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

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:15836491-15836610 -	CTGTAGCTCT-----------------------TCAA----------------T------TTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTAT-----TATTCTGTG-GTTCTGCGGGTGCC-AAAACTTAAAA------ACCG-GCTTTGTACAACGATTTCT------------
droSim1	chr3L:15181316-15181435 -	CTCTAGCTCT-----------------------TCAA----------------T------TTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT-----TATTCTGTG-GTTCTGCGGGTGCC-AAAACTTAAAA------ACCG-GCTTTATACAACGATTTCT------------
droSec1	super_0:7944386-7944505 -	CGCTAGCTCT-----------------------TCAA----------------T------TTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT-----TATTCTGTG-GTTCTGCGGGTGCC-AAAACTTAAAA------ACCG-GCTTTATACAACGATTTCT------------
droYak2	chr3L_random:2539138-2539257 -	CGATAGCTCT-----------------------TCAA----------------T------CTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTAT-----TATTCTGTG-GTTCTGCGGGTGCC-AAAATTTAATC------AACG-GCTCTATACAACGATTTCT------------
droEre2	scaffold_4784:18090156-18090270 -	CTG--GCGAT-----------------------TCAA----------------ACCA---TAGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGATTTTAT-----TATTCTGTG-GTTCTGCGGGTGCC-AAAATTTAATC------AACA-GCTCCATACAACG------------------
droAna3	scaffold_13337:11320710-11320858 +	TTGTGATTTT-----------------------TGAATCAAATATTCTGG-----ACTCTCTGCTGTCTTTGAATCTTGGCACTGGGAGAATTCACAGTTGATTTTAT-----TATTCTGTG-GTTCTGCGGGTGCC-AAAATTGAAAT------AATG-GCCTAAAACCTCAAAAAAGGATATTTATTAT
dp4	chrXR_group6:3598033-3598148 -	CGATCGTTA---------------------------------------------------TTGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTCCA---TATATTCTGTG-GTTCTGCGGGTGCC-AAAATCGAATG------TTCG-GCTCGAAACAGCAGCTGAA------------
droPer1	super_9:1894031-1894138 -	T------------------------------------------------------------TGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTTCA---TATATTCTGTG-GTTCTGCGGGTGCCCAAAATCGAATG------TTCG-GCTCGAAACAGCAGCTGAA------------
droWil1	scaffold_180727:1452378-1452537 +	CTTAAATTCTAAGAAAGATTTTCTGTGTGTGTTTGAA----------CGAAAA-TAAAGTCTGCTCACAATGCATCTTGGCACTGGGAGAATTCACAGTTGATTCTTATTCGATATTCTGTG-GTTCTGCGGGTGCC-AAAATCTAATG------TTTGAGCTGTGATCATCGAAAAAG------------
droVir3	scaffold_13049:24412507-24412633 -	TTGT-GTTCT-----------------------TCTA----------CGGAAA-GCAGAGCTACTGCCATTTCATCTTGGCACTGGGAGAATTCACAGTCGATTACAT---AATATTCTGTG-GTTCTGCGGGTGCC-AAAATGTAATG------TGTG-GACCAAGACAGC-----CT------------
droMoj3	scaffold_6473:2363995-2364108 +	ATGTAAATGT------------------------TAA----------------T------TAACTGAC------------CGTTGAGGGCATTTACATCTATGTATAA-----CAGTTTATGTAATATGCAAGTATC-TAAATATATACAGAAATACTA-TGTGTGTATAACAGTTTTT------------
droGri2	scaffold_15110:24319786-24319904 -	ATATTGTG-------------------------GAAA----------------G------CTACTGCCATTACATCTTGGCACTGGGAGAATTCACAGTTGGTTATAT---AATATTCTGTG-GTTCTGCGGGTGCC-AAACTGTAATG------TGTG-GACATAGA-AACAACCTGA------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:15836491-15836610 -	CTGTAGCTCTTCAA-----------------------------------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTGTACAACGATTTCT------------
