Secondary structure and small RNA-seq evidence for dme-mir-285

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12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:11939178-11939306 -	AC-----TTGCC---CT---------------GCCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAGAACCCACTCA---------ATTTAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droSim1	chr3L:11307954-11308082 -	AC-----TTGCC---CA---------------GCCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAAAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droSec1	super_0:4127812-4127940 -	AC-----TTGCC---CA---------------TCCACTTCAAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAAAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droYak2	chr3L:11984774-11984902 -	TC-----TTGCC---CT---------------ACCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGACAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droEre2	scaffold_4784:11929878-11930011 -	TCAGGAGCTGCA---CT---------------CCCACTTCGAGTCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGAAGCCCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGGA------------GTGTC
droAna3	scaffold_13337:6191341-6191461 -	GC---------C---AG---------------GATAATTCGAATCAAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGGAGATCCGATCA---------TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAACCACTCAACAGA-----------------
dp4	chrXR_group6:1929779-1929903 -	TC-----TTACA---AT---------------TACAGTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGAGGACTCGCTAAT--------TTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----------------
droPer1	gnl\|ti\|738578230:636-763 +	TC-----TTACA---AT-------------T-TACAGTGGGAATCGAAGAACCTGAGATCGATTGGTGCATAGATATC----AAGAGGACTCGATAAT--------TTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----------------
droWil1	scaffold_180949:5768880-5769006 +	AC-----A------------------------AATTGTTCGAATTAAAGAAC-TGAGATCGATTGGTGCATAGATAAT----ATGCGAATTCTATCATTTGATTTCATTCAATTCTAGCACCATTCGAAATCAGTGCTTTTGATTAGAACCAATCAACAAG-----------------
droVir3	scaffold_13049:21101427-21101556 +	AT-----GCAC----CA---------------GCCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATATCGCCCAAAA--AGTAATTCA---------TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTCGAACCGATCAGCGGC------------GCATC
droMoj3	scaffold_6680:15475365-15475526 +	AC-----ACACCCAGCAGACATCAAACACCACACCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATAACGCCCAAAAAG--TCATTTT----A----TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTGGAACCGATCAACGGTGTATGGGAACAAGTGTC
droGri2	scaffold_15110:22570097-22570226 -	AT-----GTAG----CA---------------GCCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATATCGTCCAAGAA---TAATTTA----A----TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTGTATTGGAACCGATCAGCGGC------------GCATT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:11939178-11939306 -	AC-----TTGCC---CT---------------GCCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAGAACCCACTCA---------ATTTAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droSim1	chr3L:11307954-11308082 -	AC-----TTGCC---CA---------------GCCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAAAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droSec1	super_0:4127812-4127940 -	AC-----TTGCC---CA---------------TCCACTTCAAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AGGAAAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droYak2	chr3L:11984774-11984902 -	TC-----TTGCC---CT---------------ACCACTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGACAACCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAA------------GTGTC
droEre2	scaffold_4784:11929878-11930011 -	TCAGGAGCTGCA---CT---------------CCCACTTCGAGTCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGAAGCCCCACTCA---------ATTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGGA------------GTGTC
droAna3	scaffold_13337:6191341-6191461 -	GC---------C---AG---------------GATAATTCGAATCAAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGGAGATCCGATCA---------TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAACCACTCAACAGA-----------------
dp4	chrXR_group6:1929779-1929903 -	TC-----TTACA---AT---------------TACAGTTCGAATCGAAGAAC-TGAGATCGATTGGTGCATAGATATC----AAGAGGACTCGCTAAT--------TTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----------------
droPer1	gnl\|ti\|738578230:636-763 +	TC-----TTACA---AT-------------T-TACAGTGGGAATCGAAGAACCTGAGATCGATTGGTGCATAGATATC----AAGAGGACTCGATAAT--------TTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----------------
droWil1	scaffold_180949:5768880-5769006 +	AC-----A------------------------AATTGTTCGAATTAAAGAAC-TGAGATCGATTGGTGCATAGATAAT----ATGCGAATTCTATCATTTGATTTCATTCAATTCTAGCACCATTCGAAATCAGTGCTTTTGATTAGAACCAATCAACAAG-----------------
droVir3	scaffold_13049:21101427-21101556 +	AT-----GCAC----CA---------------GCCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATATCGCCCAAAA--AGTAATTCA---------TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTCGAACCGATCAGCGGC------------GCATC
droMoj3	scaffold_6680:15475365-15475526 +	AC-----ACACCCAGCAGACATCAAACACCACACCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATAACGCCCAAAAAG--TCATTTT----A----TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTTTATTGGAACCGATCAACGGTGTATGGGAACAAGTGTC
droGri2	scaffold_15110:22570097-22570226 -	AT-----GTAG----CA---------------GCCAGTTCAAATTGAAGAAC-TGAGATCGATTGGTGCATAGATATCGTCCAAGAA---TAATTTA----A----TTTCAATTCTAGCACCATTCGAAATCAGTGCTTTGTATTGGAACCGATCAGCGGC------------GCATT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACTTGCCCAGCCACTTCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAGGAAAACCCACTCAATTC-AACTCTAGCACCATTCGAAATCAGTGCTTTTGATAAGAAACAATCAGCGAAGTGTC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............................................................................TAGCACCATTCGAAATCAGTGC.............................	22	1	4.00	4	4
...............................................................................TAGCACCATTCGAAATCAGTG..............................	21	1	3.00	3	3
...............................................................................TAGCACCATTCGAAATCAGTGCT............................	23	1	2.00	2	2
...........................ACTGAGATCGATTGGTGCATAGA................................................................................	23	1	2.00	2	2
...............................................................................TAGCACCATTCGAAATCAGT...............................	20	1	1.00	1	1

