Secondary structure and small RNA-seq evidence for dme-mir-277

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:5925729-5925858 +	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droSim1	chr3R:15450308-15450437 -	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droSec1	super_0:15987777-15987906 -	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droYak2	chr3R:9973459-9973588 +	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droEre2	scaffold_4770:15674279-15674408 -	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droAna3	scaffold_13340:6488981-6489110 +	A-GAAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGAAA------------------
dp4	chr2:5020571-5020711 -	G-ATTAACTGAGCA--TCCT-TTGA--AGGTTTTGGGTTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGACAAATA--TGC-GA------
droPer1	super_19:726018-726152 -	G-ATTAACTGAGCA--TCCT-TTGA--AGGTTTTGGGTTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGACAAAT---------------
droWil1	scaffold_181089:11168086-11168217 -	G-AAAACAA--GCA--TCCTTTTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAAATTTCTAAAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCTCGAATGCAAGAAA------------------
droVir3	scaffold_12855:2684186-2684333 -	GTATATAGA--GCATATCCT-T-GAGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGAAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAACAA-ATAAATGCTGAAT----
droMoj3	scaffold_6540:11885074-11885210 -	T-ATAGCAT-AGCA--TCCTCTTGAGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAACAA--CTAA-------------
droGri2	scaffold_14624:2266182-2266325 +	A--TA------TCA--TC-T-TTGAGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGAAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGAAA--TAAATGCTGAATAAAC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:5925729-5925858 +	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droSim1	chr3R:15450308-15450437 -	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droSec1	super_0:15987777-15987906 -	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droYak2	chr3R:9973459-9973588 +	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droEre2	scaffold_4770:15674279-15674408 -	G-ATAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGA-AGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA------------------
droAna3	scaffold_13340:6488981-6489110 +	A-GAAAAAT--GCA--TCCT-TTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGAAA------------------
dp4	chr2:5020571-5020711 -	G-ATTAACTGAGCA--TCCT-TTGA--AGGTTTTGGGTTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGACAAATA--TGC-GA------
droPer1	super_19:726018-726152 -	G-ATTAACTGAGCA--TCCT-TTGA--AGGTTTTGGGTTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGACAAAT---------------
droWil1	scaffold_181089:11168086-11168217 -	G-AAAACAA--GCA--TCCTTTTGA--AGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAAATTTCTAAAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCTCGAATGCAAGAAA------------------
droVir3	scaffold_12855:2684186-2684333 -	GTATATAGA--GCATATCCT-T-GAGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGAAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAACAA-ATAAATGCTGAAT----
droMoj3	scaffold_6540:11885074-11885210 -	T-ATAGCAT-AGCA--TCCTCTTGAGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGA-AGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAACAA--CTAA-------------
droGri2	scaffold_14624:2266182-2266325 +	A--TA------TCA--TC-T-TTGAGACAGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGAAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGAAA--TAAATGCTGAATAAAC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GATAAAAT--GCATCCTTTGAAGGTTTTGGGCTGCGTGTCAGGAGTGCATTTGCACTGAAACTATCTGAAGCATGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAGGAAA---------	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...........................................................................TAAATGCACTATCTGGTACGACA...........................................	23	1	3180.00	3180	3180
...........................................................................TAAATGCACTATCTGGTACGAC............................................	22	1	544.00	544	544
..................................CGTGTCAGGAGTGCATTTGCA......................................................................................	21	1	408.00	408	408
...........................................................................TAAATGCACTATCTGGTACGA.............................................	21	1	361.00	361	361
..................................CGTGTCAGGAGTGCATTTGC.......................................................................................	20	1	33.00	33	33
...........................................................................TAAATGCACTATCTGGTACG..............................................	20	1	30.00	30	30
............................................................................AAATGCACTATCTGGTACGACA...........................................	22	1	12.00	12	12
............................................................................AAATGCACTATCTGGTACGAC............................................	21	1	10.00	10	10
...................................GTGTCAGGAGTGCATTTGCA......................................................................................	20	1	8.00	8	8
...............................................................................TGCACTATCTGGTACGACA...........................................	19	1	5.00	5	5
.......................................................CTGAAACTATCTGAAGCATG..................................................................	20	1	4.00	4	4
...........................................................................TAAATGCACTATCTGGTACGACAT..........................................	24	1	4.00	4	4
..............................................................................ATGCACTATCTGGTACGACA...........................................	20	1	3.00	3	3
...................................GTGTCAGGAGTGCATTTGC.......................................................................................	19	1	2.00	2	2
..................................CGTGTCAGGAGTGCATTTGCACTGAAA................................................................................	27	1	1.00	1	1
..............................................................................ATGCACTATCTGGTACGA.............................................	18	1	1.00	1	1
.................................GCGTGTCAGGAGTGCATTTGCA......................................................................................	22	1	1.00	1	1

