Secondary structure and small RNA-seq evidence for dme-mir-1003

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:20484312-20484397 +	CAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG
droSim1	chr3R:20323145-20323230 +	GAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG
droSec1	super_0:20818704-20818789 +	GAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG
droYak2	chr3R:26013202-26013287 -	GAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGTCGTGAGCTGCG
droEre2	scaffold_4820:7574099-7574184 -	GAAACTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG
droAna3	scaffold_13340:4690326-4690418 -	CAAGCTACGCCGAAGGTGAGTATAGTGGATGTGGGTGGCTCTTATTTG--------GCCGGTCCTCTCACATCTCCATATTCACAGGCGTCGAGAGCTGCG
dp4	chr2:1751559-1751647 -	GAAGCTACGTAGAAGGTGGGTATCGTGCTTGTGGGTGGCTCTT----G--------GTCAGTCCTCTCACATCTCTATATTCACAGGCGCCGCGAGTTGCG
droPer1	super_7:1904970-1905058 -	GAAGCTACGTAGAAGGTGGGTATCGTGCTTGTGGGTGGCTCTT----G--------GTCAGTCCTCTCACATCTCTATATTCACAGGCGCCGCGAGTTGCG
droWil1	scaffold_181089:9616822-9616911 -	AAAGTTGCGCCGTAGGTGAGTATC-GGGTTGTGATTGGCTCCT----T------GTGGTAGTCCTCTCACATCTCTATATTCACAGGCGTCGCGAGCTGCG
droVir3	scaffold_13047:780932-781019 +	AAAGCTGCGTCGTAGGTGAGTAAT-CAGTTGTGGGTGGCTTTT----T--------GAAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGTGAGTTGCG
droMoj3	scaffold_6540:4775668-4775755 +	CAAGCTGCGGCGCAGGTGAGTAAT-CAGTTGTGGGTGGCTCTA----G--------TGAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGAGAGTTGCG
droGri2	scaffold_14906:5529285-5529380 -	GAAATTGCGGCGCAGGTGAGTAAT-CAGTTGTGGGTGGCTTTT----GTTCTTAGGGAAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGCGAATTGCG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:20484312-20484397 +	CAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG
droSim1	chr3R:20323145-20323230 +	GAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG
droSec1	super_0:20818704-20818789 +	GAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG
droYak2	chr3R:26013202-26013287 -	GAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGTCGTGAGCTGCG
droEre2	scaffold_4820:7574099-7574184 -	GAAACTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--------------GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG
droAna3	scaffold_13340:4690326-4690418 -	CAAGCTACGCCGAAGGTGAGTATAGTGGATGTGGGTGGCTCTTATTTG--------GCCGGTCCTCTCACATCTCCATATTCACAGGCGTCGAGAGCTGCG
dp4	chr2:1751559-1751647 -	GAAGCTACGTAGAAGGTGGGTATCGTGCTTGTGGGTGGCTCTT----G--------GTCAGTCCTCTCACATCTCTATATTCACAGGCGCCGCGAGTTGCG
droPer1	super_7:1904970-1905058 -	GAAGCTACGTAGAAGGTGGGTATCGTGCTTGTGGGTGGCTCTT----G--------GTCAGTCCTCTCACATCTCTATATTCACAGGCGCCGCGAGTTGCG
droWil1	scaffold_181089:9616822-9616911 -	AAAGTTGCGCCGTAGGTGAGTATC-GGGTTGTGATTGGCTCCT----T------GTGGTAGTCCTCTCACATCTCTATATTCACAGGCGTCGCGAGCTGCG
droVir3	scaffold_13047:780932-781019 +	AAAGCTGCGTCGTAGGTGAGTAAT-CAGTTGTGGGTGGCTTTT----T--------GAAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGTGAGTTGCG
droMoj3	scaffold_6540:4775668-4775755 +	CAAGCTGCGGCGCAGGTGAGTAAT-CAGTTGTGGGTGGCTCTA----G--------TGAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGAGAGTTGCG
droGri2	scaffold_14906:5529285-5529380 -	GAAATTGCGGCGCAGGTGAGTAAT-CAGTTGTGGGTGGCTTTT----GTTCTTAGGGAAAGCCCTCTCACATCTCTTTATTCACAGGCGGCGCGAATTGCG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GAAGCTGCGCAGAAGGTGGGTATC-TGGATGTGGTTGGCTCT--GGCGGTCCTCTCACATTTACATATTCACAGGCGCCGTGAGCTGCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
....................................................TCTCACATTTACATATTCACAG...............	22	1	42.00	42	42
....................................................TCTCACATTTACATATTCACA................	21	1	37.00	37	37
...............GTGGGTATC-TGGATGTGGTTGG...................................................	22	1	28.00	28	28
...............GTGGGTATC-TGGATGTGGTTG....................................................	21	1	7.00	7	7
......................................................TCACATTTACATATTCACAG...............	20	1	1.00	1	1
.....................................................CTCACATTTACATATTCACAG...............	21	1	1.00	1	1
........................................................ACATTTACATATTCACAG...............	18	1	1.00	1	1

dp4

GAAGCTACGTAGAAGGTGGGTATCGTGCTTGTGGGTGGCTCTTGGTCAGTCCTCTCACATCTCTATATTCACAGGCGCCGCGAGTTGCG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
....................................................TCTCACATCTCTATATTCACAG...............	22	1	636.00	636	425	211
....................................................TCTCACATCTCTATATTCACA................	21	1	236.00	236	142	94
...............GTGGGTATCGTGCTTGTGGGTGG...................................................	23	1	43.00	43	29	14
....................................................TCTCACATCTCTATATTCAC.................	20	1	12.00	12	4	8
....................................................TCTCACATCTCTATATTCA..................	19	1	3.00	3	1	2
...............GTGGGTATCGTGCTTGTGGGTG....................................................	22	1	3.00	3	3	0
...............GTGGGTATCGTGCTTGTGGGT.....................................................	21	1	3.00	3	1	2
......................................................TCACATCTCTATATTCACAG...............	20	1	3.00	3	0	3
.....................................................CTCACATCTCTATATTCACAG...............	21	1	2.00	2	1	1
.......................................................CACATCTCTATATTCACAG...............	19	1	2.00	2	2	0
......................................................TCACATCTCTATATTCACA................	19	1	2.00	2	0	2
...............GTGGGTATCGTGCTTGTGGG......................................................	20	1	2.00	2	1	1
...............GTGGGTATCGTGCTTGTGGGTGGC..................................................	24	1	1.00	1	1	0
...................................................CTCTCACATCTCTATATTCACAG...............	23	1	1.00	1	1	0
.....................................................CTCACATCTCTATATTCACA................	20	1	1.00	1	0	1
...............GTGGGTATCGTGCTTGTG........................................................	18	1	1.00	1	1	0
...................................................CTCTCACATCTCTATATTCACA................	22	1	1.00	1	1	0
...............GTGGGTATCGTGCTTGTGGGTGGCTCT...............................................	27	1	1.00	1	0	1
........................................................ACATCTCTATATTCACAG...............	18	1	1.00	1	1	0

Secondary Structure

dm3

-19.0	-19.0	-18.3

droSim1

-19.0	-19.0	-18.3

droSec1

-19.0	-19.0	-18.3

droYak2

-19.0	-19.0	-18.3

droEre2

-19.0	-19.0	-18.3

droAna3

-23.5	-22.9

dp4

-16.4	-15.9	-15.6

droPer1

-16.4	-15.9	-15.6

droWil1

-25.0

droVir3

-24.8	-24.3

droMoj3

-24.0	-23.1

droGri2

-27.4	-26.7

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