Secondary structure and small RNA-seq evidence for dme-mir-981

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:1682879-1683005 -	A-CTGCAACTTAGGAG-------------------AAACATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCAAGGCCG
droSim1	chrX_random:1085378-1085505 -	AACTGCAACTTAGGAT-------------------AAACATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCAAGGCCA
droSec1	super_10:1477754-1477881 -	AACTCCAACTTAGGAT-------------------AAACATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCAAGGCCA
droYak2	chrX:1528063-1528198 -	A------ACTTAAGAGAGAGACCAA-----GTGCAAAGCATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAAAAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCAAGGCCG
droEre2	scaffold_4644:1660954-1661093 -	A-CTGCAACTTAAGAGGG-CACCAA-----CTGCAAAGCATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCTAGGCCG
droAna3	scaffold_12929:1586917-1587049 +	A-TTATAGTTTTA-----AGA---ACTGTGTTTCATAAAGTCCTCACTGAAGCCGGGTTTCGTTAACAGCGGGCTGTCATTTCGAA--------ATCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAATAACAACGTTTAA-----
dp4	chrXL_group1a:4258914-4259036 -	A-CGAATATCTA-------------------TGCGAAAAATCCACATTGAAATCGGGTTTCGTTAACAGCGGGCTGTTATGAATAA--------ATCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAGAAACAAC----AAATGCA
droPer1	super_11:835055-835162 -	T---------G-------------------ATGCGAAAAATCCACATTGAAATCGGGTTTCGTTAACAGCGGGCTGTTATGAATAA--------ATCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAGAAACAAC-----------
droWil1	scaffold_181096:4683233-4683341 +	---------------------------------------ATCCACACTGAAATCGGGTTTCGCTAGCAGCGGACTGTCATGATAAATGTGAAAAACAAACAAGTTCGTTGTCGACGAAACCTGCATCATGTGTCGGACAAACAGCTCT--------
droVir3	scaffold_12942:51501-51599 +	A-----------------------------------ACAATCTACATTGAACTCAGATTTCGTCAGCAGCGGGCTGTGATGATTA----------TGAACAAGTTCGTTGTCGACGAAACCTGCATACTGTGT-GGAGTGGCAAC-----------
droMoj3	scaffold_6328:4397474-4397588 +	--CTGTGGATAAAAAT-------------------AGTAATCTACATTGAACTCAGGTTTCGTTAGCAACGGGCTGTGATGATTAA--------AAGAACAAGTTCGTTGTCGACGAAACCTGCATGCTATGT-GGAGAGGCAAC-----------
droGri2	scaffold_14853:795296-795391 +	----------------------------------------TCCACATTGAGCTCGGGTTTCGTCAGCAGCGGGCTGTGATGACTAA--------A-AAACAAGTTCGTTGTCGACGAAACCTGCATACTGTGT-GGAGAGTCAACG----------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:1682879-1683005 -	A-CTGCAACTTAGGAG-------------------AAACATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCAAGGCCG
droSim1	chrX_random:1085378-1085505 -	AACTGCAACTTAGGAT-------------------AAACATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCAAGGCCA
droSec1	super_10:1477754-1477881 -	AACTCCAACTTAGGAT-------------------AAACATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCAAGGCCA
droYak2	chrX:1528063-1528198 -	A------ACTTAAGAGAGAGACCAA-----GTGCAAAGCATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAAAAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCAAGGCCG
droEre2	scaffold_4644:1660954-1661093 -	A-CTGCAACTTAAGAGGG-CACCAA-----CTGCAAAGCATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAA--------TTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAAAATCAACGCTCTAGGCCG
droAna3	scaffold_12929:1586917-1587049 +	A-TTATAGTTTTA-----AGA---ACTGTGTTTCATAAAGTCCTCACTGAAGCCGGGTTTCGTTAACAGCGGGCTGTCATTTCGAA--------ATCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAATAACAACGTTTAA-----
dp4	chrXL_group1a:4258914-4259036 -	A-CGAATATCTA-------------------TGCGAAAAATCCACATTGAAATCGGGTTTCGTTAACAGCGGGCTGTTATGAATAA--------ATCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAGAAACAAC----AAATGCA
droPer1	super_11:835055-835162 -	T---------G-------------------ATGCGAAAAATCCACATTGAAATCGGGTTTCGTTAACAGCGGGCTGTTATGAATAA--------ATCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGT-GGAGAAACAAC-----------
droWil1	scaffold_181096:4683233-4683341 +	---------------------------------------ATCCACACTGAAATCGGGTTTCGCTAGCAGCGGACTGTCATGATAAATGTGAAAAACAAACAAGTTCGTTGTCGACGAAACCTGCATCATGTGTCGGACAAACAGCTCT--------
droVir3	scaffold_12942:51501-51599 +	A-----------------------------------ACAATCTACATTGAACTCAGATTTCGTCAGCAGCGGGCTGTGATGATTA----------TGAACAAGTTCGTTGTCGACGAAACCTGCATACTGTGT-GGAGTGGCAAC-----------
droMoj3	scaffold_6328:4397474-4397588 +	--CTGTGGATAAAAAT-------------------AGTAATCTACATTGAACTCAGGTTTCGTTAGCAACGGGCTGTGATGATTAA--------AAGAACAAGTTCGTTGTCGACGAAACCTGCATGCTATGT-GGAGAGGCAAC-----------
droGri2	scaffold_14853:795296-795391 +	----------------------------------------TCCACATTGAGCTCGGGTTTCGTCAGCAGCGGGCTGTGATGACTAA--------A-AAACAAGTTCGTTGTCGACGAAACCTGCATACTGTGT-GGAGAGTCAACG----------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AACTGCAACTTAGGATAAACATCCTCACTGAAGTCGGGTTTCGTTAGCAGCGGGCTGTTTTAATAAATTCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGTGGAAAATCAACGCTCAAGGCCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................................................................TTCGTTGTCGACGAAACCTGC...............................	21	1	123.00	123	123
..................................CGGGTTTCGTTAGCAGCGGGCT........................................................................	22	1	110.00	110	110
............................................................................TTCGTTGTCGACGAAACCTGCA..............................	22	1	59.00	59	59
..................................CGGGTTTCGTTAGCAGCGGGC.........................................................................	21	1	2.00	2	2
.................................TCGGGTTTCGTTAGCAGCGGGC.........................................................................	22	1	1.00	1	1
..............................................................................CGTTGTCGACGAAACCTGC...............................	19	1	1.00	1	1
............................................................................TTCGTTGTCGACGAAACCTG................................	20	1	1.00	1	1
............................................................................TTCGTTGTCGACGAAACCTGCAT.............................	23	1	1.00	1	1
.............................................................................TCGTTGTCGACGAAACCTGCATG............................	23	1	1.00	1	1

