Secondary structure and small RNA-seq evidence for dme-mir-263b

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:15836491-15836610 -	CTGTAGCTCTTCA-----------------------------A------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTGTACAACGATT------------TCT
droSim1	chr3L:15181316-15181435 -	CTCTAGCTCTTCA-----------------------------A------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTATACAACGAAT------------TCT
droSec1	super_0:7944386-7944505 -	CGCTAGCTCTTCA-----------------------------A------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTATACAACGATT------------TCT
droYak2	chr3L_random:2539138-2539257 -	CGATAGCTCTTCA-----------------------------A------TCTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTTAATCAACG-GCTCTATACAACGATT------------TCT
droEre2	scaffold_4784:18090156-18090270 -	CTG--GCGATTCA-----------------------------AACC---ATAGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGATTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTTAATCAACA-GCTCCATACAACG------------------
droAna3	scaffold_13337:11320710-11320858 +	TTGTGATTTTTGAATCAAATATTCTG--------------G----ACTCTCTGCTGTCTTTGAATCTTGGCACTGGGAGAATTCACAGTTGATTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTGAAATAATG-GCCTAAAACCTCAAAAAAGGATATTTATTAT
dp4	chrXR_group6:3598033-3598148 -	CGATCGTTA-----------------------------------------TTGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTCCAT---ATATTCTGTGGTTCTGCGGGTGCC-AAAATCGAATGTTCG-GCTCGAAACAGCAGCT------------GAA
droPer1	super_9:1894031-1894138 -	T--------------------------------------------------TGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTTCAT---ATATTCTGTGGTTCTGCGGGTGCCCAAAATCGAATGTTCG-GCTCGAAACAGCAGCT------------GAA
droWil1	scaffold_180727:1452378-1452537 +	CTTAAATTCTAAG-AAAGATTTTCTGTGTGTGTTTGAACGAAAATAAAGTCTGCTCACAATGCATCTTGGCACTGGGAGAATTCACAGTTGATTCTTATTCGATATTCTGTGGTTCTGCGGGTGCC-AAAATCTAATGTTTGAGCTGTGATCATCGAAA------------AAG
droVir3	scaffold_13049:24412507-24412633 -	TTGT-GTTCTTCT------------------------ACGGAAAGCAGAGCTACTGCCATTTCATCTTGGCACTGGGAGAATTCACAGTCGATTACATA---ATATTCTGTGGTTCTGCGGGTGCC-AAAATGTAATGTGTG-GACCAAGACAGC-----------------CT
droMoj3	Unknown	AC-TAGT---------------------------------------------------------GATTGGCACTGGGAGAATTCACAGTTGATTATATA---ATATTCTGTGGTTCTGCGGGTGCC-AAAATATAATATTCG-GAATA------------------------AT
droGri2	scaffold_15110:24319786-24319904 -	ATATTGT--GGAA-----------------------------A------GCTACTGCCATTACATCTTGGCACTGGGAGAATTCACAGTTGGTTATATA---ATATTCTGTGGTTCTGCGGGTGCC-AAACTGTAATGTGTG-GACATAGA-AACAACC------------TGA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:15836491-15836610 -	CTGTAGCTCTTCA-----------------------------A------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTGTACAACGATT------------TCT
droSim1	chr3L:15181316-15181435 -	CTCTAGCTCTTCA-----------------------------A------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTATACAACGAAT------------TCT
droSec1	super_0:7944386-7944505 -	CGCTAGCTCTTCA-----------------------------A------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTATACAACGATT------------TCT
droYak2	chr3L_random:2539138-2539257 -	CGATAGCTCTTCA-----------------------------A------TCTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTTAATCAACG-GCTCTATACAACGATT------------TCT
droEre2	scaffold_4784:18090156-18090270 -	CTG--GCGATTCA-----------------------------AACC---ATAGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGATTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTTAATCAACA-GCTCCATACAACG------------------
droAna3	scaffold_13337:11320710-11320858 +	TTGTGATTTTTGAATCAAATATTCTG--------------G----ACTCTCTGCTGTCTTTGAATCTTGGCACTGGGAGAATTCACAGTTGATTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTGAAATAATG-GCCTAAAACCTCAAAAAAGGATATTTATTAT
dp4	chrXR_group6:3598033-3598148 -	CGATCGTTA-----------------------------------------TTGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTCCA---TATATTCTGTGGTTCTGCGGGTGCC-AAAATCGAATGTTCG-GCTCGAAACAGCAGCT------------GAA
droPer1	super_9:1894031-1894138 -	T--------------------------------------------------TGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTTCA---TATATTCTGTGGTTCTGCGGGTGCCCAAAATCGAATGTTCG-GCTCGAAACAGCAGCT------------GAA
droWil1	scaffold_180727:1452378-1452537 +	CTTAAATTCTAAG-AAAGATTTTCTGTGTGTGTTTGAACGAAAATAAAGTCTGCTCACAATGCATCTTGGCACTGGGAGAATTCACAGTTGATTCTTATTCGATATTCTGTGGTTCTGCGGGTGCC-AAAATCTAATGTTTGAGCTGTGATCATCGAAA------------AAG
droVir3	scaffold_13049:24412507-24412633 -	TTGT-GTTCTTCT------------------------ACGGAAAGCAGAGCTACTGCCATTTCATCTTGGCACTGGGAGAATTCACAGTCGATTACAT---AATATTCTGTGGTTCTGCGGGTGCC-AAAATGTAATGTGTG-GACCAAGACAGC-----------------CT
droGri2	scaffold_15110:24319786-24319904 -	ATATTGT--GGAA-----------------------------A------GCTACTGCCATTACATCTTGGCACTGGGAGAATTCACAGTTGGTTATAT---AATATTCTGTGGTTCTGCGGGTGCC-AAACTGTAATGTGTG-GACATAGA-AACAACC------------TGA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTCTAGCTCTTCAATTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT--TATTCTGTGGTTCTGCGGGTGCCAAAACTTAAAAACCGGCTTTATACAACGAATTCT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................CTTGGCACTGGGAGAATTCACAG.....................................................................	23	1	3502.00	3502	3502
..............................CTTGGCACTGGGAGAATTCACA......................................................................	22	1	610.00	610	610
..............................CTTGGCACTGGGAGAATTCAC.......................................................................	21	1	224.00	224	224
...............................TTGGCACTGGGAGAATTCACAG.....................................................................	22	1	26.00	26	26
..............................CTTGGCACTGGGAGAATTCA........................................................................	20	1	24.00	24	24
..............................CTTGGCACTGGGAGAATTCACAGT....................................................................	24	1	12.00	12	12
..............................CTTGGCACTGGGAGAATTC.........................................................................	19	1	4.00	4	4
...............................TTGGCACTGGGAGAATTCACA......................................................................	21	1	4.00	4	4
.......................................................................GTGGTTCTGCGGGTGCCAAAAC.............................	22	1	3.00	3	3
...............................TTGGCACTGGGAGAATTCAC.......................................................................	20	1	2.00	2	2
.......................................................................GTGGTTCTGCGGGTGCCAAA...............................	20	1	2.00	2	2
.......................................................................GTGGTTCTGCGGGTGCCAAAA..............................	21	1	1.00	1	1
......................................................................TGTGGTTCTGCGGGTGCCAAAA..............................	22	1	1.00	1	1
..............................CTTGGCACTGGGAGAATTCACAGTT...................................................................	25	1	1.00	1	1