dp4

TCTTACAATTACAGTTCGAATCGAAGAACTGAGATCGATTGGTGCATAGATATCAAGAGGACTCGCTAATTTTCAACTCTAGCACCATTCGAAATCAGTGCTTTTGATGAGAACCATTCAACAGA-----	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...............................................................................TAGCACCATTCGAAATCAGTGCT............................	23	1	24878.00	24878	3	24875
...............................................................................TAGCACCATTCGAAATCAGTGC.............................	22	1	12336.00	12336	1	12335
...............................................................................TAGCACCATTCGAAATCAGTG..............................	21	1	1854.00	1854	0	1854
...............................................................................TAGCACCATTCGAAATCAGT...............................	20	1	1064.00	1064	0	1064
...........................ACTGAGATCGATTGGTGCATAGA................................................................................	23	1	426.00	426	2	424
...............................................................................TAGCACCATTCGAAATCAG................................	19	1	94.00	94	0	94
...........................ACTGAGATCGATTGGTGCATAG.................................................................................	22	1	73.00	73	0	73
..........................AACTGAGATCGATTGGTGCATAGA................................................................................	24	1	55.00	55	0	55
...............................................................................TAGCACCATTCGAAATCAGTGCTT...........................	24	1	44.00	44	0	44
..........................AACTGAGATCGATTGGTGCATAG.................................................................................	23	1	44.00	44	0	44
..............................................................................CTAGCACCATTCGAAATCAGTGCT............................	24	1	34.00	34	0	34
................................................................................AGCACCATTCGAAATCAGTGCT............................	22	1	33.00	33	0	33
..........................AACTGAGATCGATTGGTGCAT...................................................................................	21	1	33.00	33	0	33
..............................................................................CTAGCACCATTCGAAATCAGTGC.............................	23	1	28.00	28	0	28
...........................ACTGAGATCGATTGGTGCAT...................................................................................	20	1	22.00	22	0	22
...........................ACTGAGATCGATTGGTGCATA..................................................................................	21	1	17.00	17	0	17
................................................................................AGCACCATTCGAAATCAGTGC.............................	21	1	17.00	17	0	17
.................................................................................GCACCATTCGAAATCAGTGCT............................	21	1	13.00	13	0	13
..........................AACTGAGATCGATTGGTGCATA..................................................................................	22	1	9.00	9	0	9
..........................AACTGAGATCGATTGGTGCA....................................................................................	20	1	6.00	6	0	6
............................CTGAGATCGATTGGTGCATAGA................................................................................	22	1	6.00	6	0	6
.................................................................................GCACCATTCGAAATCAGTGC.............................	20	1	6.00	6	0	6
..............................................................................CTAGCACCATTCGAAATCAGTG..............................	22	1	5.00	5	0	5
..................................................TATCAAGAGGACTCGCTAATT...........................................................	21	1	4.00	4	0	4
.............................TGAGATCGATTGGTGCATAGA................................................................................	21	1	4.00	4	0	4
..................................................TATCAAGAGGACTCGCTAATTTTC........................................................	24	1	3.00	3	0	3

Secondary Structure

dm3

dG=-29.9, p-value=0.009901	dG=-29.8, p-value=0.009901	dG=-29.0, p-value=0.009901	dG=-29.0, p-value=0.009901	dG=-28.9, p-value=0.009901

droSim1

dG=-27.1, p-value=0.009901	dG=-26.6, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.2, p-value=0.009901

droSec1

dG=-27.1, p-value=0.009901	dG=-26.6, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.2, p-value=0.009901

droYak2

dG=-26.5, p-value=0.009901	dG=-26.0, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.6, p-value=0.009901

droEre2

dG=-26.7, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.3, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.8, p-value=0.009901

droAna3

dG=-29.2, p-value=0.009901	dG=-28.7, p-value=0.009901	dG=-28.3, p-value=0.009901

dp4

dG=-28.2, p-value=0.009901	dG=-27.4, p-value=0.009901	dG=-27.3, p-value=0.009901	dG=-27.3, p-value=0.009901

droPer1

dG=-25.5, p-value=0.009901	dG=-25.3, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.5, p-value=0.009901

droWil1

dG=-30.8, p-value=0.009901	dG=-30.3, p-value=0.009901	dG=-29.9, p-value=0.009901

droVir3

dG=-27.3, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.4, p-value=0.009901

droMoj3

dG=-27.5, p-value=0.009901	dG=-27.3, p-value=0.009901	dG=-27.2, p-value=0.009901	dG=-26.6, p-value=0.009901	dG=-26.6, p-value=0.009901

droGri2

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

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