Secondary structure and small RNA-seq evidence for dme-mir-310

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:16471242-16471360 -	AAAAGTGTTT------GC----G-----------------------AAAACATAAACATTTGCAGGGC-GGGTCGTGTGTCAGTGTATTTAT-------------ATCT-TAGC----------TATATTGCACACTTCCCGGCCTTTAAATGTCCA---ATGTTTCAACATT-------------TAAATCT-----
droSim1	chr2R:15132542-15132660 -	AAAAGTGCTT------GC----A-----------------------AAAACATAAACATTTGCAGGAC-GGGTCGTGTGTCAGTGTATTTAC-------------TTCT-TAGC----------TATATTGCACACTTCCCGGCCTTTAAATGTCCA---ATGTTTCAACTTT-------------AATATCT-----
droSec1	super_1:14025465-14025583 -	AAAAGTGCTT------GC----A-----------------------AAAACATAAACATTTGCAGGAC-GGGTCGTGTGTCAGTGTATTTAC-------------TTCT-TAAC----------TATATTGCACACTTCCCGGCCTTTAAATGTCCA---ATGTTTCAACTTT-------------AATATCT-----
droYak2	chr2R:12724925-12725037 +	CTT-------------GC----A-----------------------AATACACAAACATTTGCAGGAC-GGGTCGTGTGGCAGTGTATTGAT-------------TTCT-TAGC----------TATATTGCACACTTCCCGCCCTTTAAATGTCCA---GTGTTTCGACTTG-------------GATATCT-----
droEre2	scaffold_4845:10616419-10616531 -	CTT-------------GC----A-----------------------AATACACAAATATTTGCAGGAC-GGGTCGTGTGTCAATGTATTGAT-------------CTCT-TAGC----------TATATTGCACACTTCCCGCCCTTTAAATGTCCA---GTGTTTCAACTTG-------------AATATCT-----
droAna3	scaffold_13266:4133041-4133158 +	AATAGC----------------------------------------AAAACATAAACACTTGCAGGAC-GGGGAGCGTGACAATATATATAT-------------TTTA-TAAA--------CATATATTGCACACCTCCCGGCCTATAAGTGTAAA----TGTTCCTACAGG-------------TAAAACTTCTAA
dp4	chr3:8679992-8680133 +	ATTATAGTGT------GCGGAGTATGTGCTGTGTAT--T-------TGTACACCAACATTTGTGCGTCTAAGATCTGT-GCAGTATATACAT-------ACATAG-AA-TACAA----------AATATTGCAGACTTCTCAGACTACAAATGTGAA---CTGTCTGGTCTTC-------------AAAAAAT-----
droPer1	super_4:2566796-2566912 +	CTGTGCATTT------G-------------------------------TACACCAACATTTGTTCGTCTAAGTTCTGTG-CAGTATATACAT-------ACATAG-TT-TAAAA----------AATATTGCACACTTCTCAGACTACAAATGTGAA---CTGTCTGGTCTTC-------------AAAA--------
droWil1	scaffold_180700:3453399-3453550 +	GAAGGAGTCAATGACCAC----A-----------------------AATTTTCAAACATTCTTTGGAC-GGACTT-GT-CAAATATGTTTGG-------ATATAAAATT-CAACAATTGGACAACATATTGATCAAAACCGGGCCAAAAATTGTTGG---AAAATTCTTCAAAGTTGTTGGACTTGACAATTT-----
droVir3	scaffold_12875:13668721-13668866 -	AAAACAATTT------GG----TAAATACTGCGCATAGCCTTGCGCCTTATGTAATCATTTTTAGGCC-GTGCTCTGTGTGAATATGTTTTT-------------AACTATAAT----------CATATTGCACATCTCCCGGCCTATAAGTGTAGATGCATAATTCATCAAA-------------TATAAAT-----
droMoj3	scaffold_6496:9090283-9090389 -	TGT--------------------------------------------------ATCCATTTTTAGGCC-GTGCTATGTGACAATATGTATTT-------AAATTG-TA-TTTAT----------CATATTGCACATCTCCCGGCCTACAAGTGTAAATGCACAATTCAACT----------------ATGTAC-----
droGri2	scaffold_15245:17564471-17564548 +	C--------------------------------------------------------------AGGAT-GGAAGCTGTGACAATATGTAGGTTTTAATTAATTTA-TA-TTTCA----------TATATTGCACACCTCCCGGCCTATAAATG---------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:16471242-16471360 -	AAAAGTGTTT------GC----G-----------------------AAAACATAAACATTTGCAGGGC-GGGTCGTGTGTCAGTGTATTTAT-------------ATCT-TAGC----------TATATTGCACACTTCCCGGCCTTTAAATGTCCA---ATGTTTCAACATT-------------TAAATCT-----
droSim1	chr2R:15132542-15132660 -	AAAAGTGCTT------GC----A-----------------------AAAACATAAACATTTGCAGGAC-GGGTCGTGTGTCAGTGTATTTAC-------------TTCT-TAGC----------TATATTGCACACTTCCCGGCCTTTAAATGTCCA---ATGTTTCAACTTT-------------AATATCT-----
droSec1	super_1:14025465-14025583 -	AAAAGTGCTT------GC----A-----------------------AAAACATAAACATTTGCAGGAC-GGGTCGTGTGTCAGTGTATTTAC-------------TTCT-TAAC----------TATATTGCACACTTCCCGGCCTTTAAATGTCCA---ATGTTTCAACTTT-------------AATATCT-----
droYak2	chr2R:12724925-12725037 +	CTT-------------GC----A-----------------------AATACACAAACATTTGCAGGAC-GGGTCGTGTGGCAGTGTATTGAT-------------TTCT-TAGC----------TATATTGCACACTTCCCGCCCTTTAAATGTCCA---GTGTTTCGACTTG-------------GATATCT-----
droEre2	scaffold_4845:10616419-10616531 -	CTT-------------GC----A-----------------------AATACACAAATATTTGCAGGAC-GGGTCGTGTGTCAATGTATTGAT-------------CTCT-TAGC----------TATATTGCACACTTCCCGCCCTTTAAATGTCCA---GTGTTTCAACTTG-------------AATATCT-----
