Secondary structure and small RNA-seq evidence for dme-mir-279

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:25041292-25041421 +	ACTGG--------AGCTGGAATTGG-AATTCATACTACTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droSim1	chr3R:24712183-24712312 +	ACTGG--------AGCTGGAATTGG-AATTCATACTGCTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droSec1	super_4:3904072-3904201 +	ACTGG--------AGCTGGAATTGG-AATTCATACTGCTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droYak2	chr3R:21456037-21456166 -	ACTGG--------AACTAGAATTGA-AATTCATACTACTGTTTTTAGTGGGTGAGGGTCCAGTGCTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droEre2	scaffold_4820:2989050-2989173 -	ACTGG--------------AATTGG-AATTCATACTACTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droAna3	scaffold_13340:14200293-14200422 -	GGCGG--------CGATACTAATAC-TACTACTACTACTGTTTTTAGTGGGTGAGGGTCCAGTGTTTCACATTGATTT-C---TGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCAGCAAG-----------GCCCACGT
dp4	chr2:1881900-1882031 +	AGTGG--------TTTTA-AGTTCG-CGATCATACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCAACAGA-----------ATGCACGT
droPer1	super_7:2045298-2045429 +	AGTGG--------TTTTA-AGTTCG-CGATCATACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCAACAGA-----------ATGCACGT
droWil1	scaffold_181108:1734340-1734482 +	ACTAC--------TACTACGACTAG-AACAACTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTAAATAT-TT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCGAAAATAAAAAAAGAAACACGT
droVir3	scaffold_12822:2330907-2331031 +	ACGAG-----------TGGA-TCGAATATGCGTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTCGTTTTTTCAAGTATTTGTGACTAGATCCACACTCATTAACAACGGTAGTTCAATCAGCAAA--------------TA---
droMoj3	scaffold_6540:26447118-26447234 +	AC-GG--------TTCTG-A-TCGGAAATACGTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGTTTG-CTTAAGTATTTGTGACTAGATCCACACTCATTAAAAACGGTAGTTCAATC-------------------------
droGri2	scaffold_14624:3249724-3249850 +	ATAAGGGAAGTGATTTA-----TGGATAACCGTATTACTGTTTTTAGTGGGTGAGGGTCCAGTGTTTCACATTGTTT--ATT-TGTATTTGTGACTAGATCCACACTCATTAAAAACGGTAGTTCAATCAACA-------------------GT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:25041292-25041421 +	ACTGG--------AGCTGGAATTGG-AATTCATACTACTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droSim1	chr3R:24712183-24712312 +	ACTGG--------AGCTGGAATTGG-AATTCATACTGCTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droSec1	super_4:3904072-3904201 +	ACTGG--------AGCTGGAATTGG-AATTCATACTGCTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droYak2	chr3R:21456037-21456166 -	ACTGG--------AACTAGAATTGA-AATTCATACTACTGTTTTTAGTGGGTGAGGGTCCAGTGCTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droEre2	scaffold_4820:2989050-2989173 -	ACTGG--------------AATTGG-AATTCATACTACTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAAG--------------CACGT
droAna3	scaffold_13340:14200293-14200422 -	GGCGG--------CGATACTAATAC-TACTACTACTACTGTTTTTAGTGGGTGAGGGTCCAGTGTTTCACATTGATTT-C---TGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCAGCAAG-----------GCCCACGT
dp4	chr2:1881900-1882031 +	AGTGG--------TTTTA-AGTTCG-CGATCATACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCAACAGA-----------ATGCACGT
droPer1	super_7:2045298-2045429 +	AGTGG--------TTTTA-AGTTCG-CGATCATACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGATTTTCTT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCAACAGA-----------ATGCACGT
droWil1	scaffold_181108:1734340-1734482 +	ACTAC--------TACTACGACTAG-AACAACTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTAAATAT-TT-AGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCGAAAATAAAAAAAGAAACACGT
droVir3	scaffold_12822:2330907-2331031 +	ACGAG-----------TGGA-TCGAATATGCGTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTCGTTTTTTCAAGTATTTGTGACTAGATCCACACTCATTAACAACGGTAGTTCAATCAGCAAA--------------TA---
droMoj3	scaffold_6540:26447118-26447234 +	AC-GG--------TTCTG-A-TCGGAAATACGTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGTTTG-CTTAAGTATTTGTGACTAGATCCACACTCATTAAAAACGGTAGTTCAATC-------------------------