dp4

A-CGAATATCTATGCGAAAAATCCACATTGAAATCGGGTTTCGTTAACAGCGGGCTGTTATGAATAAATCAACAAGTTCGTTGTCGACGAAACCTGCATGCTGTGTGGAGAAACAAC----AAATGCA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................................................................TTCGTTGTCGACGAAACCTGC...............................	21	1	2035.00	2035	165	1870
............................................................................TTCGTTGTCGACGAAACCTGCA..............................	22	1	983.00	983	194	789
............................................................................TTCGTTGTCGACGAAACCTG................................	20	1	229.00	229	0	229
..................................CGGGTTTCGTTAACAGCGGGCT........................................................................	22	1	206.00	206	148	58
............................................................................TTCGTTGTCGACGAAACCTGCAT.............................	23	1	25.00	25	1	24
............................................................................TTCGTTGTCGACGAAACCT.................................	19	1	24.00	24	0	24
..................................CGGGTTTCGTTAACAGCGGGC.........................................................................	21	1	20.00	20	13	7
..................................CGGGTTTCGTTAACAGCGGG..........................................................................	20	1	10.00	10	1	9
...............................................................................GTTGTCGACGAAACCTGC...............................	18	1	4.00	4	2	2
.............................................................................TCGTTGTCGACGAAACCTGC...............................	20	1	3.00	3	0	3
...................................GGGTTTCGTTAACAGCGGGCT........................................................................	21	1	2.00	2	1	1
..................................CGGGTTTCGTTAACAGCGG...........................................................................	19	1	1.00	1	0	1
...............................................................................GTTGTCGACGAAACCTGCA..............................	19	1	1.00	1	1	0
.............................................................................TCGTTGTCGACGAAACCTGCA..............................	21	1	1.00	1	0	1
..............................................................................CGTTGTCGACGAAACCTGCA..............................	20	1	1.00	1	0	1

Secondary Structure

dm3

dG=-30.2, p-value=0.009901	dG=-30.2, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-29.7, p-value=0.009901

droSim1

dG=-30.2, p-value=0.009901	dG=-30.2, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-29.7, p-value=0.009901

droSec1

dG=-30.2, p-value=0.009901	dG=-30.2, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-29.7, p-value=0.009901

droYak2

dG=-30.2, p-value=0.009901	dG=-30.2, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-29.7, p-value=0.009901

droEre2

dG=-30.2, p-value=0.009901	dG=-30.2, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-30.0, p-value=0.009901	dG=-29.7, p-value=0.009901

droAna3

dG=-30.6, p-value=0.009901	dG=-30.1, p-value=0.009901	dG=-30.1, p-value=0.009901	dG=-29.7, p-value=0.009901	dG=-29.6, p-value=0.009901

dp4

dG=-31.1, p-value=0.009901	dG=-31.1, p-value=0.009901	dG=-31.0, p-value=0.009901	dG=-30.8, p-value=0.009901	dG=-30.8, p-value=0.009901

droPer1

dG=-31.1, p-value=0.009901	dG=-31.1, p-value=0.009901	dG=-31.0, p-value=0.009901	dG=-30.8, p-value=0.009901	dG=-30.8, p-value=0.009901

droWil1

dG=-25.6, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.5, p-value=0.009901	dG=-25.3, p-value=0.009901

droVir3

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

droMoj3

dG=-31.2, p-value=0.009901	dG=-31.2, p-value=0.009901	dG=-30.4, p-value=0.009901

droGri2

dG=-32.3, p-value=0.009901	dG=-32.3, p-value=0.009901	dG=-31.4, p-value=0.009901

Generated: 03/07/2013 at 07:19 PM