Secondary structure and small RNA-seq evidence for dme-mir-124

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:17566355-17566484 +	C-CCA----------------A--------------------GTGTCCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTACTCATACCCAATA
droSim1	chr2L:17270490-17270619 +	C-CCA----------------A--------------------GTGTCCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTACTCATACCCAATG
droSec1	super_7:1207305-1207434 +	C-CCA----------------A--------------------GTGTCCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTACTCATACCCAATG
droYak2	chr2R:3533165-3533294 -	C-CCA----------------A--------------------GTGTTCTTCATCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTTCTCATACCCAATG
droEre2	scaffold_4845:6683953-6684082 -	C-CCA----------------A--------------------GTGTCCTTCATCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTACTCATACCCAATG
droAna3	scaffold_12916:3309677-3309806 -	C-CAG----------------A--------------------GGCTTTTGTGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAA-----ACTACAAATGACATATT
dp4	chr4_group3:10867616-10867737 -	T-CTC----------------A--------------------GTGC---TCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAAACTCTACTA----------TCAAAAACAGCA
droPer1	super_8:2078713-2078834 -	T-CTC----------------A--------------------GTGC---TCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAAACTCTACTA----------TCAAAAACAGCA
droWil1	scaffold_180764:940183-940306 -	T-TCT---------------CA--------------------GA-------GTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGCAGGCCTATATGTTATTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAATTCTACAA-----AA-ACCAAAACGCAAAA
droVir3	scaffold_12963:16493143-16493272 +	G-ACAACATT---------------------------CGTGAGTG----CCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGAATTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAA-----TTAACAAA-----AATA
droMoj3	scaffold_6500:21419441-21419593 +	CGACAA--TTGCCCTGCGCTCAGCGTGCGGGACTCGCCGTGAGTG----ACGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGAATTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAA-----AA--------TCCAACA
droGri2	scaffold_15252:13906813-13906947 +	G-TGG----------------T--------------------GTGTGTGCCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGTTTTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACACTTCCATTCAAATATAACCAGCA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:17566355-17566484 +	C-CCA----------------A--------------------GTGTCCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTACTCATACCCAATA
droSim1	chr2L:17270490-17270619 +	C-CCA----------------A--------------------GTGTCCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTACTCATACCCAATG
droSec1	super_7:1207305-1207434 +	C-CCA----------------A--------------------GTGTCCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTACTCATACCCAATG
droYak2	chr2R:3533165-3533294 -	C-CCA----------------A--------------------GTGTTCTTCATCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTTCTCATACCCAATG
droEre2	scaffold_4845:6683953-6684082 -	C-CCA----------------A--------------------GTGTCCTTCATCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAA-----ATTACTCATACCCAATG
droAna3	scaffold_12916:3309677-3309806 -	C-CAG----------------A--------------------GGCTTTTGTGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAA-----ACTACAAATGACATATT
dp4	chr4_group3:10867616-10867737 -	T-CTC----------------A--------------------GTGC---TCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAAACTCTACTA----------TCAAAAACAGCA
droPer1	super_8:2078713-2078834 -	T-CTC----------------A--------------------GTGC---TCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAAACTCTACTA----------TCAAAAACAGCA
droWil1	scaffold_180764:940183-940306 -	T-TCT---------------CA--------------------GA-------GTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGCAGGCCTATATGTTATTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAATTCTACAA-----AA-ACCAAAACGCAAAA
droVir3	scaffold_12963:16493143-16493272 +	G-ACAACATT---------------------------CGTGAGTG----CCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGAATTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAA-----TTAACAAA-----AATA
droMoj3	scaffold_6500:21419441-21419593 +	CGACAA--TTGCCCTGCGCTCAGCGTGCGGGACTCGCCGTGAGTG----ACGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGAATTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAA-----AA--------TCCAACA
droGri2	scaffold_15252:13906813-13906947 +	G-TGG----------------T--------------------GTGTGTGCCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGTTTTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACACTTCCATTCAAATATAACCAGCA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCCAAGTGTCCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAAATTACTCATACCCAATG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................................................TAAGGCACGCGGTGAATGCCA......................................	21	1	3087.00	3087	3087
.......................................................................TAAGGCACGCGGTGAATGCCAA.....................................	22	1	1416.00	1416	1416
.......................................................................TAAGGCACGCGGTGAATGCCAAG....................................	23	1	578.00	578	578
.......................................................................TAAGGCACGCGGTGAATGCC.......................................	20	1	287.00	287	287
.....................................GGTATCCACTGTAGGCCTATATG......................................................................	23	1	231.00	231	231
....................................TGGTATCCACTGTAGGCCTATATG......................................................................	24	1	22.00	22	22
.....................................GGTATCCACTGTAGGCCTATA........................................................................	21	1	21.00	21	21
........................................................................AAGGCACGCGGTGAATGCCA......................................	20	1	9.00	9	9
.....................................GGTATCCACTGTAGGCCTATAT.......................................................................	22	1	8.00	8	8
.....................................GGTATCCACTGTAGGCCTAT.........................................................................	20	1	4.00	4	4
.......................................................................TAAGGCACGCGGTGAATGCCAAGA...................................	24	1	4.00	4	4
.......................................................................TAAGGCACGCGGTGAATG.........................................	18	1	4.00	4	4
....................................TGGTATCCACTGTAGGCCTATA........................................................................	22	1	3.00	3	3
.......................................................................TAAGGCACGCGGTGAATGC........................................	19	1	3.00	3	3
........................................................................AAGGCACGCGGTGAATGCCAAG....................................	22	1	2.00	2	2
........................................................................AAGGCACGCGGTGAATGCCAA.....................................	21	1	2.00	2	2
.........................................................................AGGCACGCGGTGAATGCCAAG....................................	21	1	1.00	1	1
.........................................................................AGGCACGCGGTGAATGCCA......................................	19	1	1.00	1	1
.....................................GGTATCCACTGTAGGCCTATATGT.....................................................................	24	1	1.00	1	1
.....................................GGTATCCACTGTAGGCCTA..........................................................................	19	1	1.00	1	1
.........................................................................AGGCACGCGGTGAATGCCAAGA...................................	22	1	1.00	1	1

