Secondary structure and small RNA-seq evidence for dme-mir-316

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:21661799-21661917 -	GAAAA--------------------------------------------GTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCAATTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGCTCAGCGATT------------------------------TGCA------------------------------------
droSim1	chr3L:21004826-21004944 -	GAAAA--------------------------------------------GTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGCCCAGCGACT------------------------------TGCA------------------------------------
droSec1	super_11:1581867-1581985 -	GAAAA--------------------------------------------GTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGCCCAGCGACT------------------------------TGCA------------------------------------
droYak2	chr3L:18849495-18849613 +	GAAAA--------------------------------------------GTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCAACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGACCAGCGATT------------------------------TGCA------------------------------------
droEre2	scaffold_4784:21318808-21318933 -	GAAA-------------------------------------TACACAAAGTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCAACAACGACAGGAAAGGGAAAAAGGCGTATTCACTATGAGTTTGGCCAGCGACT------------------------------TGCA------------------------------------
droAna3	scaffold_13337:3985740-3985858 -	CAAGA--------------------------------------------ACATATATTC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTAATTCAAACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGGTCAACATTT------------------------------CGTC------------------------------------
dp4	chrXR_group6:4548558-4548677 +	GTAAA----------------------------------A-TATACAAAG-----ATC-AAAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTCGATCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTATCCAACAA---------------------------------ACA------------------------------------
droPer1	super_9:2845596-2845715 +	GTAAA----------------------------------A-TATACAAAG-----ATC-AAAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTCGATCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTATCCAACAA---------------------------------ACA------------------------------------
droWil1	scaffold_180698:1092691-1092806 +	ATATA--------------------------------------------ATGTATGTAT-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTTAACTAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTAATCAACAAAT------------------------------T---------------------------------------
droVir3	scaffold_13049:24266823-24266971 +	ATATC--------------------------------------------TTTGATCTATAAAGTTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATT-GAGCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAATTTGTTCAACCAATCTGTTTAAACACCTATTCAATGAAAAGAAATGCT------------------------------------
droMoj3	scaffold_6680:18891183-18891347 +	GATCTA--ACTGAATCGATTTT--------------------------------TATATAAAGTTCTAGTCGATTTGTCTTTTTCCGCTTACTGACGTTTTATT-GAACAACGGCAGGGAAGGGAAAAAGGCGTATTTACTATGAATTATTTCAACGATA------------------------------TAAAAATTTCTATTAAAATAATAATCAGAGTGAGAGAGGG
droGri2	scaffold_15110:9482044-9482193 -	TACCAGAGACTAAA-CATTTTGTGTATAAGTATTGTATGATTAAGCAATC-----TTC-AGAGTTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATT-GAGCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAATGTAATCAACAA------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:21661799-21661917 -	GAAAA--------------------------------------------GTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCAATTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGCTCAGCGATT------------------------------TGCA------------------------------------
droSim1	chr3L:21004826-21004944 -	GAAAA--------------------------------------------GTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGCCCAGCGACT------------------------------TGCA------------------------------------
droSec1	super_11:1581867-1581985 -	GAAAA--------------------------------------------GTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGCCCAGCGACT------------------------------TGCA------------------------------------
droYak2	chr3L:18849495-18849613 +	GAAAA--------------------------------------------GTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCAACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGACCAGCGATT------------------------------TGCA------------------------------------
droEre2	scaffold_4784:21318808-21318933 -	GAAA-------------------------------------TACACAAAGTGGATACAC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCAACAACGACAGGAAAGGGAAAAAGGCGTATTCACTATGAGTTTGGCCAGCGACT------------------------------TGCA------------------------------------
droAna3	scaffold_13337:3985740-3985858 -	CAAGA--------------------------------------------ACATATATTC-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTAATTCAAACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGGTCAACATTT------------------------------CGTC------------------------------------
dp4	chrXR_group6:4548558-4548677 +	GTAAA----------------------------------A-TATACAAAG-----ATC-AAAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTCGATCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTATCCAACAA---------------------------------ACA------------------------------------
droPer1	super_9:2845596-2845715 +	GTAAA----------------------------------A-TATACAAAG-----ATC-AAAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTCGATCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTATCCAACAA---------------------------------ACA------------------------------------
droWil1	scaffold_180698:1092691-1092806 +	ATATA--------------------------------------------ATGTATGTAT-AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTTAACTAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTAATCAACAAAT------------------------------T---------------------------------------
droVir3	scaffold_13049:24266823-24266971 +	ATATC--------------------------------------------TTTGATCTATAAAGTTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATT-GAGCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAATTTGTTCAACCAATCTGTTTAAACACCTATTCAATGAAAAGAAATGCT------------------------------------
droMoj3	scaffold_6680:18891183-18891347 +	GATCTA--ACTGAATCGATTTT--------------------------------TATATAAAGTTCTAGTCGATTTGTCTTTTTCCGCTTACTGACGTTTTATT-GAACAACGGCAGGGAAGGGAAAAAGGCGTATTTACTATGAATTATTTCAACGATA------------------------------TAAAAATTTCTATTAAAATAATAATCAGAGTGAGAGAGGG
droGri2	scaffold_15110:9482044-9482193 -	TACCAGAGACTAAA-CATTTTGTGTATAAGTATTGTATGATTAAGCAATC-----TTC-AGAGTTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATT-GAGCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAATGTAATCAACAA------------------------------------------------------------------------