droGri2	scaffold_14624:3249724-3249850 +	ATAAGGGAAGTGATTTA-----TGGATAACCGTATTACTGTTTTTAGTGGGTGAGGGTCCAGTGTTTCACATTGTTT--ATT-TGTATTTGTGACTAGATCCACACTCATTAAAAACGGTAGTTCAATCAACA-------------------GT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACTGGAGCTGGAATTGGAATTCATACTGCTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATTTTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCATCAA---GCACGT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.................................................................................TGACTAGATCCACACTCATT................................	20	1	1375.00	1375	1375
.................................................................................TGACTAGATCCACACTCATTA...............................	21	1	1032.00	1032	1032
.................................................................................TGACTAGATCCACACTCATTAA..............................	22	1	871.00	871	871
.................................................................................TGACTAGATCCACACTCAT.................................	19	1	256.00	256	256
....................................AGTGGGTGGGGGTCCAGTGTTTCACA.......................................................................	26	1	179.00	179	179
.....................................GTGGGTGGGGGTCCAGTGTTTCACA.......................................................................	25	1	70.00	70	70
....................................AGTGGGTGGGGGTCCAGTGTTTCA.........................................................................	24	1	17.00	17	17
....................................AGTGGGTGGGGGTCCAGTGTTTCAC........................................................................	25	1	14.00	14	14
.................................................................................TGACTAGATCCACACTCATTAAT.............................	23	1	11.00	11	11
.....................................GTGGGTGGGGGTCCAGTGTTTCA.........................................................................	23	1	8.00	8	8
.....................................GTGGGTGGGGGTCCAGTGTTTCAC........................................................................	24	1	7.00	7	7
..................................................................................GACTAGATCCACACTCATT................................	19	1	4.00	4	4
....................................AGTGGGTGGGGGTCCAGTGTT............................................................................	21	1	3.00	3	3
....................................AGTGGGTGGGGGTCCAGTGT.............................................................................	20	1	3.00	3	3
....................................AGTGGGTGGGGGTCCAGTGTTT...........................................................................	22	1	3.00	3	3
..........................................TGGGGGTCCAGTGTTTCACA.......................................................................	20	1	2.00	2	2
....................................................................................CTAGATCCACACTCATTA...............................	18	1	1.00	1	1
..............................................................TTGATTTTCTTAGTATTTG....................................................	19	1	1.00	1	1
....................................AGTGGGTGGGGGTCCAGT...............................................................................	18	1	1.00	1	1
.................................................................................TGACTAGATCCACACTCA..................................	18	1	1.00	1	1
.....................................................................................TAGATCCACACTCATTAA..............................	18	1	1.00	1	1
....................................AGTGGGTGGGGGTCCAGTG..............................................................................	19	1	1.00	1	1
.....................................GTGGGTGGGGGTCCAGTGTTT...........................................................................	21	1	1.00	1	1
......................................TGGGTGGGGGTCCAGTGTTTCACA.......................................................................	24	1	1.00	1	1