dp4

TCTCAGTGC---TCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAAACTCTACTA-----TCAAAAACAGCA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................................................................TAAGGCACGCGGTGAATGCCA......................................	21	1	37470.00	37470	3038	34432
.......................................................................TAAGGCACGCGGTGAATGCCAAG....................................	23	1	10075.00	10075	4518	5557
.......................................................................TAAGGCACGCGGTGAATGCCAA.....................................	22	1	5869.00	5869	2270	3599
.......................................................................TAAGGCACGCGGTGAATGCC.......................................	20	1	5677.00	5677	207	5470
....................................TGGTATCCACTGTAGGCCTATATG......................................................................	24	1	466.00	466	346	120
.......................................................................TAAGGCACGCGGTGAATGC........................................	19	1	256.00	256	4	252
.....................................GGTATCCACTGTAGGCCTATATG......................................................................	23	1	208.00	208	194	14
.......................................................................TAAGGCACGCGGTGAATGCCAAGA...................................	24	1	195.00	195	24	171
........................................................................AAGGCACGCGGTGAATGCCA......................................	20	1	118.00	118	5	113
........................................................................AAGGCACGCGGTGAATGCCAAG....................................	22	1	96.00	96	45	51
.......................................................................TAAGGCACGCGGTGAATG.........................................	18	1	41.00	41	3	38
....................................TGGTATCCACTGTAGGCCTATA........................................................................	22	1	27.00	27	26	1
....................................TGGTATCCACTGTAGGCCTA..........................................................................	20	1	25.00	25	1	24
....................................TGGTATCCACTGTAGGCCTATAT.......................................................................	23	1	25.00	25	18	7
........................................................................AAGGCACGCGGTGAATGCCAA.....................................	21	1	18.00	18	5	13
.....................................GGTATCCACTGTAGGCCTATA........................................................................	21	1	15.00	15	15	0
........................................................................AAGGCACGCGGTGAATGCC.......................................	19	1	15.00	15	0	15
.........................................................................AGGCACGCGGTGAATGCCAAG....................................	21	1	13.00	13	7	6
.........................................................................AGGCACGCGGTGAATGCCA......................................	19	1	10.00	10	2	8
....................................TGGTATCCACTGTAGGCCTAT.........................................................................	21	1	9.00	9	5	4
....................................TGGTATCCACTGTAGGCCT...........................................................................	19	1	8.00	8	0	8
.....................................GGTATCCACTGTAGGCCTATAT.......................................................................	22	1	7.00	7	6	1
.........................................................................AGGCACGCGGTGAATGCCAA.....................................	20	1	6.00	6	2	4

Secondary Structure

dm3

dG=-27.2, p-value=0.009901

droSim1

dG=-27.2, p-value=0.009901

droSec1

dG=-27.2, p-value=0.009901

droYak2

dG=-27.2, p-value=0.009901

droEre2

dG=-27.2, p-value=0.009901

droAna3

dG=-27.2, p-value=0.009901

dp4

dG=-27.2, p-value=0.009901

droPer1

dG=-27.2, p-value=0.009901

droWil1

dG=-28.5, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-27.5, p-value=0.009901

droVir3

dG=-27.7, p-value=0.009901

droMoj3

dG=-27.7, p-value=0.009901

droGri2

dG=-27.6, p-value=0.009901	dG=-27.6, p-value=0.009901	dG=-27.2, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.8, p-value=0.009901

Generated: 03/07/2013 at 04:49 PM