Secondary structure and small RNA-seq evidence for dme-mir-92b

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:21477105-21477234 +	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCATTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAATGAGTGTCGCAGTCGACGATCTACACAGTGCA
droSim1	chr3R:21305387-21305516 +	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCGACGATCTACACAGTGCA
droSec1	super_13:263913-264042 +	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCGACGATCTACACAGTGCA
droYak2	chr3R:24996445-24996574 -	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCAGCGATCTGCACAGTGCG
droEre2	scaffold_4820:6565044-6565173 -	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCAGCGATCTACACAGTGCA
droAna3	scaffold_13340:3732627-3732749 +	AGTGCAGT------GAAGCATTAAA---ACGTCACCTGATGTAGGCCGTGCCCGGTGCTTATTTGTTACT-TTTGGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCAAAGGCAGCTATCTTCAC------
dp4	chr2:23630755-23630875 -	-GTACAGT-----TGGAGCATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTCGTTGTTTGAAAATACAAATTGCACTAGTCCCGGCCTGCAGAGAGTGTCGCACACAACGAGCT----------
droPer1	super_3:6405653-6405778 -	AGTGCAGTACAGTTGGAGCATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTCGTTGTTTGAAAATACAAATTGCACTAGTCCCGGCCTGCAGAGAGTGTCGCACACAACGAGCT----------
droWil1	scaffold_181130:14574160-14574279 -	TGCGGAA----ATTGTATCTTTAAAAATACGTCACATGATGTAGACCGTGCCTGGTGCTTATTTGTTGCTATTTAAATATACAAATTGCACTAGTCCCGGCCTGCAGTAAGTGTCGCAAACAAC---------------
droVir3	scaffold_12855:6883792-6883910 +	AGTGGTGT------GCAACATTAAA---ACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGCGAAAATCCAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGCCAACGTTC-----------
droMoj3	scaffold_6540:25731646-25731761 -	AGTGCTGT------GCAACATTAAA---ACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGCGAAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAAACAACG--------------
droGri2	scaffold_14906:3026528-3026659 +	AGTGATGT---GGTGCAACATTAAA---ACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGTGAAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAAACAACAAACAACA-ACAGCA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:21477105-21477234 +	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCATTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAATGAGTGTCGCAGTCGACGATCTACACAGTGCA
droSim1	chr3R:21305387-21305516 +	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCGACGATCTACACAGTGCA
droSec1	super_13:263913-264042 +	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCGACGATCTACACAGTGCA
droYak2	chr3R:24996445-24996574 -	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCAGCGATCTGCACAGTGCG
droEre2	scaffold_4820:6565044-6565173 -	AGTGCAGT------GGTACATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCAGCGATCTACACAGTGCA
droAna3	scaffold_13340:3732627-3732749 +	AGTGCAGT------GAAGCATTAAA---ACGTCACCTGATGTAGGCCGTGCCCGGTGCTTATTTGTTACT-TTTGGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCAAAGGCAGCTATCTTCAC------
dp4	chr2:23630755-23630875 -	-GTACAGT-----TGGAGCATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTCGTTGTTTGAAAATACAAATTGCACTAGTCCCGGCCTGCAGAGAGTGTCGCACACAACGAGCT----------
droPer1	super_3:6405653-6405778 -	AGTGCAGTACAGTTGGAGCATTAAA---ACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTCGTTGTTTGAAAATACAAATTGCACTAGTCCCGGCCTGCAGAGAGTGTCGCACACAACGAGCT----------
droWil1	scaffold_181130:14574160-14574279 -	TGCGGAA----ATTGTATCTTTAAAAATACGTCACATGATGTAGACCGTGCCTGGTGCTTATTTGTTGCTATTTAAATATACAAATTGCACTAGTCCCGGCCTGCAGTAAGTGTCGCAAACAAC---------------
droVir3	scaffold_12855:6883792-6883910 +	AGTGGTGT------GCAACATTAAA---ACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGCGAAAATCCAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGCCAACGTTC-----------
droMoj3	scaffold_6540:25731646-25731761 -	AGTGCTGT------GCAACATTAAA---ACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGCGAAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAAACAACG--------------
droGri2	scaffold_14906:3026528-3026659 +	AGTGATGT---GGTGCAACATTAAA---ACGTCACCTGATGTAGGTCGTGCCTGGTGCTTATTTGTTGTTATGTGAAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAAACAACAAACAACA-ACAGCA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AGTGCAGT-GGTACATTAAAACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTTGCCTTTTCGAAATACAAATTGCACTAGTCCCGGCCTGCAGTGAGTGTCGCAGTCGACGATCTACACAGTGCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...........................................................................AATTGCACTAGTCCCGGCCTGC..................................	22	1	2817.00	2817	2817
...........................................................................AATTGCACTAGTCCCGGCCTG...................................	21	1	2235.00	2235	2235
...........................................................................AATTGCACTAGTCCCGGCCT....................................	20	1	266.00	266	266
..................................AGGCCGTGCCCAGTGCTTATTTG..........................................................................	23	1	108.00	108	108
...........................................................................AATTGCACTAGTCCCGGCCTGCA.................................	23	1	99.00	99	99
............................................................................ATTGCACTAGTCCCGGCCTGC..................................	21	1	16.00	16	16
..........................................................................AAATTGCACTAGTCCCGGCCTGC..................................	23	1	12.00	12	12
...........................................................................AATTGCACTAGTCCCGGCC.....................................	19	1	12.00	12	12
............................................................................ATTGCACTAGTCCCGGCCTG...................................	20	1	12.00	12	12
..........................................................................AAATTGCACTAGTCCCGGCCTG...................................	22	1	7.00	7	7
..........................................................................AAATTGCACTAGTCCCGGCCT....................................	21	1	5.00	5	5
...........................................................................AATTGCACTAGTCCCGGC......................................	18	1	5.00	5	5
..................................AGGCCGTGCCCAGTGCTTATTTGT.........................................................................	24	1	4.00	4	4
............................................................................ATTGCACTAGTCCCGGCCTGCA.................................	22	1	2.00	2	2
..................................AGGCCGTGCCCAGTGCTTATTT...........................................................................	22	1	2.00	2	2
.........................................................TTGCCTTTTCGAAATACAA.......................................................	19	1	1.00	1	1
.........................................................TTGCCTTTTCGAAATACAAA......................................................	20	1	1.00	1	1
............................................................................ATTGCACTAGTCCCGGCCT....................................	19	1	1.00	1	1
..................................AGGCCGTGCCCAGTGCTTATT............................................................................	21	1	1.00	1	1
..............................................................................TGCACTAGTCCCGGCCTG...................................	18	1	1.00	1	1
.............................................................................TTGCACTAGTCCCGGCCTGC..................................	20	1	1.00	1	1

