Secondary structure and small RNA-seq evidence for dme-mir-125

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:18472300-18472439 +	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAATAAGGC
droSim1	chr2L:18161211-18161350 +	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAATAAGGC
droSec1	super_7:2098251-2098391 +	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA-----------------------AAAAAATAAGGC
droYak2	chr2R:4989099-4989238 +	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAATAAGGC
droEre2	scaffold_4845:5799089-5799228 -	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAATAAGGC
droAna3	scaffold_12916:2379461-2379598 +	AAT-----ATTGGTATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAATA------------------------CAAAA--AAGA
dp4	chr4_group3:3635996-3636136 +	AGT-----ATTGGTATGAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTATAC-----------------------AAAAAAAAAAGC
droPer1	super_2335:2506-2645 +	AGT-----ATTGGTATGAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTATAC------------------------AAAAAAAAAGC
droWil1	scaffold_180708:11623324-11623458 +	ATT-----ATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTGGCA------------------------AAA-----AGC
droVir3	scaffold_12963:18451638-18451806 +	TATTACACATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTAACAAAAAAACAAAAACAATTACAAAAAAATAAGAA
droMoj3	scaffold_6500:6184266-6184401 -	CAC-----ATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAGTA----
droGri2	scaffold_15252:6428908-6429045 +	CAC-----ATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAA--AAAC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:18472300-18472439 +	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAATAAGGC
droSim1	chr2L:18161211-18161350 +	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAATAAGGC
droSec1	super_7:2098251-2098391 +	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA-----------------------AAAAAATAAGGC
droYak2	chr2R:4989099-4989238 +	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAATAAGGC
droEre2	scaffold_4845:5799089-5799228 -	AAT-----ATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAATAAGGC
droAna3	scaffold_12916:2379461-2379598 +	AAT-----ATTGGTATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAATA------------------------CAAAA--AAGA
dp4	chr4_group3:3635996-3636136 +	AGT-----ATTGGTATGAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTATAC-----------------------AAAAAAAAAAGC
droPer1	super_2335:2506-2645 +	AGT-----ATTGGTATGAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTATAC------------------------AAAAAAAAAGC
droWil1	scaffold_180708:11623324-11623458 +	ATT-----ATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTGGCA------------------------AAA-----AGC
droVir3	scaffold_12963:18451638-18451806 +	TATTACACATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTAACAAAAAAACAAAAACAATTACAAAAAAATAAGAA
droMoj3	scaffold_6500:6184266-6184401 -	CAC-----ATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAGTA----
droGri2	scaffold_15252:6428908-6429045 +	CAC-----ATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA------------------------AAAAA--AAAC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AATATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTA-GTAAAAAATAAGGC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...........................................TCCCTGAGACCCTAACTTGTGA............................................................................	22	1	20.00	20	20
...........................................TCCCTGAGACCCTAACTTGTG.............................................................................	21	1	1.00	1	1

dp4

AGTATTGGTATGAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGACCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTATACAAAAAAAAAAGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...........................................TCCCTGAGACCCTAACTTGTGA............................................................................	22	1	7563.00	7563	13	7550
...........................................TCCCTGAGACCCTAACTTGTG.............................................................................	21	1	2246.00	2246	0	2246
...........................................TCCCTGAGACCCTAACTTGT..............................................................................	20	1	1091.00	1091	0	1091
.............................................CCTGAGACCCTAACTTGTGA............................................................................	20	1	44.00	44	0	44
..................................................................................ACAAGTTTTGATCTCCGGTAT......................................	21	1	30.00	30	0	30
...........................................TCCCTGAGACCCTAACTTG...............................................................................	19	1	28.00	28	0	28
.............................................CCTGAGACCCTAACTTGTG.............................................................................	19	1	14.00	14	0	14
...........................................TCCCTGAGACCCTAACTTGTGACT..........................................................................	24	1	9.00	9	0	9
..............................................CTGAGACCCTAACTTGTGA............................................................................	19	1	8.00	8	0	8
.............................................CCTGAGACCCTAACTTGT..............................................................................	18	1	6.00	6	0	6
............................................CCCTGAGACCCTAACTTGTGA............................................................................	21	1	4.00	4	0	4
...........................................TCCCTGAGACCCTAACTTGTGAC...........................................................................	23	1	3.00	3	0	3
...........................................TCCCTGAGACCCTAACTT................................................................................	18	1	2.00	2	0	2
..................................................................................ACAAGTTTTGATCTCCGGT........................................	19	1	2.00	2	0	2
..............................................CTGAGACCCTAACTTGTG.............................................................................	18	1	2.00	2	0	2
................................................................................TCACAAGTTTTGATCTCCGGTAT......................................	23	1	2.00	2	0	2
...........................................TCCCTGAGACCCTAACTTGTGACTT.........................................................................	25	1	2.00	2	0	2
................................................................................TCACAAGTTTTGATCTCCGGTA.......................................	22	1	1.00	1	0	1
..................................................................................ACAAGTTTTGATCTCCGGTA.......................................	20	1	1.00	1	0	1
..............................................CTGAGACCCTAACTTGTGACT..........................................................................	21	1	1.00	1	0	1
..................................................................................ACAAGTTTTGATCTCCGGTATT.....................................	22	1	1.00	1	0	1

Secondary Structure

dm3

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droSim1

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droSec1

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droYak2

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droEre2

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droAna3

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

dp4

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droPer1

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droWil1

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droVir3

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droMoj3

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

droGri2

dG=-18.5, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.5, p-value=0.009901

Generated: 03/07/2013 at 04:50 PM