Secondary structure and small RNA-seq evidence for dme-mir-317

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:5916833-5916954 +	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CATCCT-TGCTGCACCA-------------CA-
droSim1	chr3R:15459127-15459249 -	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CATCCTTTGCTGCTCCA-------------CA-
droSec1	super_0:15996573-15996694 -	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CATCCT-TGCTGCTCCA-------------CA-
droYak2	chr3R:9963959-9964079 +	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CGTCCT-TGCTGCTCCAG---------------
droEre2	scaffold_4770:15683457-15683577 -	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CGTCCT-TGCTGCTCCAG---------------
droAna3	scaffold_13340:6479980-6480089 +	AA----GC------TCATTT---G-------------TGTGCATCGGCTGCTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TTG-CATCCT-TTC-----------------------
dp4	chr2:5029980-5030116 -	AA----GC---------TCTTCCGTGTCTCGTGTCTCTGTGCAACTGCCGTTGGGATAC-ACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCGTT--CTG-CAACAA-TGCAACATCAGC---------AACAA
droPer1	super_19:735499-735629 -	AA----GC---------TCTTCCGTGTCTCGTGTCTCTGTGCAACTGCCGTTGGGATAC-ACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCGTT--CTG-CAACAA-TGCAACATCAG---------------
droWil1	scaffold_181089:11180051-11180176 -	AA----GCTTTCTAGATTCTTC---------------TGTGCAACTGCCACTGGGATAC-ACCCTGTGCTCGCTTTGAATATTGTGCAAACAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTTTTG-CATCCA-TGCAACACCA----------------
droVir3	scaffold_12855:2698510-2698638 -	AA----GC---------TTTTTC--------------AGTGCAATTGCCGCTGGGATAC-ACCCTGTGCTCGCTTTGAATT--GTGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT---GGCAGCCAA-TGCAACAATTGCAACAACTGCAACA-
droMoj3	scaffold_6540:11898843-11898966 -	GAGTAAGC----------TTTCT-----------CTCTGTGCAATTGCCGCTGGGATAC-ACCCTGTGCTCGCTTTGAGTT-TATGT-TGCAAGTGAACACAGCTGGTGGTATCCAGAGGCCGTT---GACAGCCAA-TGCAACAACAGC---------A--A-
droGri2	scaffold_14624:2253109-2253242 +	AAA-AAGC---------TTTTCGC-------------TGTGCAATTGCCACTGGGATATTGCCCTGTGCTCGCTTTGAATATTGTGTAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CGCACA-TGCAACAACAACAACAAGAGCA--A-

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:5916833-5916954 +	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CATCCT-TGCTGCACCA-------------CA-
droSim1	chr3R:15459127-15459249 -	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CATCCTTTGCTGCTCCA-------------CA-
droSec1	super_0:15996573-15996694 -	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CATCCT-TGCTGCTCCA-------------CA-
droYak2	chr3R:9963959-9964079 +	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CGTCCT-TGCTGCTCCAG---------------
droEre2	scaffold_4770:15683457-15683577 -	AA----GC------GAATTTTCCA-------------TATGCAACTGCCATTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CGTCCT-TGCTGCTCCAG---------------
droAna3	scaffold_13340:6479980-6480089 +	AA----GC------TCATTT---G-------------TGTGCATCGGCTGCTGGGATAC-ACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TTG-CATCCT-TTC-----------------------
dp4	chr2:5029980-5030116 -	AA----GC---------TCTTCCGTGTCTCGTGTCTCTGTGCAACTGCCGTTGGGATAC-ACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCGTT--CTG-CAACAA-TGCAACATCAGC---------AACAA
droPer1	super_19:735499-735629 -	AA----GC---------TCTTCCGTGTCTCGTGTCTCTGTGCAACTGCCGTTGGGATAC-ACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCGTT--CTG-CAACAA-TGCAACATCAG---------------
droWil1	scaffold_181089:11180051-11180176 -	AA----GCTTTCTAGATTCTTC---------------TGTGCAACTGCCACTGGGATAC-ACCCTGTGCTCGCTTTGAATATTGTGCAAACAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTTTTG-CATCCA-TGCAACACCA----------------
droVir3	scaffold_12855:2698510-2698638 -	AA----GC---------TTTTTC--------------AGTGCAATTGCCGCTGGGATAC-ACCCTGTGCTCGCTTTGAATT--GTGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT---GGCAGCCAA-TGCAACAATTGCAACAACTGCAACA-
droMoj3	scaffold_6540:11898843-11898966 -	GAGTAAGC----------TTTCT-----------CTCTGTGCAATTGCCGCTGGGATAC-ACCCTGTGCTCGCTTTGAGTT-TATGT-TGCAAGTGAACACAGCTGGTGGTATCCAGAGGCCGTT---GACAGCCAA-TGCAACAACAGC---------A--A-
droGri2	scaffold_14624:2253109-2253242 +	AAA-AAGC---------TTTTCGC-------------TGTGCAATTGCCACTGGGATATTGCCCTGTGCTCGCTTTGAATATTGTGTAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTT--TGG-CGCACA-TGCAACAACAACAACAAGAGCA--A-

