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

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:11953395-11953518 -	CCATCTAAT----------------------------------------GGT--ATATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCAAAATGAA
droSim1	chr2L:11760450-11760573 -	CCATCTAAT----------------------------------------GGT--ATATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCAAAATGAA
droSec1	super_16:152684-152807 -	CCTTCTAAT----------------------------------------GGT--ATATAGATCTCGACACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCAAAGTGAA
droYak2	chr2L:8374818-8374940 -	CCAGCTGCT----------------------------------------GGT--ATATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTACTTTTTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCAA-ATGAA
droEre2	scaffold_4929:13456433-13456555 +	CCATCTGAT----------------------------------------GGT--GTATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTACTTTTGA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCGA-ATGAA
droAna3	scaffold_12943:2289700-2289819 +	ACA----------------------------------------------AGT--TTCTCCATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTCTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGATTAAAACATCAAA------A-AAGTGA-
dp4	chr4_group3:7322788-7322905 +	ACTCATAAG----------------------------------------TGT--ATCCACATCCCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTT-TTTCAA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGACT----CAT---------CTCA-ATCAA
droPer1	super_1:8768281-8768398 +	ACTCATAAG----------------------------------------TGT--ATCCACATCCCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTT-TTTCAA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGACT----CAT---------CTCA-ATCAA
droWil1	scaffold_180708:2657721-2657853 -	CTTTCGATT----------------------------------------GG---TTCTGCATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTTTTTATTTAACAC-ACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGATTTAAGCATACAGAACATCCGACATCAA
droVir3	scaffold_12963:13235091-13235216 +	CTTAATGTT----------------------------------------GCTTGCTCTGCATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTTTTTATAA--CAC-GCCCGTGATCTCTTAGTGGCATCTATGGTGCGGGA-TATTACGTACAA------C-AAATGAA
droMoj3	Unknown	ACT-------------------------------------------------------------------AGTGATTGGCACTGGGAGAATTCACAGTTGA-TTATAT--AATATTCTGTGGTTCTGC-----------GGGTGCCAAAATATAATAT---------TCGGAATAAT
droGri2	scaffold_15126:6621358-6621517 -	CTACCTGAATTTCTGCTGGGTAAGTTATTTTTTTCAAGTGATTTTTCTTGTT-GTTCTGCATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTTATTTTAA--CAC-GCCCGTGATCTCTTAGTGGCATCTATGGTGCGGGA-TATTACGT---------GCAGA---AA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:11953395-11953518 -	CCATCTAAT----------------------------------------GGT--ATATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCAAAATGAA
droSim1	chr2L:11760450-11760573 -	CCATCTAAT----------------------------------------GGT--ATATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCAAAATGAA
droSec1	super_16:152684-152807 -	CCTTCTAAT----------------------------------------GGT--ATATAGATCTCGACACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCAAAGTGAA
droYak2	chr2L:8374818-8374940 -	CCAGCTGCT----------------------------------------GGT--ATATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTACTTTTTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCAA-ATGAA
droEre2	scaffold_4929:13456433-13456555 +	CCATCTGAT----------------------------------------GGT--GTATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTACTTTTGA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACAT---------CCGA-ATGAA
droAna3	scaffold_12943:2289700-2289819 +	ACA----------------------------------------------AGT--TTCTCCATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTCTA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGATTAAAACATCAAA------A-AAGTGA-
dp4	chr4_group3:7322788-7322905 +	ACTCATAAG----------------------------------------TGT--ATCCACATCCCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTT-TTTCAA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGACT----CAT---------CTCA-ATCAA
droPer1	super_1:8768281-8768398 +	ACTCATAAG----------------------------------------TGT--ATCCACATCCCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTT-TTTCAA--TACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGACT----CAT---------CTCA-ATCAA
droWil1	scaffold_180708:2657721-2657853 -	CTTTCGATT----------------------------------------GG---TTCTGCATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTTTTTATTTAACAC-ACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGATTTAAGCATACAGAACATCCGACATCAA
droVir3	scaffold_12963:13235091-13235216 +	CTTAATGTT----------------------------------------GCTTGCTCTGCATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTTTTTATAA--CAC-GCCCGTGATCTCTTAGTGGCATCTATGGTGCGGGA-TATTACGTACAA------C-AAATGAA
droMoj3	Unknown	ACT-------------------------------------------------------------------AGTGATTGGCACTGGGAGAATTCACAGTTGA-TTATAT--AATATTCTGTGGTTCTGC-----------GGGTGCCAAAATATAATAT---------TCGGAATAAT
droGri2	scaffold_15126:6621358-6621517 -	CTACCTGAATTTCTGCTGGGTAAGTTATTTTTTTCAAGTGATTTTTCTTGTT-GTTCTGCATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTTATTTTAA--CAC-GCCCGTGATCTCTTAGTGGCATCTATGGTGCGGGA-TATTACGT---------GCAGA---AA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCATCTAATGGTATATAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTT-ATACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAAAACATCCAAAATGAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................AATGGCACTGGAAGAATTCACGGG.....................................................................	24	1	24604.00	24604	24604
................................AATGGCACTGGAAGAATTCACGG......................................................................	23	1	1977.00	1977	1977
................................AATGGCACTGGAAGAATTCAC........................................................................	21	1	1804.00	1804	1804
................................AATGGCACTGGAAGAATTCACG.......................................................................	22	1	1516.00	1516	1516
................................AATGGCACTGGAAGAATTCA.........................................................................	20	1	151.00	151	151
..........................................................................CGTGATCTCTTAGTGGCATCTA.............................	22	1	150.00	150	150
..........................................................................CGTGATCTCTTAGTGGCATCT..............................	21	1	31.00	31	31
................................AATGGCACTGGAAGAATTC..........................................................................	19	1	24.00	24	24
.................................ATGGCACTGGAAGAATTCACGGG.....................................................................	23	1	19.00	19	19
...................................GGCACTGGAAGAATTCACGGG.....................................................................	21	1	4.00	4	4
......................................ACTGGAAGAATTCACGGG.....................................................................	18	1	4.00	4	4
................................AATGGCACTGGAAGAATTCACGGGG....................................................................	25	1	3.00	3	3
....................................GCACTGGAAGAATTCACGGG.....................................................................	20	1	3.00	3	3
.....................................CACTGGAAGAATTCACGGG.....................................................................	19	1	3.00	3	3
.................................ATGGCACTGGAAGAATTCACG.......................................................................	21	1	2.00	2	2