dp4

AGTGGTT-TTAAGTTCGCGATCATACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGATTTTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTTCAATCAACAGAATGCACGT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.................................................................................TGACTAGATCCACACTCATT................................	20	1	2474.00	2474	1142	1332
.................................................................................TGACTAGATCCACACTCATTA...............................	21	1	1955.00	1955	1611	344
.................................................................................TGACTAGATCCACACTCATTAA..............................	22	1	1714.00	1714	1511	203
.................................................................................TGACTAGATCCACACTCAT.................................	19	1	435.00	435	216	219
....................................AGTGAGTGAGGGTCCAGTGTTTCACA.......................................................................	26	1	322.00	322	302	20
.....................................GTGAGTGAGGGTCCAGTGTTTCACA.......................................................................	25	1	89.00	89	80	9
.....................................GTGAGTGAGGGTCCAGTGTTTCA.........................................................................	23	1	45.00	45	24	21
....................................AGTGAGTGAGGGTCCAGTGTTTCAC........................................................................	25	1	26.00	26	26	0
.....................................GTGAGTGAGGGTCCAGTGTTTCAC........................................................................	24	1	25.00	25	20	5
....................................AGTGAGTGAGGGTCCAGTG..............................................................................	19	1	22.00	22	1	21
....................................AGTGAGTGAGGGTCCAGTGTTTCA.........................................................................	24	1	20.00	20	18	2
.....................................GTGAGTGAGGGTCCAGTGTT............................................................................	20	1	12.00	12	1	11
....................................AGTGAGTGAGGGTCCAGTGT.............................................................................	20	1	10.00	10	1	9
.................................................................................TGACTAGATCCACACTCATTAAT.............................	23	1	10.00	10	10	0
....................................AGTGAGTGAGGGTCCAGTGTTTC..........................................................................	23	1	9.00	9	8	1
.....................................GTGAGTGAGGGTCCAGTGTTTC..........................................................................	22	1	9.00	9	3	6
....................................AGTGAGTGAGGGTCCAGTGTTT...........................................................................	22	1	8.00	8	7	1
.....................................GTGAGTGAGGGTCCAGTGTTT...........................................................................	21	1	5.00	5	1	4
....................................AGTGAGTGAGGGTCCAGTGTT............................................................................	21	1	5.00	5	0	5
..............................................................TTGATTTTCTTAGTATTTG....................................................	19	1	3.00	3	3	0
....................................................................................CTAGATCCACACTCATTA...............................	18	1	2.00	2	2	0
....................................AGTGAGTGAGGGTCCAGT...............................................................................	18	1	2.00	2	1	1
.....................................GTGAGTGAGGGTCCAGTGTTTCACAT......................................................................	26	1	2.00	2	2	0
.....................................GTGAGTGAGGGTCCAGTG..............................................................................	18	1	2.00	2	0	2
..................................................................................GACTAGATCCACACTCATT................................	19	1	1.00	1	0	1
.................................................................................TGACTAGATCCACACTCA..................................	18	1	1.00	1	1	0
..................................................................................GACTAGATCCACACTCATTAA..............................	21	1	1.00	1	0	1

Secondary Structure

dm3

dG=-23.1, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-22.2, p-value=0.009901

droSim1

dG=-23.1, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-22.2, p-value=0.009901

droSec1

dG=-23.1, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-22.2, p-value=0.009901

droYak2

dG=-22.7, p-value=0.009901	dG=-22.5, p-value=0.009901	dG=-22.0, p-value=0.009901	dG=-21.8, p-value=0.009901

droEre2

dG=-23.1, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-22.2, p-value=0.009901

droAna3

dG=-22.2, p-value=0.009901	dG=-22.0, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.6, p-value=0.009901	dG=-21.6, p-value=0.009901

dp4

dG=-23.6, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.7, p-value=0.009901

droPer1

dG=-23.6, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.7, p-value=0.009901

droWil1

dG=-23.0, p-value=0.009901	dG=-22.8, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-22.3, p-value=0.009901

droVir3

dG=-22.6, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.6, p-value=0.009901

droMoj3

dG=-25.4, p-value=0.009901	dG=-25.2, p-value=0.009901	dG=-25.2, p-value=0.009901	dG=-25.0, p-value=0.009901	dG=-24.7, p-value=0.009901

droGri2

dG=-24.0, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.6, p-value=0.009901	dG=-23.5, p-value=0.009901

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