Secondary structure and small RNA-seq evidence for dme-mir-31a

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:13671285-13671406 -	CGATC---------------GTAT--ATC---AACTCCGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTT--GAAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAGCGAG---ATC------------------------------------------
droSim1	chr2R:12409842-12409963 -	CGATC---------------GTAT--AGC---ACCTCCGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTT--GAAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAGCGAG---ATC------------------------------------------
droSec1	super_1:11168758-11168879 -	CGATC---------------GTAT--AGC---ACCTCCGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTT--GAAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAGCGAG---ATC------------------------------------------
droYak2	chr2R:15512007-15512128 +	CGATC---------------GTAT--AGC---ACCTCTGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTT--GAAGATCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACACTCAGCGAG---ATC------------------------------------------
droEre2	scaffold_4845:7899182-7899303 -	CGATC---------------GTAT--AGC---ACCTCCGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGCTTTT--AAAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAGCGAG---ATC------------------------------------------
droAna3	scaffold_13266:10515593-10515725 +	CGATC---------------ATAT--AGCCAAGAATCTGTTGTT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGGAAAACGAATTT--TGAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAACAAG---ATCGAAACTCT----------------------------------
dp4	chr3:16483204-16483318 -	CG---------------------T--ACC---GCATCTGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGAAGTTGAAAAGCGATCTT--TGAGAACGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACAGTCAACA-G---ATC------------------------------------------
droPer1	super_4:278992-279106 +	CG---------------------T--ACC---GCATCTGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGAAGTTGAAAAGCGATCTT--TGAGAACGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACAGTCAACA-G---ATC------------------------------------------
droWil1	scaffold_180700:4557862-4557981 -	CA-TC---------------ATCATTAT-----CATCTGTTTTTCGAATTGGCAAGATGTCGGCATAGCTGATA-------AT-ATTTTTAGAAAAGCGCTATGCTGCATCTAGTCAGTTTATTCAATAGAGCAATCGACAATATTATC------------------------------------------
droVir3	scaffold_12875:16937652-16937767 -	---TC---------------GCCT--C-----GCATCTGTTGTT-CAATTGGCAAGATGTCGGCATAGCTGACGTTTGAAAGCGCATTT--TTATAGCGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACAATCAACAAA---A--------------------------------------------
droMoj3	scaffold_6496:11065442-11065572 +	CTATATTTATAAATATTTCGGTTT--ATC---GCATCTATTGTT-GAATTGGCAAGATGTCGGCATAGCTGACGTTTCAAAGCGCAT-T--GCATAGCGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACAGTCAACA--------------------------------------------------
droGri2	scaffold_15245:16476618-16476778 -	CTCTC---------------GCGA--TTC---TCATCTGTTGGT-GAATTGGCAAGATGTCGGCATAGCTGACGTTTGAAAGCGCATCT---TATAGCGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACACTCAACA-T---ATCCATAC-CTGAAATGCTTAGAAACTTGGAGTATCTACGGATTA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:13671285-13671406 -	CGATC---------------GTAT--ATC---AACTCCGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTT--GAAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAGCGAG---ATC------------------------------------------
droSim1	chr2R:12409842-12409963 -	CGATC---------------GTAT--AGC---ACCTCCGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTT--GAAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAGCGAG---ATC------------------------------------------
droSec1	super_1:11168758-11168879 -	CGATC---------------GTAT--AGC---ACCTCCGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTT--GAAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAGCGAG---ATC------------------------------------------
droYak2	chr2R:15512007-15512128 +	CGATC---------------GTAT--AGC---ACCTCTGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTT--GAAGATCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACACTCAGCGAG---ATC------------------------------------------
droEre2	scaffold_4845:7899182-7899303 -	CGATC---------------GTAT--AGC---ACCTCCGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGCTTTT--AAAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAGCGAG---ATC------------------------------------------
droAna3	scaffold_13266:10515593-10515725 +	CGATC---------------ATAT--AGCCAAGAATCTGTTGTT-AAATTGGCAAGATGTCGGCATAGCTGACGTTGGAAAACGAATTT--TGAGAGCGCTATGCTGCATCTAGTCAGT-TGTTCAATGGAACAGTCAACAAG---ATCGAAACTCT----------------------------------
