Secondary structure and small RNA-seq evidence for dme-mir-3

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:15549085-15549183 -	GCCA-C------------CTAA-GGTCCCGATCCTGGGATGCATCTTGTGCAGTTATGTTTC--AAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACATCG--------------TCG
droSim1	chr2R:14254518-14254616 -	ACCA-C------------CAAA-GGTCCCGATCCTGGGATGCATCTTGTGCAGTTATGTTCC--AAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACATCG--------------TCG
droSec1	super_1:13063812-13063910 -	ATCA-C------------CAAA-GGTCCCGATCCTGGGATGCATCTTGTGCAGTTATGTTTC--AAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACATCG--------------TCG
droYak2	chr2R:13623606-13623704 +	ACCA-T------------CAAA-GGTCCTGATCCTGGGATGCATCTTGTGCAGTCATGTTTC--CAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCTTGGCCACTTCG--------------ACG
droEre2	scaffold_4845:9749329-9749427 -	ACCC-A------------CCAA-GGTCCTGATCCTGGGATGCATCTTGTGCAGTTATGTTTC--TAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACTTCG--------------ACG
droAna3	scaffold_13266:9731210-9731313 +	GCCC-C------------CAACTGGCTACGATCTTGGGACGCATTTTGTGCAGTTATGCACC--AAA-AATA------TATCCATCACTGGGCAAAGTGTGTCTCAGGATCTTGGCCATCTCA--------------ACG
dp4	chr3:12677741-12677846 -	ACGA-CGA--------TACCGA-GGCAACGATCCTGGGATGCATTTTGTGCAGTTATGTCTA--CGTGATCA------TCCTCATCACTGGGCAAAGTGTGTCTCAGGATTGCAGCCCCGCCA--------------A--
droPer1	super_2:8905820-8905925 +	ACGA-CGA--------TACCGA-GGCAACGATCCTGGGATGCATTTTGTGCAGTTATGTCTA--CGTGATCA------TCCTCATCACTGGGCAAAGTGTGTCTCAGGATTGCAGCCCCGCCA--------------A--
droWil1	scaffold_180701:1651920-1652025 -	TCGA-A------------TTTA-GACCATGATTTTGGGATGCATTTTGTGCAGTTATGTCTTCATGTGATAATTCT----CTCATCACTGGGCAAAGTGTGTCTCATAATTTTGGTAACCATA--------------T--
droVir3	scaffold_12875:4111929-4112038 +	AATAAAAATACCAGAATCTCAT-AGCTCTGCTTTTGGGATGCATTTTGTGCGGTTATGTCTG--CCT-------CCAAAACCCATCACTGGGCAAAGTGTGTCTCAAAATTGTGGCTACC--------------------
droMoj3	scaffold_6496:20936961-20937077 -	AACT-C------------TCGC-AGCTCTACTTTTGGGATGCATTTTGTGCAGATGTCTAAC--GAT-------TGGAAACCCATCACTGGGCAAAGTGTGTCTCAAAATTGGGGCAACTAGCACAAAGGAGGAGTGTTT
droGri2	scaffold_15112:2109003-2109099 -	AATT-T------------TCAT-AGCTCTGCTTTTGGGATGCATTCTGTACAGTAATGTTGA--CTCTTGTA------AAACCATCACTGGGCAAAGTGTGTCTCAAAATTGTGGCAA---------------------G