dp4

ACTCATAAGTGTATCCACATCCCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGT--TTTTCAATACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGGGACT----CATCT-CAATCAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................AATGGCACTGGAAGAATTCACGGG.....................................................................	24	1	18174.00	18174	14926	3248
................................AATGGCACTGGAAGAATTCACG.......................................................................	22	1	5146.00	5146	1322	3824
................................AATGGCACTGGAAGAATTCAC........................................................................	21	1	5059.00	5059	1463	3596
................................AATGGCACTGGAAGAATTCACGG......................................................................	23	1	3001.00	3001	1578	1423
................................AATGGCACTGGAAGAATTCA.........................................................................	20	1	2698.00	2698	218	2480
................................AATGGCACTGGAAGAATTC..........................................................................	19	1	465.00	465	13	452
..........................................................................CGTGATCTCTTAGTGGCATCTA.............................	22	1	280.00	280	266	14
..........................................................................CGTGATCTCTTAGTGGCATCT..............................	21	1	51.00	51	46	5
.................................ATGGCACTGGAAGAATTCACGGG.....................................................................	23	1	34.00	34	22	12
................................AATGGCACTGGAAGAATT...........................................................................	18	1	21.00	21	2	19
................................AATGGCACTGGAAGAATTCACGGGG....................................................................	25	1	10.00	10	8	2
.................................ATGGCACTGGAAGAATTCACG.......................................................................	21	1	10.00	10	0	10
...................................GGCACTGGAAGAATTCACGGG.....................................................................	21	1	5.00	5	5	0
.................................ATGGCACTGGAAGAATTCACGG......................................................................	22	1	5.00	5	1	4
.................................ATGGCACTGGAAGAATTCA.........................................................................	19	1	5.00	5	0	5
.................................ATGGCACTGGAAGAATTCAC........................................................................	20	1	5.00	5	1	4
.....................................CACTGGAAGAATTCACGGG.....................................................................	19	1	4.00	4	4	0

Secondary Structure

dm3

dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901

droSim1

dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901

droSec1

dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901

droYak2

dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901

droEre2

dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901

droAna3

dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901

dp4

dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901

droPer1

dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901

droWil1

dG=-24.5, p-value=0.009901	dG=-24.4, p-value=0.009901	dG=-24.3, p-value=0.009901	dG=-24.3, p-value=0.009901	dG=-24.2, p-value=0.009901

droVir3

dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.8, p-value=0.009901

droMoj3

dG=-13.4, p-value=0.009901	dG=-13.4, p-value=0.009901	dG=-12.6, p-value=0.009901	dG=-12.6, p-value=0.009901	dG=-12.6, p-value=0.009901

droGri2

dG=-24.0, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.8, p-value=0.009901

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