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAGCGAATTTTCCAT-------------ATGCAACTGCCATTGGGATACACCCTGTGCTCGCTTTGAATGAAATGCAAGCAAGTGAACACAGCTGGTGGTATCCAGTGGCCGTTTGGCATCCTTTGCTGCTCCA----C-A	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...................................................................................TGAACACAGCTGGTGGTATCC.....................................	21	1	56.00	56	56
...................................................................................TGAACACAGCTGGTGGTATCCA....................................	22	1	51.00	51	51
.........................................TGGGATACACCCTGTGCTCGCT..............................................................................	22	1	16.00	16	16
...................................................................................TGAACACAGCTGGTGGTATC......................................	20	1	12.00	12	12
...................................................................................TGAACACAGCTGGTGGTATCCAGT..................................	24	1	9.00	9	9
...................................................................................TGAACACAGCTGGTGGTAT.......................................	19	1	5.00	5	5
...................................................................................TGAACACAGCTGGTGGTATCCAG...................................	23	1	3.00	3	3
.........................................TGGGATACACCCTGTGCTCGC...............................................................................	21	1	2.00	2	2
...................................................................................TGAACACAGCTGGTGGTA........................................	18	1	1.00	1	1

dp4

AAGC---TCTTCCGTGTCTCGTGTCTCTGTGCAACTGCCGTTGGGATACACCCTGTGCTCGCTTTGAATATGGTGCAAGCAAGTGAACACAGCTGGTGGTATCCAATGGCCGTTCTGCAACAA-TGCAACATCAGCAACAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...................................................................................TGAACACAGCTGGTGGTATCC.....................................	21	1	7103.00	7103	32	7071
...................................................................................TGAACACAGCTGGTGGTATC......................................	20	1	5593.00	5593	27	5566
...................................................................................TGAACACAGCTGGTGGTATCCAAT..................................	24	1	4093.00	4093	187	3906
...................................................................................TGAACACAGCTGGTGGTAT.......................................	19	1	3240.00	3240	9	3231
...................................................................................TGAACACAGCTGGTGGTATCCA....................................	22	1	1570.00	1570	34	1536
.........................................TGGGATACACCCTGTGCTCGCT..............................................................................	22	1	574.00	574	22	552
...................................................................................TGAACACAGCTGGTGGTATCCAA...................................	23	1	164.00	164	4	160
...................................................................................TGAACACAGCTGGTGGTA........................................	18	1	73.00	73	0	73
.........................................TGGGATACACCCTGTGCTCG................................................................................	20	1	31.00	31	0	31
.........................................TGGGATACACCCTGTGCTCGC...............................................................................	21	1	28.00	28	0	28
...............................................................TTGAATATGGTGCAAGCAAG..........................................................	20	1	24.00	24	3	21
....................................................................................GAACACAGCTGGTGGTATCC.....................................	20	1	6.00	6	0	6
..................................................................................GTGAACACAGCTGGTGGTATC......................................	21	1	6.00	6	1	5
..................................................................................GTGAACACAGCTGGTGGTAT.......................................	20	1	5.00	5	0	5
....................................................................................GAACACAGCTGGTGGTATCCA....................................	21	1	2.00	2	0	2
.........................................TGGGATACACCCTGTGCTCGCTT.............................................................................	23	1	2.00	2	0	2

Secondary Structure

dm3

dG=-29.3, p-value=0.009901	dG=-29.3, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901

droSim1

dG=-29.3, p-value=0.009901	dG=-29.3, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901

droSec1

dG=-29.3, p-value=0.009901	dG=-29.3, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901

droYak2

dG=-29.3, p-value=0.009901	dG=-29.3, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901

droEre2

dG=-29.3, p-value=0.009901	dG=-29.3, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901	dG=-28.9, p-value=0.009901

droAna3

dG=-28.3, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901	dG=-27.9, p-value=0.009901

dp4

dG=-26.7, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.4, p-value=0.009901

droPer1

dG=-26.7, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.4, p-value=0.009901

droWil1

dG=-29.9, p-value=0.009901	dG=-29.5, p-value=0.009901	dG=-29.5, p-value=0.009901	dG=-29.5, p-value=0.009901	dG=-29.5, p-value=0.009901

droVir3

dG=-29.5, p-value=0.009901	dG=-29.1, p-value=0.009901	dG=-29.1, p-value=0.009901	dG=-29.1, p-value=0.009901	dG=-29.1, p-value=0.009901

droMoj3

dG=-26.2, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.8, p-value=0.009901

droGri2

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

Generated: 03/07/2013 at 05:20 PM