dp4

CGATCGTTA------TTGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTCCATATATTCTGTGGTTCTGCGGGTGCCAAAATCGAATGTTCGGCTCGAAACAGCAGCTGAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................CTTGGCACTGGGAGAATTCACAG.....................................................................	23	1	1269.00	1269	421	848
..............................CTTGGCACTGGGAGAATTCACA......................................................................	22	1	1267.00	1267	163	1104
..............................CTTGGCACTGGGAGAATTCAC.......................................................................	21	1	1202.00	1202	44	1158
..............................CTTGGCACTGGGAGAATTCA........................................................................	20	1	1189.00	1189	20	1169
..............................CTTGGCACTGGGAGAATTC.........................................................................	19	1	336.00	336	7	329
..............................CTTGGCACTGGGAGAATT..........................................................................	18	1	30.00	30	0	30
..............................CTTGGCACTGGGAGAATTCACAGT....................................................................	24	1	15.00	15	1	14
...............................TTGGCACTGGGAGAATTCACAG.....................................................................	22	1	14.00	14	7	7
...............................TTGGCACTGGGAGAATTCAC.......................................................................	20	1	10.00	10	1	9
...............................TTGGCACTGGGAGAATTCACA......................................................................	21	1	9.00	9	2	7
...............................TTGGCACTGGGAGAATTCA........................................................................	19	1	5.00	5	0	5
.......................................................................GTGGTTCTGCGGGTGCCAAAA..............................	21	1	2.00	2	2	0
...............................TTGGCACTGGGAGAATTC.........................................................................	18	1	2.00	2	0	2
..............................CTTGGCACTGGGAGAATTCACAGTT...................................................................	25	1	1.00	1	0	1
........................................................................TGGTTCTGCGGGTGCCAAAA..............................	20	1	1.00	1	1	0
......TTA------TTGCTGGCATTGGCT............................................................................................	18	1	1.00	1	1	0
........................................................................TGGTTCTGCGGGTGCCAAAAT.............................	21	1	1.00	1	1	0
...............................TTGGCACTGGGAGAATTCACAGT....................................................................	23	1	1.00	1	0	1

Secondary Structure

dm3

dG=-27.3, p-value=0.009901	dG=-27.3, p-value=0.009901	dG=-27.1, p-value=0.009901	dG=-27.1, p-value=0.009901

droSim1

dG=-27.3, p-value=0.009901	dG=-27.3, p-value=0.009901	dG=-27.1, p-value=0.009901	dG=-27.1, p-value=0.009901

droSec1

dG=-27.3, p-value=0.009901	dG=-27.3, p-value=0.009901	dG=-27.1, p-value=0.009901	dG=-27.1, p-value=0.009901

droYak2

dG=-25.0, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.8, p-value=0.009901	dG=-24.8, p-value=0.009901

droEre2

dG=-25.6, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.9, p-value=0.009901

droAna3

dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-22.8, p-value=0.009901

dp4

dG=-23.5, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.5, p-value=0.009901

droPer1

dG=-21.3, p-value=0.009901	dG=-21.3, p-value=0.009901	dG=-20.3, p-value=0.009901	dG=-20.3, p-value=0.009901

droWil1

dG=-24.1, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.3, p-value=0.009901

droVir3

dG=-25.6, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-24.8, p-value=0.009901	dG=-24.8, p-value=0.009901	dG=-24.8, p-value=0.009901

droMoj3

dG=-23.6, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.8, p-value=0.009901

droGri2

dG=-26.8, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-26.0, p-value=0.009901

Generated: 03/07/2013 at 05:01 PM