dp4

GATTAACTGAGCATCCTTTGAAGGTTTTGGGTTGCGTGTCAGGAGTGCATTTGCACTGAAACATTCTGAAGCTTGTAAATGCACTATCTGGTACGACATTCCAGAACGTACAATCTTCCCGAATGCAAGACAAATATGCGA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...........................................................................TAAATGCACTATCTGGTACGACA...........................................	23	1	79776.00	79776	3469	76307
...........................................................................TAAATGCACTATCTGGTACGA.............................................	21	1	6883.00	6883	749	6134
...........................................................................TAAATGCACTATCTGGTACGAC............................................	22	1	5851.00	5851	472	5379
...........................................................................TAAATGCACTATCTGGTACG..............................................	20	1	2200.00	2200	115	2085
..................................CGTGTCAGGAGTGCATTTGCA......................................................................................	21	1	872.00	872	694	178
..................................CGTGTCAGGAGTGCATTTGC.......................................................................................	20	1	117.00	117	25	92
............................................................................AAATGCACTATCTGGTACGACA...........................................	22	1	115.00	115	5	110
...........................................................................TAAATGCACTATCTGGTACGACAT..........................................	24	1	58.00	58	1	57
.............................................................................AATGCACTATCTGGTACGACA...........................................	21	1	43.00	43	4	39
...................................GTGTCAGGAGTGCATTTGCA......................................................................................	20	1	26.00	26	19	7
...........................................................................TAAATGCACTATCTGGTAC...............................................	19	1	26.00	26	3	23
..............................................................................ATGCACTATCTGGTACGACA...........................................	20	1	24.00	24	1	23
...............................................................................TGCACTATCTGGTACGACA...........................................	19	1	22.00	22	7	15
................................................................................GCACTATCTGGTACGACA...........................................	18	1	18.00	18	7	11
.......................................................CTGAAACATTCTGAAGCTTG..................................................................	20	1	16.00	16	5	11
............................................................................AAATGCACTATCTGGTACGAC............................................	21	1	6.00	6	1	5
..................................CGTGTCAGGAGTGCATTTG........................................................................................	19	1	6.00	6	1	5
............................................................................AAATGCACTATCTGGTACGA.............................................	20	1	5.00	5	0	5
..................................CGTGTCAGGAGTGCATTTGCACTGAA.................................................................................	26	1	5.00	5	1	4
.............................................................................AATGCACTATCTGGTACGAC............................................	20	1	5.00	5	0	5

Secondary Structure

dm3

dG=-26.4, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.5, p-value=0.009901

droSim1

dG=-26.4, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.5, p-value=0.009901

droSec1

dG=-26.4, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.5, p-value=0.009901

droYak2

dG=-26.4, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.5, p-value=0.009901

droEre2

dG=-26.4, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.9, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.5, p-value=0.009901

droAna3

dG=-26.1, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.2, p-value=0.009901

dp4

dG=-26.9, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.0, p-value=0.009901

droPer1

dG=-26.9, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.0, p-value=0.009901

droWil1

dG=-26.0, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.1, p-value=0.009901

droVir3

dG=-26.0, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.3, p-value=0.009901	dG=-25.1, p-value=0.009901

droMoj3

dG=-26.1, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.2, p-value=0.009901

droGri2

dG=-26.0, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.3, p-value=0.009901	dG=-25.1, p-value=0.009901

Generated: 03/07/2013 at 05:02 PM