droAna3	scaffold_13266:4133041-4133158 +	AATAGC----------------------------------------AAAACATAAACACTTGCAGGAC-GGGGAGCGTGACAATATATATAT-------------TTTA-TAAA--------CATATATTGCACACCTCCCGGCCTATAAGTGTAAA----TGTTCCTACAGG-------------TAAAACTTCTAA
dp4	chr3:8679992-8680133 +	ATTATAGTGT------GCGGAGTATGTGCTGTGTAT--T-------TGTACACCAACATTTGTGCGTCTAAGATCTGT-GCAGTATATACAT-------ACATAG-AA-TACAA----------AATATTGCAGACTTCTCAGACTACAAATGTGAA---CTGTCTGGTCTTC-------------AAAAAAT-----
droPer1	super_4:2566796-2566912 +	CTGTGCATTT------G-------------------------------TACACCAACATTTGTTCGTCTAAGTTCTGTG-CAGTATATACAT-------ACATAG-TT-TAAAA----------AATATTGCACACTTCTCAGACTACAAATGTGAA---CTGTCTGGTCTTC-------------AAAA--------
droWil1	scaffold_180700:3453399-3453550 +	GAAGGAGTCAATGACCAC----A-----------------------AATTTTCAAACATTCTTTGGAC-GGACTT-GT-CAAATATGTTTGG-------ATATAAAATT-CAACAATTGGACAACATATTGATCAAAACCGGGCCAAAAATTGTTGG---AAAATTCTTCAAAGTTGTTGGACTTGACAATTT-----
droVir3	scaffold_12875:13668721-13668866 -	AAAACAATTT------GG----TAAATACTGCGCATAGCCTTGCGCCTTATGTAATCATTTTTAGGCC-GTGCTCTGTGTGAATATGTTTTT-------------AACTATAAT----------CATATTGCACATCTCCCGGCCTATAAGTGTAGATGCATAATTCATCAAA-------------TATAAAT-----
droMoj3	scaffold_6496:9090283-9090389 -	TGT--------------------------------------------------ATCCATTTTTAGGCC-GTGCTATGTGACAATATGTATTT-------AAATTG-TA-TTTAT----------CATATTGCACATCTCCCGGCCTACAAGTGTAAATGCACAATTCAACT----------------ATGTAC-----
droGri2	scaffold_15245:17564471-17564548 +	C--------------------------------------------------------------AGGAT-GGAAGCTGTGACAATATGTAGGTTTTAATTAATTTA-TA-TTTCA----------TATATTGCACACCTCCCGGCCTATAAATG---------------------------------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAAAGTGCTTGCAAAAACATAAACATTTGCAGGACGGGTCGTGTGTCAGTGTATTTACTTCTTAGCT---------------------------------------ATATTGCACACTTCCCGGCCTTTAAATGTCCAATGTTTCAACTTTAATATCT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...........................................................................................................TATTGCACACTTCCCGGCCTTT.............................	22	1	1479.00	1479	1479
...........................................................................................................TATTGCACACTTCCCGGCCTT..............................	21	1	441.00	441	441
...........................................................................................................TATTGCACACTTCCCGGCCTTTA............................	23	1	75.00	75	75
...........................................................................................................TATTGCACACTTCCCGGCCT...............................	20	1	74.00	74	74
...........................................................................................................TATTGCACACTTCCCGGCCTTTAA...........................	24	1	48.00	48	48
............................................................................................................ATTGCACACTTCCCGGCCTTT.............................	21	1	8.00	8	8
...........................................................................................................TATTGCACACTTCCCGGCCTTTAAA..........................	25	1	8.00	8	8
..............................AGGACGGGTCGTGTGTCAGT............................................................................................................	20	1	4.00	4	4
............................................................................................................ATTGCACACTTCCCGGCCT...............................	19	1	1.00	1	1
............................................................................................................ATTGCACACTTCCCGGCCTT..............................	20	1	1.00	1	1
...............................................................................................................GCACACTTCCCGGCCTTT.............................	18	1	1.00	1	1
...........................................................................................................TATTGCACACTTCCCGGCC................................	19	1	1.00	1	1