dp4	chr3:16483204-16483318 -	CG---------------------T--ACC---GCATCTGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGAAGTTGAAAAGCGATCTT--TGAGAACGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACAGTCAACA-G---ATC------------------------------------------
droPer1	super_4:278992-279106 +	CG---------------------T--ACC---GCATCTGTTGGT-AAATTGGCAAGATGTCGGCATAGCTGAAGTTGAAAAGCGATCTT--TGAGAACGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACAGTCAACA-G---ATC------------------------------------------
droWil1	scaffold_180700:4557862-4557981 -	CA-TC---------------ATCATTAT-----CATCTGTTTTTCGAATTGGCAAGATGTCGGCATAGCTGATA-------AT-ATTTTTAGAAAAGCGCTATGCTGCATCTAGTCAGTTTATTCAATAGAGCAATCGACAATATTATC------------------------------------------
droVir3	scaffold_12875:16937652-16937767 -	---TC---------------GCCT--C-----GCATCTGTTGTT-CAATTGGCAAGATGTCGGCATAGCTGACGTTTGAAAGCGCATTT--TTATAGCGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACAATCAACAAA---A--------------------------------------------
droMoj3	scaffold_6496:11065442-11065572 +	CTATATTTATAAATATTTCGGTTT--ATC---GCATCTATTGTT-GAATTGGCAAGATGTCGGCATAGCTGACGTTTCAAAGCGCAT-T--GCATAGCGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACAGTCAACA--------------------------------------------------
droGri2	scaffold_15245:16476618-16476778 -	CTCTC---------------GCGA--TTC---TCATCTGTTGGT-GAATTGGCAAGATGTCGGCATAGCTGACGTTTGAAAGCGCATCT---TATAGCGCTATGCTGCATCTAGTCAGT-TATTCAATGGAACACTCAACA-T---ATCCATAC-CTGAAATGCTTAGAAACTTGGAGTATCTACGGATTA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CGATCGTATAGCACCTCCGTTGGTAAATTGGCAAGATGTCGGCATAGCTGACGTTGAAAAGCGATTTTGAAGAGCGCTATGCTGCATCTAGTCAGTTGTTCAATGGAACAGTCAGCGAGATC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................TGGCAAGATGTCGGCATAGCTGA.......................................................................	23	1	16655.00	16655	16655
............................TGGCAAGATGTCGGCATAGCTG........................................................................	22	1	1149.00	1149	1149
..........................................................................CGCTATGCTGCATCTAGTCAGT..........................	22	1	194.00	194	194
............................TGGCAAGATGTCGGCATAGCT.........................................................................	21	1	85.00	85	85
................................AAGATGTCGGCATAGCTGA.......................................................................	19	1	18.00	18	18
............................TGGCAAGATGTCGGCATAGCTGAC......................................................................	24	1	13.00	13	13
............................TGGCAAGATGTCGGCATAGCTGACGTT...................................................................	27	1	11.00	11	11
............................TGGCAAGATGTCGGCATAGCTGACG.....................................................................	25	1	10.00	10	10
.............................GGCAAGATGTCGGCATAGCTGA.......................................................................	22	1	9.00	9	9
..............................GCAAGATGTCGGCATAGCTGA.......................................................................	21	1	5.00	5	5
............................TGGCAAGATGTCGGCATAGC..........................................................................	20	1	5.00	5	5
............................TGGCAAGATGTCGGCATAG...........................................................................	19	1	4.00	4	4
..........................................................................CGCTATGCTGCATCTAGTCAG...........................	21	1	2.00	2	2
...........................................................................GCTATGCTGCATCTAGTCAGT..........................	21	1	2.00	2	2
..............................GCAAGATGTCGGCATAGCTGACGT....................................................................	24	1	1.00	1	1
..............................GCAAGATGTCGGCATAGCTG........................................................................	20	1	1.00	1	1
..........................................................................CGCTATGCTGCATCTAGTCAGTT.........................	23	1	1.00	1	1
.............................GGCAAGATGTCGGCATAGCTG........................................................................	21	1	1.00	1	1
............................TGGCAAGATGTCGGCATAGCTGACGT....................................................................	26	1	1.00	1	1
..........................................................................CGCTATGCTGCATCTAGTC.............................	19	1	1.00	1	1