droSim1	chr3L:15181316-15181435 -	CTCTAGCTCTTCAA-----------------------------------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTATACAACGATTTCT------------
droSec1	super_0:7944386-7944505 -	CGCTAGCTCTTCAA-----------------------------------TTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAACTTAAAAACCG-GCTTTATACAACGATTTCT------------
droYak2	chr3L_random:2539138-2539257 -	CGATAGCTCTTCAA-----------------------------------TCTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTTAATCAACG-GCTCTATACAACGATTTCT------------
droEre2	scaffold_4784:18090156-18090270 -	CTG--GCGATTCAA-----------------------------ACC---ATAGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGATTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTTAATCAACA-GCTCCATACAACG------------------
droAna3	scaffold_13337:11320710-11320858 +	TTGTGATTTTTGAATCAAATATTCTG--------------G----ACTCTCTGCTGTCTTTGAATCTTGGCACTGGGAGAATTCACAGTTGATTTTAT-----TATTCTGTGGTTCTGCGGGTGCC-AAAATTGAAATAATG-GCCTAAAACCTCAAAAAAGGATATTTATTAT
dp4	chrXR_group6:3598033-3598148 -	CGATCGTTA-----------------------------------------TTGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTCCA---TATATTCTGTGGTTCTGCGGGTGCC-AAAATCGAATGTTCG-GCTCGAAACAGCAGCTGAA------------
droPer1	super_9:1894031-1894138 -	T--------------------------------------------------TGCTGGCATTGGCTCTTGGCACTGGGAGAATTCACAGTTGGTTTTCA---TATATTCTGTGGTTCTGCGGGTGCCCAAAATCGAATGTTCG-GCTCGAAACAGCAGCTGAA------------
droWil1	scaffold_180727:1452378-1452537 +	CTTAAATTCTAAGA-AAGATTTTCTGTGTGTGTTTGAACGAAAATAAAGTCTGCTCACAATGCATCTTGGCACTGGGAGAATTCACAGTTGATTCTTATTCGATATTCTGTGGTTCTGCGGGTGCC-AAAATCTAATGTTTGAGCTGTGATCATCGAAAAAG------------
droVir3	scaffold_13049:24412507-24412633 -	TTGT-GTTCTTCTA------------------------CGGAAAGCAGAGCTACTGCCATTTCATCTTGGCACTGGGAGAATTCACAGTCGATTACAT---AATATTCTGTGGTTCTGCGGGTGCC-AAAATGTAATGTGTG-GACCAAGACAGC-----CT------------
droGri2	scaffold_15110:24319786-24319904 -	ATATTGT--GGAAA-----------------------------------GCTACTGCCATTACATCTTGGCACTGGGAGAATTCACAGTTGGTTATAT---AATATTCTGTGGTTCTGCGGGTGCC-AAACTGTAATGTGTG-GACATAGA-AACAACCTGA------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTCTAGCTCTTCAATTTGCTGACTTTGAGTCTTGGCACTGGGAGAATTCACAGTTGACTTGAT--TATTCTGTGGTTCTGCGGGTGCCAAAACTTAAAAACCGGCTTTATACAACGATTTCT	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

Secondary Structure

dm3

-33.2	-33.2	-33.0	-33.0	-32.2	-32.2

droSim1

-33.2	-33.2	-33.0	-33.0	-32.2	-32.2

droSec1

-33.2	-33.2	-33.0	-33.0	-32.2	-32.2

droYak2

-30.5	-30.5	-30.3	-30.3	-29.5	-29.5

droEre2

-33.5	-33.5	-32.9	-32.9	-32.8	-32.8

droAna3

-29.5	-29.5	-28.9	-28.9	-28.8	-28.8

dp4

-32.3	-32.3	-32.3	-32.3	-31.3	-31.3

droPer1

-29.0	-29.0	-29.0	-29.0	-28.8	-28.8

droWil1

-29.9	-29.9	-29.8	-29.8	-29.6	-29.6

droVir3

-32.6	-32.6	-32.2	-32.2	-32.0	-32.0

droMoj3

-10.1	-10.0	-9.9	-9.8	-9.7	-9.7

droGri2

-36.0	-36.0	-35.4	-35.4	-35.2	-35.2

Generated: 01/05/2013 at 05:12 PM