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

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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

Secondary Structure

dm3

-40.6	-40.4	-40.1	-39.9	-39.9	-39.9

droSim1

-40.6	-40.4	-40.1	-39.9	-39.9	-39.9

droSec1

-41.5	-41.3	-40.8	-40.7	-40.6	-40.5

droYak2

-47.8	-47.0	-46.8

droEre2

-48.5	-48.0	-47.8	-47.8	-47.8	-47.7

droAna3

-41.8	-41.8	-41.0	-41.0	-40.8	-40.8

dp4

-41.0	-40.9	-40.9	-40.9	-40.8	-40.8

droPer1

-41.0	-40.9	-40.9	-40.9	-40.8	-40.8

droWil1

-33.3	-33.1	-33.0	-32.9	-32.9	-32.7

droVir3

-41.3	-40.6	-40.5	-40.5	-40.3

droMoj3

-43.5	-43.5	-42.7	-42.7	-42.7	-42.7

droGri2

-44.0	-44.0	-44.0	-44.0	-44.0	-44.0

Generated: 01/05/2013 at 05:16 PM