dp4

ATTATAGTGTGC----------------GGAGTATGTGCTGTGTATTTGTACACCAACATTTGTGCGTCTAAGATCTGTGCAGTATATACATACATAGAATACAAAATATTGCAGACTTCTCAGACTACAAATGTGAACTGTCTGGTCTTCAAAAAAT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...............................................................TGCGTCTAAGATCTGTGCAGTAT........................................................................	23	1	19.00	19	18	1
.............................................................................................................TTGCAGACTTCTCAGACTACA............................	21	1	8.00	8	8	0
...........................................................................................................TATTGCAGACTTCTCAGACTAC.............................	22	1	5.00	5	5	0
...............................................................TGCGTCTAAGATCTGTGCAGT..........................................................................	21	1	4.00	4	3	1
...........................................................................................................TATTGCAGACTTCTCAGACTACA............................	23	1	2.00	2	2	0
...........................................................................................................TATTGCAGACTTCTCAGACT...............................	20	1	2.00	2	2	0
...........................................................................................................TATTGCAGACTTCTCAGACTA..............................	21	1	2.00	2	2	0
.............................................................TGTGCGTCTAAGATCTGTGCAG...........................................................................	22	1	2.00	2	1	1
.............................................................TGTGCGTCTAAGATCTGTGCAGTA.........................................................................	24	1	1.00	1	1	0
...........................................................................................................TATTGCAGACTTCTCAGACTACAA...........................	24	1	1.00	1	1	0
.............................................................................................................TTGCAGACTTCTCAGACTA..............................	19	1	1.00	1	1	0
..............................................................GTGCGTCTAAGATCTGTGCA............................................................................	20	1	1.00	1	1	0
.............................................................TGTGCGTCTAAGATCTGTGCA............................................................................	21	1	1.00	1	1	0
.................................................................CGTCTAAGATCTGTGCAGTAT........................................................................	21	1	1.00	1	1	0
...............................................................TGCGTCTAAGATCTGTGCAG...........................................................................	20	1	1.00	1	0	1
.............................................................................................................TTGCAGACTTCTCAGACTAC.............................	20	1	1.00	1	1	0
...............................................................TGCGTCTAAGATCTGTGCAGTA.........................................................................	22	1	1.00	1	1	0

Secondary Structure

dm3

dG=-28.3, p-value=0.009901	dG=-28.0, p-value=0.009901	dG=-28.0, p-value=0.009901

droSim1

dG=-24.5, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.5, p-value=0.009901

droSec1

dG=-24.8, p-value=0.009901	dG=-24.5, p-value=0.009901	dG=-24.5, p-value=0.009901

droYak2

dG=-25.2, p-value=0.009901	dG=-25.2, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.9, p-value=0.009901

droEre2

dG=-25.2, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.3, p-value=0.009901	dG=-24.2, p-value=0.009901

droAna3

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

dp4

dG=-17.5, p-value=0.009901	dG=-17.2, p-value=0.009901

droPer1

dG=-17.9, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.2, p-value=0.009901	dG=-16.9, p-value=0.009901

droWil1

dG=-16.6, p-value=0.009901	dG=-16.6, p-value=0.009901	dG=-16.6, p-value=0.009901	dG=-16.6, p-value=0.009901	dG=-16.6, p-value=0.009901

droVir3

dG=-20.7, p-value=0.009901	dG=-20.3, p-value=0.009901	dG=-20.3, p-value=0.009901	dG=-19.9, p-value=0.009901	dG=-19.8, p-value=0.009901

droMoj3

dG=-23.6, p-value=0.009901	dG=-23.1, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.7, p-value=0.009901

droGri2

dG=-18.2, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.0, p-value=0.009901	dG=-17.9, p-value=0.009901	dG=-17.7, p-value=0.009901

Generated: 03/07/2013 at 05:15 PM