Secondary structure and small RNA-seq evidence for dme-mir-281-1

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:8057863-8057982 -	AATCGAATC-CAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--AACTA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTGTGAG
droSim1	chr2R_random:2148092-2148211 -	AATCGAATC-CAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--AAGCA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTGTGAG
droSec1	super_1:5602965-5603084 -	AATCGAATC-CAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--AACCA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTGTGAT
droYak2	chr2R:8893333-8893452 +	AATCGAATC-CATATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--ATTCA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTATGAG
droEre2	scaffold_4845:17736182-17736301 +	AATCGAATA-CATATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--AACCA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCACTATGAG
droAna3	scaffold_13266:2568740-2568853 +	CT---ATCT-CGAATGCGAATACGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--TACCT---ATAAC---ACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGCTTCGCTCCGAT
dp4	chr3:418413-418523 -	AA---AACA-CGAATGCGAATAGGTGAATAAAGAGAGCTGTCCGTCGACAGTCAACG--TACCAATT-TAAT---ACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGTTGCGC----AG
droPer1	super_2:605310-605420 -	AA---AACA-CGAATGCGAATAGGTGAATAAAGAGAGCTGTCCGTCGACAGTCAACG--TACCAATT-TAAT---ACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGTTGCGC----AG
droWil1	scaffold_181141:3241875-3241979 +	AG---A-----AAAAGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGTTAAACGA-TTTTAAA---ACTGTCATGGAATTGCTCTCTTTGTATGATATTCGACGT--------GAC
droVir3	scaffold_12875:19829913-19830024 +	AATCGTACC-CAAAAGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGT--AACAA-ATGTAAT---ACTGTCATGGAATTGCTCTCTTTGTATGATATTCGACGTTGCCC------
droMoj3	scaffold_6496:6376225-6376337 -	AATCGTAGCGAAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGT--AAAGA-TTGTAAA---ACTGTCATGGAATTGCTCTCTTTGTATGATATTCGACGTTGCCC------
droGri2	scaffold_15245:18178188-18178294 +	AATT---AT-GAAAAGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGT--ATAAA-TTTTAAT---ACTGTCATGGAATTGCTCTCTTTGTATGATATTCGACGTTGC--------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:8057863-8057982 -	AATCGAATC-CAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--AACTA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTGTGAG
droSim1	chr2R_random:2148092-2148211 -	AATCGAATC-CAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--AAGCA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTGTGAG
droSec1	super_1:5602965-5603084 -	AATCGAATC-CAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--AACCA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTGTGAT
droYak2	chr2R:8893333-8893452 +	AATCGAATC-CATATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--ATTCA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTATGAG
droEre2	scaffold_4845:17736182-17736301 +	AATCGAATA-CATATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--AACCA-TT-TAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCACTATGAG
droAna3	scaffold_13266:2568740-2568853 +	CT---ATCT-CGAATGCGAATACGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGA--TACCT---ATAAC---ACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGCTTCGCTCCGAT
dp4	chr3:418413-418523 -	AA---AACA-CGAATGCGAATAGGTGAATAAAGAGAGCTGTCCGTCGACAGTCAACG--TACCAATT-TAAT---ACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGTTGCGC----AG
droPer1	super_2:605310-605420 -	AA---AACA-CGAATGCGAATAGGTGAATAAAGAGAGCTGTCCGTCGACAGTCAACG--TACCAATT-TAAT---ACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGTTGCGC----AG
droWil1	scaffold_181141:3241875-3241979 +	AG---A-----AAAAGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGTTAAACGA-TTTTAAA---ACTGTCATGGAATTGCTCTCTTTGTATGATATTCGACGT--------GAC
droVir3	scaffold_12875:19829913-19830024 +	AATCGTACC-CAAAAGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGT--AACAA-ATGTAAT---ACTGTCATGGAATTGCTCTCTTTGTATGATATTCGACGTTGCCC------
droMoj3	scaffold_6496:6376225-6376337 -	AATCGTAGCGAAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGT--AAAGA-TTGTAAA---ACTGTCATGGAATTGCTCTCTTTGTATGATATTCGACGTTGCCC------
droGri2	scaffold_15245:18178188-18178294 +	AATT---AT-GAAAAGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGT--ATAAA-TTTTAAT---ACTGTCATGGAATTGCTCTCTTTGTATGATATTCGACGTTGC--------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AATCGAATCCAAATGCGAATAAGTGAATAAAGAGAGCTGTCCGTCGACAGTCCAGAAAGC-ATTTAATATCACTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGATGCGCTGTGAG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................AAAGAGAGCTGTCCGTCGACAGT......................................................................	23	1	587.00	587	587
........................................................................CTGTCATGGAATTGCTCTCTTTG..........................	23	2	530.00	1060	1060
............................AAAGAGAGCTGTCCGTCGACAG.......................................................................	22	1	268.00	268	268
.........................................................................TGTCATGGAATTGCTCTCTTTG..........................	22	2	213.50	427	427
.............................AAGAGAGCTGTCCGTCGACAGTC.....................................................................	23	1	15.00	15	15
..............................AGAGAGCTGTCCGTCGACAGTC.....................................................................	22	1	11.00	11	11
.........................................................................TGTCATGGAATTGCTCTCTTT...........................	21	2	10.50	21	21
.............................AAGAGAGCTGTCCGTCGACAGT......................................................................	22	1	6.00	6	6
............................AAAGAGAGCTGTCCGTCGACAGTC.....................................................................	24	1	6.00	6	6
............................AAAGAGAGCTGTCCGTCGACA........................................................................	21	1	4.00	4	4
..............................AGAGAGCTGTCCGTCGACAGT......................................................................	21	1	3.00	3	3
........................................................................CTGTCATGGAATTGCTCTCTTTGT.........................	24	2	2.00	4	4
..........................................................................GTCATGGAATTGCTCTCTTTGT.........................	22	2	1.50	3	3
............................AAAGAGAGCTGTCCGTCGACAGTCC....................................................................	25	1	1.00	1	1
...........................TAAAGAGAGCTGTCCGTCGACAG.......................................................................	23	1	1.00	1	1
......................................GTCCGTCGACAGTCCAGAAAGC-A...........................................................	23	1	1.00	1	1
........................................................................CTGTCATGGAATTGCTCTCTT............................	21	2	0.50	1	1

