Secondary structure and small RNA-seq evidence for dme-mir-306

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:16698389-16698503 +	GTGAATAG-TTTAAA------AG--------------TCCACTC-G-----ATGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTGGGACATA-ATCTACA----AATA-------------A
droSim1	zdv96e12.b1:525-640 +	GTGAATAG-TTTAAA------AG--------------TCCACTC-G-----ATGGCTCAGGTACTTAGTGACTCTCAAT--------GCCTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTGGGACATA-ATCTACA----AATA-------------A
droSec1	super_7:345406-345520 +	GTGAACAG-TTTAAA------AT--------------TCCACTC-G-----ATGGCTCAGGTACTTAGTGACTCTCAAT--------GCCTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTGGGACATA-ATCTACA----AATA-------------A
droYak2	chr2R:4404548-4404662 -	GTGAAAAG-TTTTAA------AG--------------TCCACTC-G-----GTGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTAGGACATA-ATCCACA----AATA-------------A
droEre2	scaffold_4845:19768040-19768155 +	GTGAATAG-TTTAAG------TG--------------TCCACTC-G-----GTGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTGGGACGCA-ATCAACA---AAATA-------------A
droAna3	scaffold_12916:15864848-15864962 -	GTGAAAGT-GCCAGA------AG--------------TCCACTT-G-----GTAGCTCAGGTACTTAGTGACTCTCAAT--------GCATTTGA--CATTTTGGGAGCCACTTTGTGCCTGGGCCA-----TCAGTGCGACTAT-ATCTTCT----ATTA-------------A
dp4	chr4_group3:8443802-8443917 +	GTGATTTA-TCTACA------AG--------------CACACTTTG-----CCGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTCGA--CATCTTGAGAGTCTCTCTGTGCCTGCACTG-----GCGGTGGTGCAAC-TGCAACG----ATTA-------------A
droPer1	super_1:9894921-9895036 +	GTGATTTA-TCTACA------AG--------------CACACTTTG-----CCGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTCGA--CATCTTGAGAGTCTCTCTGTGCCTGCACTG-----GCGGTGGTGCAAC-TGCAACG----ATTA-------------A
droWil1	scaffold_181132:873705-873839 -	GTGACTATACAAAGTGATACGAG--------------TTATCTCTGCCTAAACAGCTCAGGTACTTAGTGACTCTCAAA--------GAATATATATAGACTTGAGAGACGCTCTGTACCTAGACTGTTGTGTCTGCGGAATGTC-AACATCA----TGTG-------------T
droVir3	scaffold_12963:12863192-12863320 -	GTGCTG--------A------ACTC-CTCCCGCCCTGCACACCC-C-----GCTGCTCAGGTACTTAGTGACTCTCAATCATCTATTGCTTTGCA--TACCTTGAGGGTCGCTCTGTGCCTGTGCCG-----CCTGTGCTGCACA-ACCAACG----ACGA-------------G
droMoj3	scaffold_6500:7201931-7202062 +	ATTCATGA-TGTCC-------AG--------------CACACGC-T-----GCAGCTCAGGTACTTAGTGACTCTCAATCACATATTGCTTTGCA--TACTTTGAGGGTCGCTCTGTGCCTGTGCCG-----CCCGTGTTGCACACAGCCACA----CA---ATTGTGA-ATTCG
droGri2	scaffold_14978:830883-831041 +	GTGTTAAA-TGTGGAAAAACCAATCCAATCCG--CTGCACACGT-T-----GCTGCTCAGGTACTTAGTGACTCTCAATTCAACATTGTATTGCA-CGCCTTTGAGGGTCGCTCTGTGCCTGTGTTG-----CACGTGTTGCATT-CACACCATCCGAGTGATTTGTGTCCTTTG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:16698389-16698503 +	GTGAATAG-TTTAAA------AG--------------TCCACTC-G-----ATGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTGGGACATA-ATCTACA----AATA-------------A
droSim1	zdv96e12.b1:525-640 +	GTGAATAG-TTTAAA------AG--------------TCCACTC-G-----ATGGCTCAGGTACTTAGTGACTCTCAAT--------GCCTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTGGGACATA-ATCTACA----AATA-------------A
droSec1	super_7:345406-345520 +	GTGAACAG-TTTAAA------AT--------------TCCACTC-G-----ATGGCTCAGGTACTTAGTGACTCTCAAT--------GCCTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTGGGACATA-ATCTACA----AATA-------------A
droYak2	chr2R:4404548-4404662 -	GTGAAAAG-TTTTAA------AG--------------TCCACTC-G-----GTGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTAGGACATA-ATCCACA----AATA-------------A
droEre2	scaffold_4845:19768040-19768155 +	GTGAATAG-TTTAAG------TG--------------TCCACTC-G-----GTGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTTGA--CATTTTGGGGGTCACTCTGTGCCTGTGCTG-----CCAGTGGGACGCA-ATCAACA---AAATA-------------A
