Secondary structure and small RNA-seq evidence for dme-mir-iab-4

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:12681982-12682079 +	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAGAGCACTAACAAC
droSim1	chr3R:8791202-8791299 -	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGATAGCACGAGCAAC
droSec1	super_12:1472230-1472327 -	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGATAGCACGAGCAAC
droYak2	chr3R:11708953-11709050 -	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAAAGCACGAGCAAC
droEre2	scaffold_4770:8952402-8952499 -	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAAAGCACGAGCAAC
droAna3	scaffold_13340:7215188-7215285 -	TGATTTTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGTAACACCTTCAAC
dp4	chr2:17671752-17671849 +	-GAACCTGTGCGACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC
droPer1	super_0:11526558-11526655 +	-GAACCTGTGCGACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC
droWil1	scaffold_181130:4905585-4905682 -	TGAATCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATGCTATCCGGTATACCTTCAGTATACGTAACACGATGAAACACCAACAAC
droVir3	scaffold_12855:414691-414788 -	AGAGCCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCGAC
droMoj3	scaffold_6540:1943729-1943826 +	TGAGCCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC
droGri2	scaffold_14906:12815108-12815201 +	-----CTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:12681982-12682079 +	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAGAGCACTAACAAC
droSim1	chr3R:8791202-8791299 -	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGATAGCACGAGCAAC
droSec1	super_12:1472230-1472327 -	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGATAGCACGAGCAAC
droYak2	chr3R:11708953-11709050 -	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAAAGCACGAGCAAC
droEre2	scaffold_4770:8952402-8952499 -	CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAAAGCACGAGCAAC
droAna3	scaffold_13340:7215188-7215285 -	TGATTTTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGTAACACCTTCAAC
dp4	chr2:17671752-17671849 +	-GAACCTGTGCGACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC
droPer1	super_0:11526558-11526655 +	-GAACCTGTGCGACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC
droWil1	scaffold_181130:4905585-4905682 -	TGAATCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATGCTATCCGGTATACCTTCAGTATACGTAACACGATGAAACACCAACAAC
droVir3	scaffold_12855:414691-414788 -	AGAGCCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCGAC
droMoj3	scaffold_6540:1943729-1943826 +	TGAGCCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC
droGri2	scaffold_14906:12815108-12815201 +	-----CTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CGATTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGATAGCACGAGCAAC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.....................ACGTATACTGAATGTATCCT.........................................................	20	2	2.00	4	4
..........................................................TATACCTTCAGTATACGTAACA..................	22	2	1.50	3	3
.......................GTATACTGAATGTATCCTGA.......................................................	20	2	0.50	1	1
.......................................................CGGTATACCTTCAGTATACGTAA....................	23	2	0.50	1	1

dp4

-GAACCTGTGCGACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAAC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.....................ACGTATACTGAATGTATCCTG........................................................	21	2	7.00	14	14	0
..........................................................TATACCTTCAGTATACGTAACA..................	22	2	2.50	5	5	0
.....................ACGTATACTGAATGTATCCTGA.......................................................	22	2	2.50	5	0	5
......................CGTATACTGAATGTATCCTGA.......................................................	21	2	1.50	3	3	0
.......................................................CGGTATACCTTCAGTATACGTAA....................	23	2	0.50	1	1	0
.......................................................CGGTATACCTTCAGTATACGTAAC...................	24	2	0.50	1	1	0
.....................ACGTATACTGAATGTATCC..........................................................	19	2	0.50	1	1	0

Secondary Structure

dm3

-24.6	-24.2	-23.7

droSim1

-24.6	-24.2	-23.7

droSec1

-24.6	-24.2	-23.7

droYak2

-24.6	-24.2	-23.7

droEre2

-24.6	-24.2	-23.7

droAna3

-26.2	-25.8	-25.3

dp4

-26.2	-25.8	-25.3

droPer1

-26.2	-25.8	-25.3

droWil1

-26.2	-25.8	-25.8	-25.6	-25.4	-25.3

droVir3

-26.2	-25.8	-25.3

droMoj3

-26.2	-25.8	-25.3

droGri2

-26.2	-25.8	-25.3

Generated: 01/05/2013 at 05:37 PM