dp4

AA---AACACGAATGCGAATAGGTGAATAAAGAGAGCTGTCCGTCGACAGTCAACGTACCAATTTAATA---CTGTCATGGAATTGCTCTCTTTGTATAATATTCGACGTTGCGC----AG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................AAAGAGAGCTGTCCGTCGACAGT......................................................................	23	1	1156.00	1156	776	380
........................................................................CTGTCATGGAATTGCTCTCTTTG..........................	23	2	1084.00	2168	804	1364
............................AAAGAGAGCTGTCCGTCGACAG.......................................................................	22	1	593.00	593	341	252
.........................................................................TGTCATGGAATTGCTCTCTTT...........................	21	2	116.00	232	0	232
............................AAAGAGAGCTGTCCGTCGACA........................................................................	21	1	115.00	115	5	110
........................................................................CTGTCATGGAATTGCTCTCTT............................	21	2	37.50	75	3	72
............................AAAGAGAGCTGTCCGTCGAC.........................................................................	20	1	25.00	25	1	24
.............................AAGAGAGCTGTCCGTCGACAGT......................................................................	22	1	7.00	7	4	3
........................................................................CTGTCATGGAATTGCTCTCT.............................	20	2	6.00	12	0	12
............................AAAGAGAGCTGTCCGTCGA..........................................................................	19	1	5.00	5	1	4
.........................................................................TGTCATGGAATTGCTCTCTTTGTA........................	24	2	4.00	8	8	0
........................................................................CTGTCATGGAATTGCTCTCTTTGT.........................	24	2	4.00	8	8	0
............................AAAGAGAGCTGTCCGTCGACAGTC.....................................................................	24	1	4.00	4	2	2
.............................AAGAGAGCTGTCCGTCGACAGTC.....................................................................	23	1	3.00	3	2	1
.........................................................................TGTCATGGAATTGCTCTCT.............................	19	2	2.00	4	0	4
.............................AAGAGAGCTGTCCGTCGACAG.......................................................................	21	1	1.00	1	0	1
..............................AGAGAGCTGTCCGTCGACAGT......................................................................	21	1	1.00	1	1	0
.....................GGTGAATAAAGAGAGCTGTCCGTC............................................................................	24	1	1.00	1	1	0
.........................................................................TGTCATGGAATTGCTCTCTTTGTAT.......................	25	2	1.00	2	0	2

Secondary Structure

dm3

dG=-26.7, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.7, p-value=0.009901

droSim1

dG=-26.7, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.7, p-value=0.009901

droSec1

dG=-26.7, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.7, p-value=0.009901

droYak2

dG=-26.7, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.9, p-value=0.009901

droEre2

dG=-26.7, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.7, p-value=0.009901

droAna3

dG=-27.0, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.0, p-value=0.009901

dp4

dG=-26.7, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.7, p-value=0.009901

droPer1

dG=-26.7, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.7, p-value=0.009901

droWil1

dG=-27.2, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.7, p-value=0.009901	dG=-26.5, p-value=0.009901

droVir3

dG=-27.2, p-value=0.009901	dG=-27.1, p-value=0.009901	dG=-26.7, p-value=0.009901	dG=-26.7, p-value=0.009901	dG=-26.6, p-value=0.009901

droMoj3

dG=-28.3, p-value=0.009901	dG=-27.8, p-value=0.009901

droGri2

dG=-26.7, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-25.9, p-value=0.009901

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