droAna3	scaffold_12916:15864848-15864962 -	GTGAAAGT-GCCAGA------AG--------------TCCACTT-G-----GTAGCTCAGGTACTTAGTGACTCTCAAT--------GCATTTGA--CATTTTGGGAGCCACTTTGTGCCTGGGCCA-----TCAGTGCGACTAT-ATCTTCT----ATTA-------------A
dp4	chr4_group3:8443802-8443917 +	GTGATTTA-TCTACA------AG--------------CACACTTTG-----CCGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTCGA--CATCTTGAGAGTCTCTCTGTGCCTGCACTG-----GCGGTGGTGCAAC-TGCAACG----ATTA-------------A
droPer1	super_1:9894921-9895036 +	GTGATTTA-TCTACA------AG--------------CACACTTTG-----CCGGCTCAGGTACTTAGTGACTCTCAAT--------GCTTTCGA--CATCTTGAGAGTCTCTCTGTGCCTGCACTG-----GCGGTGGTGCAAC-TGCAACG----ATTA-------------A
droWil1	scaffold_181132:873705-873839 -	GTGACTATACAAAGTGATACGAG--------------TTATCTCTGCCTAAACAGCTCAGGTACTTAGTGACTCTCAAA--------GAATATATATAGACTTGAGAGACGCTCTGTACCTAGACTGTTGTGTCTGCGGAATGTC-AACATCA----TGTG-------------T
droVir3	scaffold_12963:12863192-12863320 -	GTGCTG--------A------ACTC-CTCCCGCCCTGCACACCC-C-----GCTGCTCAGGTACTTAGTGACTCTCAATCATCTATTGCTTTGCA--TACCTTGAGGGTCGCTCTGTGCCTGTGCCG-----CCTGTGCTGCACA-ACCAACG----ACGA-------------G
droMoj3	scaffold_6500:7201931-7202062 +	ATTCATGA-TGTCC-------AG--------------CACACGC-T-----GCAGCTCAGGTACTTAGTGACTCTCAATCACATATTGCTTTGCA--TACTTTGAGGGTCGCTCTGTGCCTGTGCCG-----CCCGTGTTGCACACAGCCACA----CA---ATTGTGA-ATTCG
droGri2	scaffold_14978:830883-831041 +	GTGTTAAA-TGTGGAAAAACCAATCCAATCCG--CTGCACACGT-T-----GCTGCTCAGGTACTTAGTGACTCTCAATTCAACATTGTATTGCA-CGCCTTTGAGGGTCGCTCTGTGCCTGTGTTG-----CACGTGTTGCATT-CACACCATCCGAGTGATTTGTGTCCTTTG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GTGAATAGTTTAAAAGTCCACT-CGATGGCTCAGGTACTTAGTGACTCTCAATGCCTTTGACATTTTGGGGGTCACTCTGTGCCTGTGCTGCCAGTGGGACATAATCTACAAATAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................TCAGGTACTTAGTGACTCTCA.................................................................	21	1	2506.00	2506	2506
..............................TCAGGTACTTAGTGACTCTCAA................................................................	22	1	1235.00	1235	1235
..............................TCAGGTACTTAGTGACTCTC..................................................................	20	1	142.00	142	142
...................................................................GGGGGTCACTCTGTGCCTGTGC...........................	22	1	77.00	77	77
................................AGGTACTTAGTGACTCTCA.................................................................	19	1	17.00	17	17
................................AGGTACTTAGTGACTCTCAA................................................................	20	1	13.00	13	13
...................................................................GGGGGTCACTCTGTGCCTGTG............................	21	1	10.00	10	10
..............................TCAGGTACTTAGTGACTCT...................................................................	19	1	9.00	9	9
..............................TCAGGTACTTAGTGACTCTCAAT...............................................................	23	1	6.00	6	6
...............................CAGGTACTTAGTGACTCTCAA................................................................	21	1	3.00	3	3
................................AGGTACTTAGTGACTCTC..................................................................	18	1	1.00	1	1
...............................CAGGTACTTAGTGACTCTCA.................................................................	20	1	1.00	1	1
.............................CTCAGGTACTTAGTGACTCTCA.................................................................	22	1	1.00	1	1
..............................TCAGGTACTTAGTGACTCTCAATGC.............................................................	25	1	1.00	1	1
..............................TCAGGTACTTAGTGACTC....................................................................	18	1	1.00	1	1

