Secondary structure and small RNA-seq evidence for dme-mir-276a

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:10358313-10358440 +	CC-AA----------GA---------TATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droSim1	chr3L:9747980-9748107 +	CC-AA----------GA---------TATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droSec1	super_0:2571151-2571278 +	CC-AA----------GA---------TATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droYak2	chr3L:10348871-10348998 +	GC-AA----------GA---------TATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droEre2	scaffold_4784:10353122-10353248 +	GC-AA----------GA---------TAT-TTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droAna3	scaffold_13337:15274238-15274391 +	CC-AA----------GA---------TATTTCTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTAACATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCTAAAATCAAC-GA-----AA------ACATAAAGCGGAGTTGGTTTCCCCTTCAACCA-AAAAAT-C
dp4	chrXR_group6:8756376-8756505 +	CG-AACGGAGGAGAAGATGTGTGTATT--TTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAGACAAC-GA------------------------------------------------------
droPer1	super_27:1191188-1191317 +	CG-AACGGAGGAGAAGATGTGTGTATT--TTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAGACAAC-GA------------------------------------------------------
droWil1	scaffold_181024:222598-222734 -	CTGAA----------AA---------TA--TGCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATTTAATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-GTTACGAAA------ACAG----------------------CAACAAGAAA-AAAC
droVir3	scaffold_13049:16143973-16144087 +	TG-AA----------AA---------TAT--GCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCAATTTATATACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-GAAGTG--------------------------------------------------
droMoj3	scaffold_6680:20621809-20621940 -	CC-AA----------AG---------TAT--GCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCAATTTAAATACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAACACAACTCAAACAAAAACGAAAACG----------------------------------AGCG
droGri2	scaffold_15110:12521926-12522042 -	CA-AA----------AA---------TAT--GCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTAAATTTAAATACTCATAGGAACTTCATACCGTGCTCTTGGAAGACCAAAACACAAC-AAAG------------------------------------------------AAAC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:10358313-10358440 +	CC-AA----------GA---------TATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droSim1	chr3L:9747980-9748107 +	CC-AA----------GA---------TATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droSec1	super_0:2571151-2571278 +	CC-AA----------GA---------TATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droYak2	chr3L:10348871-10348998 +	GC-AA----------GA---------TATTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droEre2	scaffold_4784:10353122-10353248 +	GC-AA----------GA---------TAT-TTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-CAAGTGAATGCAAAA-------------------------------------ATCC
droAna3	scaffold_13337:15274238-15274391 +	CC-AA----------GA---------TATTTCTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTAACATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCTAAAATCAAC-GA-----AA------ACATAAAGCGGAGTTGGTTTCCCCTTCAACCA-AAAAAT-C
dp4	chrXR_group6:8756376-8756505 +	CG-AACGGAGGAGAAGATGTGTGTATT--TTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAGACAAC-GA------------------------------------------------------
droPer1	super_27:1191188-1191317 +	CG-AACGGAGGAGAAGATGTGTGTATT--TTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAGACAAC-GA------------------------------------------------------
droWil1	scaffold_181024:222598-222734 -	CTGAA----------AA---------TA--TGCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATTTAATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-GTTACGAAA------ACAG----------------------CAACAAGAAA-AAAC
droVir3	scaffold_13049:16143973-16144087 +	TG-AA----------AA---------TAT--GCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCAATTTATATACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAAC-GAAGTG--------------------------------------------------
droMoj3	scaffold_6680:20621809-20621940 -	CC-AA----------AG---------TAT--GCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCAATTTAAATACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAACACAACTCAAACAAAAACGAAAACG----------------------------------AGCG
droGri2	scaffold_15110:12521926-12522042 -	CA-AA----------AA---------TAT--GCTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTAAATTTAAATACTCATAGGAACTTCATACCGTGCTCTTGGAAGACCAAAACACAAC-AAAG------------------------------------------------AAAC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CCA----------AGATA-------TTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCA--TTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAAACAACCAAGTGAATGCAAAAATCC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................................................................TAGGAACTTCATACCGTGCTCT......................................	22	2	9748.00	19496	19496
................................................AGCGAGGTATAGAGTTCCTACG.............................................................................	22	4	5579.25	22317	22317
.......................................................................................TAGGAACTTCATACCGTGCTC.......................................	21	2	51.00	102	102
.......................................................................................TAGGAACTTCATACCGTGCT........................................	20	2	10.00	20	20
................................................AGCGAGGTATAGAGTTCCTA...............................................................................	20	4	1.75	7	7
................................................AGCGAGGTATAGAGTTCCTACGT............................................................................	23	4	1.25	5	5

dp4

CGAACGGAGGAGAAGATGTGTGTATTTTTTTACCTGGTTTTTGCCATCAGCGAGGTATAGAGTTCCTACGTTCATATTATAAACTCGTAGGAACTTCATACCGTGCTCTTGGAAGACCAAAAGACAACGA-----------------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................................................................................TAGGAACTTCATACCGTGCTCT......................................	22	2	41665.00	83330	0	83330
.......................................................................................TAGGAACTTCATACCGTGCTC.......................................	21	2	14083.00	28166	353	27813
.......................................................................................TAGGAACTTCATACCGTGCT........................................	20	2	1175.00	2350	36	2314
.......................................................................................TAGGAACTTCATACCGTGCTCTT.....................................	23	2	68.50	137	137	0
................................................AGCGAGGTATAGAGTTCCTA...............................................................................	20	4	42.75	171	0	171
.......................................................................................TAGGAACTTCATACCGTGC.........................................	19	2	21.00	42	0	42
........................................................................................AGGAACTTCATACCGTGCTCT......................................	21	2	12.50	25	0	25
................................................AGCGAGGTATAGAGTTCCTACGTT...........................................................................	24	2	4.50	9	0	9
...................................................................................CTCGTAGGAACTTCATACCGTG..........................................	22	2	1.50	3	0	3

Secondary Structure

dm3

-39.1	-38.5

droSim1

-39.1	-38.5

droSec1

-39.1	-38.5

droYak2

-39.1	-38.5

droEre2

-39.1	-38.5

droAna3

-37.4	-36.8

dp4

-39.0	-38.4

droPer1

-39.0	-38.4

droWil1

-39.0	-38.4

droVir3

-39.0	-38.4

droMoj3

-39.0	-38.4

droGri2

-33.2	-32.6	-32.6

Generated: 01/05/2013 at 05:12 PM