG=-23.9, p-value=0.009901

droYak2

dG=-24.4, p-value=0.009901	dG=-23.9, p-value=0.009901

droEre2

dG=-24.4, p-value=0.009901	dG=-23.9, p-value=0.009901

droAna3

dG=-24.4, p-value=0.009901	dG=-24.3, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.8, p-value=0.009901

dp4

dG=-24.4, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.7, p-value=0.009901

droPer1

dG=-24.4, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.7, p-value=0.009901

droWil1

dG=-24.3, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.6, p-value=0.009901

droVir3

dG=-24.4, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.5, p-value=0.009901

droMoj3

dG=-25.2, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.5, p-value=0.009901	dG=-24.4, p-value=0.009901	dG=-24.2, p-value=0.009901

droGri2

dG=-24.4, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.7, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.4, p-value=0.009901

Generated: 03/07/2013 at 05:04 PM