dp4

GTGATTTATCTACAAGCACACTTTGCCGGCTCAGGTACTTAGTGACTCTCAATGCTTTCGACATCTTGAGAGTCTCTCTGTGCCTGCACTGGCGGTGGTGCAACTGCAACGATTAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................TCAGGTACTTAGTGACTCTCA.................................................................	21	1	3587.00	3587	3156	431
..............................TCAGGTACTTAGTGACTCTCAA................................................................	22	1	2713.00	2713	2140	573
..............................TCAGGTACTTAGTGACTCTC..................................................................	20	1	347.00	347	151	196
..............................TCAGGTACTTAGTGACTCT...................................................................	19	1	59.00	59	17	42
................................AGGTACTTAGTGACTCTCA.................................................................	19	1	25.00	25	22	3
................................AGGTACTTAGTGACTCTCAA................................................................	20	1	25.00	25	21	4
...................................................................GAGAGTCTCTCTGTGCCTGCAC...........................	22	1	15.00	15	12	3
..............................TCAGGTACTTAGTGACTCTCAAT...............................................................	23	1	13.00	13	9	4
................................AGGTACTTAGTGACTCTC..................................................................	18	1	5.00	5	2	3
...............................CAGGTACTTAGTGACTCTCAA................................................................	21	1	5.00	5	5	0
.............................CTCAGGTACTTAGTGACTCTCA.................................................................	22	1	4.00	4	3	1
...............................CAGGTACTTAGTGACTCTCA.................................................................	20	1	4.00	4	4	0
...................................................................GAGAGTCTCTCTGTGCCTGC.............................	20	1	4.00	4	4	0
...................................................................GAGAGTCTCTCTGTGCCTGCA............................	21	1	3.00	3	3	0
.............................CTCAGGTACTTAGTGACTCTCAA................................................................	23	1	2.00	2	0	2
..................................GTACTTAGTGACTCTCAA................................................................	18	1	1.00	1	1	0
.........CTACAAGCACACTTTGCCGGC......................................................................................	21	1	1.00	1	1	0
...............................CAGGTACTTAGTGACTCTC..................................................................	19	1	1.00	1	1	0
........TCTACAAGCACACTTTGCCGGC......................................................................................	22	1	1.00	1	1	0
..............................TCAGGTACTTAGTGACTCTCAATGC.............................................................	25	1	1.00	1	1	0
...............................................................TCTTGAGAGTCTCTCTGTG..................................	19	1	1.00	1	1	0

Secondary Structure

dm3

dG=-33.6, p-value=0.009901	dG=-33.5, p-value=0.009901	dG=-32.9, p-value=0.009901	dG=-32.8, p-value=0.009901	dG=-32.7, p-value=0.009901

droSim1

dG=-33.6, p-value=0.009901	dG=-33.5, p-value=0.009901	dG=-32.9, p-value=0.009901	dG=-32.8, p-value=0.009901	dG=-32.7, p-value=0.009901

droSec1

dG=-33.6, p-value=0.009901	dG=-33.5, p-value=0.009901	dG=-32.9, p-value=0.009901	dG=-32.8, p-value=0.009901	dG=-32.7, p-value=0.009901

droYak2

dG=-36.1, p-value=0.009901	dG=-35.3, p-value=0.009901	dG=-35.1, p-value=0.009901

droEre2

dG=-36.1, p-value=0.009901	dG=-35.3, p-value=0.009901	dG=-35.1, p-value=0.009901

droAna3

dG=-32.8, p-value=0.009901	dG=-32.0, p-value=0.009901	dG=-31.8, p-value=0.009901

dp4

dG=-31.3, p-value=0.009901	dG=-31.2, p-value=0.009901	dG=-31.1, p-value=0.009901	dG=-30.4, p-value=0.009901	dG=-30.3, p-value=0.009901

droPer1

dG=-31.3, p-value=0.009901	dG=-31.2, p-value=0.009901	dG=-31.1, p-value=0.009901	dG=-30.4, p-value=0.009901	dG=-30.3, p-value=0.009901

droWil1

dG=-26.7, p-value=0.009901	dG=-26.6, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.2, p-value=0.009901

droVir3

dG=-35.0, p-value=0.009901	dG=-34.2, p-value=0.009901	dG=-34.2, p-value=0.009901

droMoj3

dG=-35.6, p-value=0.009901	dG=-34.8, p-value=0.009901	dG=-34.8, p-value=0.009901	dG=-34.7, p-value=0.009901

droGri2

dG=-33.9, p-value=0.009901	dG=-33.9, p-value=0.009901	dG=-33.3, p-value=0.009901

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