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GAAAAGTGGATACAC------AAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTCATTTCCACAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTGCCCAGCGACTTGCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
....................................TGTCTTTTTCCGCTTACTGGCG...................................................................	22	1	2443.00	2443	2443
....................................TGTCTTTTTCCGCTTACTGGCGT..................................................................	23	1	299.00	299	299
....................................TGTCTTTTTCCGCTTACTGGC....................................................................	21	1	98.00	98	98
....................................TGTCTTTTTCCGCTTACTGGCGTT.................................................................	24	1	23.00	23	23
..........................................................................ACAGGAAAGGGAAAAAGGCGTA.............................	22	1	21.00	21	21
.......................................CTTTTTCCGCTTACTGGCG...................................................................	19	1	4.00	4	4
....................................TGTCTTTTTCCGCTTACTGG.....................................................................	20	1	4.00	4	4
.........................................................................GACAGGAAAGGGAAAAAGGCGTA.............................	23	1	3.00	3	3
......................................TCTTTTTCCGCTTACTGGCG...................................................................	20	1	2.00	2	2
.....................................GTCTTTTTCCGCTTACTGGCGTT.................................................................	23	1	1.00	1	1
....................................TGTCTTTTTCCGCTTACTGGCGTTT................................................................	25	1	1.00	1	1
.....................................GTCTTTTTCCGCTTACTGGCG...................................................................	21	1	1.00	1	1
..........................................................................ACAGGAAAGGGAAAAAGGCG...............................	20	1	1.00	1	1
........................................TTTTTCCGCTTACTGGCGT..................................................................	19	1	1.00	1	1

dp4

GTAAAAT--ATACAAAGATCAAAATTCTAGTCGATTTGTCTTTTTCCGCTTACTGGCGTTTTATTCGATCAACGACAGGAAAGGGAAAAAGGCGTATTTACTATGAGTTTATCCAACAA---ACA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
....................................TGTCTTTTTCCGCTTACTGGCG...................................................................	22	1	4648.00	4648	3220	1428
....................................TGTCTTTTTCCGCTTACTGGCGT..................................................................	23	1	754.00	754	496	258
....................................TGTCTTTTTCCGCTTACTGGC....................................................................	21	1	198.00	198	137	61
....................................TGTCTTTTTCCGCTTACTGG.....................................................................	20	1	51.00	51	19	32
....................................TGTCTTTTTCCGCTTACTGGCGTT.................................................................	24	1	48.00	48	26	22
..........................................................................ACAGGAAAGGGAAAAAGGCGTA.............................	22	1	40.00	40	38	2
........................................TTTTTCCGCTTACTGGCG...................................................................	18	1	6.00	6	6	0
.........................................................................GACAGGAAAGGGAAAAAGGCGTA.............................	23	1	5.00	5	5	0
..........................................................................ACAGGAAAGGGAAAAAGGC................................	19	1	4.00	4	3	1
....................................TGTCTTTTTCCGCTTACTGGCGTTT................................................................	25	1	4.00	4	1	3
.......................................CTTTTTCCGCTTACTGGCG...................................................................	19	1	3.00	3	3	0
.....................................GTCTTTTTCCGCTTACTGGCG...................................................................	21	1	3.00	3	3	0

Secondary Structure

dm3

-28.8	-28.7	-27.9	-27.8

droSim1

-28.8	-28.7	-27.9	-27.8

droSec1

-28.8	-28.7	-27.9	-27.8

droYak2

-28.8	-28.7	-27.9	-27.8

droEre2

-28.8	-28.7	-27.9	-27.8

droAna3

-28.8	-28.7	-27.9	-27.8

dp4

-28.8	-28.7	-27.9	-27.8

droPer1

-28.8	-28.7	-27.9	-27.8

droWil1

-29.6	-29.5	-28.7

droVir3

-28.9	-28.8	-28.3	-28.2	-28.1	-27.9

droMoj3

-28.7	-28.3	-27.9	-27.9	-27.7

droGri2

-28.1	-27.4	-27.1

Generated: 01/05/2013 at 05:17 PM