dp4

-GTACAGTTGGAGCATTAAAACGTCACCTGATGTAGGCCGTGCCCAGTGCTTATTTGTCGTTGTTTGAAAATACAAATTGCACTAGTCCCGGCCTGCAGAGAGTGTCGCACACAACGAGCT----------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...........................................................................AATTGCACTAGTCCCGGCCTGC..................................	22	1	3406.00	3406	3262	144
...........................................................................AATTGCACTAGTCCCGGCCTG...................................	21	1	3329.00	3329	3288	41
...........................................................................AATTGCACTAGTCCCGGCCT....................................	20	1	866.00	866	850	16
..................................AGGCCGTGCCCAGTGCTTATTTG..........................................................................	23	1	122.00	122	121	1
...........................................................................AATTGCACTAGTCCCGGCC.....................................	19	1	71.00	71	69	2
............................................................................ATTGCACTAGTCCCGGCCTGC..................................	21	1	63.00	63	52	11
............................................................................ATTGCACTAGTCCCGGCCTG...................................	20	1	52.00	52	40	12
...........................................................................AATTGCACTAGTCCCGGCCTGCA.................................	23	1	48.00	48	48	0
............................................................................ATTGCACTAGTCCCGGCCT....................................	19	1	22.00	22	12	10
...........................................................................AATTGCACTAGTCCCGGC......................................	18	1	18.00	18	18	0
..........................................................................AAATTGCACTAGTCCCGGCCTGC..................................	23	1	7.00	7	7	0
.........................................................TCGTTGTTTGAAAATACA........................................................	18	1	5.00	5	5	0
..................................AGGCCGTGCCCAGTGCTTATTT...........................................................................	22	1	5.00	5	5	0
...............................................................................GCACTAGTCCCGGCCTGC..................................	18	1	3.00	3	3	0
..................................AGGCCGTGCCCAGTGCTTATT............................................................................	21	1	3.00	3	3	0
..........................................................................AAATTGCACTAGTCCCGGCCTG...................................	22	1	3.00	3	3	0
.........................................................TCGTTGTTTGAAAATACAAA......................................................	20	1	2.00	2	2	0
.............................................................................TTGCACTAGTCCCGGCCTGC..................................	20	1	2.00	2	2	0
..............................................................................TGCACTAGTCCCGGCCTGC..................................	19	1	1.00	1	1	0

Secondary Structure

dm3

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

droSim1

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

droSec1

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

droYak2

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

droEre2

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

droAna3

dG=-26.4, p-value=0.009901	dG=-26.1, p-value=0.009901

dp4

dG=-27.3, p-value=0.009901	dG=-27.0, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.5, p-value=0.009901

droPer1

dG=-27.3, p-value=0.009901	dG=-27.0, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.5, p-value=0.009901

droWil1

dG=-23.4, p-value=0.009901	dG=-22.7, p-value=0.009901

droVir3

dG=-26.5, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.5, p-value=0.009901

droMoj3

dG=-28.5, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901

droGri2

dG=-28.5, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901

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