dp4

CG------TACCGCATCTGTTGGTAAATTGGCAAGATGTCGGCATAGCTGAAGTTGAAAAGCGATCTTTGAGAACGCTATGCTGCATCTAGTCAGTTATTCAATGGAACAGTCAAC-AGATC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................TGGCAAGATGTCGGCATAGCTGA.......................................................................	23	1	24100.00	24100	19346	4754
............................TGGCAAGATGTCGGCATAGCTG........................................................................	22	1	4415.00	4415	1314	3101
............................TGGCAAGATGTCGGCATAGCT.........................................................................	21	1	2063.00	2063	129	1934
..........................................................................CGCTATGCTGCATCTAGTCAGT..........................	22	1	893.00	893	737	156
............................TGGCAAGATGTCGGCATAGC..........................................................................	20	1	256.00	256	14	242
............................TGGCAAGATGTCGGCATAGCTGAA......................................................................	24	1	148.00	148	71	77
............................TGGCAAGATGTCGGCATAG...........................................................................	19	1	89.00	89	8	81
............................TGGCAAGATGTCGGCATAGCTGAAGTT...................................................................	27	1	37.00	37	28	9
................................AAGATGTCGGCATAGCTGA.......................................................................	19	1	24.00	24	22	2
.............................GGCAAGATGTCGGCATAGCTGA.......................................................................	22	1	23.00	23	20	3
..........................................................................CGCTATGCTGCATCTAGTCAG...........................	21	1	22.00	22	21	1
............................TGGCAAGATGTCGGCATAGCTGAAGT....................................................................	26	1	15.00	15	15	0
............................TGGCAAGATGTCGGCATAGCTGAAG.....................................................................	25	1	14.00	14	7	7
..........................................................................CGCTATGCTGCATCTAGTCA............................	20	1	9.00	9	1	8
..........................................................................CGCTATGCTGCATCTAGTCAGTT.........................	23	1	9.00	9	9	0
............................TGGCAAGATGTCGGCATA............................................................................	18	1	8.00	8	2	6
..............................GCAAGATGTCGGCATAGCTGA.......................................................................	21	1	8.00	8	4	4
..........................................................................CGCTATGCTGCATCTAGTC.............................	19	1	6.00	6	2	4
.............................GGCAAGATGTCGGCATAGCTG........................................................................	21	1	5.00	5	1	4
.................................AGATGTCGGCATAGCTGA.......................................................................	18	1	4.00	4	4	0
...........................................................................GCTATGCTGCATCTAGTCAGT..........................	21	1	3.00	3	2	1

Secondary Structure

dm3

dG=-29.5, p-value=0.009901	dG=-28.8, p-value=0.009901	dG=-28.6, p-value=0.009901

droSim1

dG=-29.5, p-value=0.009901	dG=-28.8, p-value=0.009901	dG=-28.6, p-value=0.009901

droSec1

dG=-29.5, p-value=0.009901	dG=-28.8, p-value=0.009901	dG=-28.6, p-value=0.009901

droYak2

dG=-32.4, p-value=0.009901	dG=-31.7, p-value=0.009901

droEre2

dG=-29.7, p-value=0.009901	dG=-29.0, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.7, p-value=0.009901	dG=-28.7, p-value=0.009901

droAna3

dG=-28.2, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.8, p-value=0.009901	dG=-27.5, p-value=0.009901	dG=-27.4, p-value=0.009901

dp4

dG=-28.5, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.2, p-value=0.009901	dG=-27.8, p-value=0.009901	dG=-27.8, p-value=0.009901

droPer1

dG=-28.5, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.2, p-value=0.009901	dG=-27.8, p-value=0.009901	dG=-27.8, p-value=0.009901

droWil1

dG=-27.5, p-value=0.009901	dG=-27.2, p-value=0.009901	dG=-26.6, p-value=0.009901	dG=-26.5, p-value=0.009901

droVir3

dG=-28.5, p-value=0.009901	dG=-28.1, p-value=0.009901	dG=-28.0, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901

droMoj3

dG=-28.8, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.1, p-value=0.009901

droGri2

dG=-28.8, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.1, p-value=0.009901

Generated: 03/07/2013 at 05:21 PM