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:15549085-15549183 -	GCCA-C------------CTAA-GGTCCCGATCCTGGGATGCATCTTGTGCAGTTATGTTTC--AAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACATCG--------------TCG
droSim1	chr2R:14254518-14254616 -	ACCA-C------------CAAA-GGTCCCGATCCTGGGATGCATCTTGTGCAGTTATGTTCC--AAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACATCG--------------TCG
droSec1	super_1:13063812-13063910 -	ATCA-C------------CAAA-GGTCCCGATCCTGGGATGCATCTTGTGCAGTTATGTTTC--AAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACATCG--------------TCG
droYak2	chr2R:13623606-13623704 +	ACCA-T------------CAAA-GGTCCTGATCCTGGGATGCATCTTGTGCAGTCATGTTTC--CAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCTTGGCCACTTCG--------------ACG
droEre2	scaffold_4845:9749329-9749427 -	ACCC-A------------CCAA-GGTCCTGATCCTGGGATGCATCTTGTGCAGTTATGTTTC--TAT-------CT----CACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACTTCG--------------ACG
droAna3	scaffold_13266:9731210-9731313 +	GCCC-C------------CAACTGGCTACGATCTTGGGACGCATTTTGTGCAGTTATGCACC--AAA-AATA------TATCCATCACTGGGCAAAGTGTGTCTCAGGATCTTGGCCATCTCA--------------ACG
dp4	chr3:12677741-12677846 -	ACGA-CGA--------TACCGA-GGCAACGATCCTGGGATGCATTTTGTGCAGTTATGTCTA--CGTGATCA------TCCTCATCACTGGGCAAAGTGTGTCTCAGGATTGCAGCCCCGCCA--------------A--
droPer1	super_2:8905820-8905925 +	ACGA-CGA--------TACCGA-GGCAACGATCCTGGGATGCATTTTGTGCAGTTATGTCTA--CGTGATCA------TCCTCATCACTGGGCAAAGTGTGTCTCAGGATTGCAGCCCCGCCA--------------A--
droWil1	scaffold_180701:1651920-1652025 -	TCGA-A------------TTTA-GACCATGATTTTGGGATGCATTTTGTGCAGTTATGTCTTCATGTGATAATTCT----CTCATCACTGGGCAAAGTGTGTCTCATAATTTTGGTAACCATA--------------T--
droVir3	scaffold_12875:4111929-4112038 +	AATAAAAATACCAGAATCTCAT-AGCTCTGCTTTTGGGATGCATTTTGTGCGGTTATGTCTG--CCT-------CCAAAACCCATCACTGGGCAAAGTGTGTCTCAAAATTGTGGCTACC--------------------
droMoj3	scaffold_6496:20936961-20937077 -	AACT-C------------TCGC-AGCTCTACTTTTGGGATGCATTTTGTGCAGATGTCTAAC--GAT-------TGGAAACCCATCACTGGGCAAAGTGTGTCTCAAAATTGGGGCAACTAGCACAAAGGAGGAGTGTTT
droGri2	scaffold_15112:2109003-2109099 -	AATT-T------------TCAT-AGCTCTGCTTTTGGGATGCATTCTGTACAGTAATGTTGA--CTCTTGTA------AAACCATCACTGGGCAAAGTGTGTCTCAAAATTGTGGCAA---------------------G

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACCAC----CAAAGGTCCCGATCCTGGGATGCATCTTGTGCAGTTATGTTCC-------AATCTCACATCACTGGGCAAAGTGTGTCTCAAGATCCTGGCCACATCGTCG-	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
....................................................................TCACTGGGCAAAGTGTGTCTCA.....................	22	1	7742.00	7742	7742
....................................................................TCACTGGGCAAAGTGTGTCTC......................	21	1	173.00	173	173
......................................................................ACTGGGCAAAGTGTGTCTCA.....................	20	1	46.00	46	46
....................................................................TCACTGGGCAAAGTGTGTCT.......................	20	1	25.00	25	25
....................................................................TCACTGGGCAAAGTGTGTCTCAA....................	23	1	15.00	15	15
...AC----CAAAGGTCCCGATCCTG.....................................................................................	19	1	13.00	13	13
..........................GGATGCATCTTGTGCAGTTATG...............................................................	22	1	8.00	8	8
.....................................................................CACTGGGCAAAGTGTGTCTCA.....................	21	1	7.00	7	7
..CAC----CAAAGGTCCCGATCCTG.....................................................................................	20	1	4.00	4	4
.......................................................................CTGGGCAAAGTGTGTCTCA.....................	19	1	2.00	2	2
......................................................................ACTGGGCAAAGTGTGTCTC......................	19	1	1.00	1	1
.....................................................................CACTGGGCAAAGTGTGTCTCAA....................	22	1	1.00	1	1
ACCAC----CAAAGGTCCCGATCCTG.....................................................................................	22	1	1.00	1	1

dp4

ACGACGATACCGAGGCAACGATCCTGGGATGCATTTTGTGCAGTTATGTCTACGTGATCATC--CTCATCACTGGGCAAAGTGTGTCTCAGGATTGCAGCCCC---GCCAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
....................................................................TCACTGGGCAAAGTGTGTCTCA.....................	22	1	11230.00	11230	11228	2
....................................................................TCACTGGGCAAAGTGTGTCTC......................	21	1	320.00	320	320	0
......................................................................ACTGGGCAAAGTGTGTCTCA.....................	20	1	84.00	84	84	0
....................................................................TCACTGGGCAAAGTGTGTCT.......................	20	1	81.00	81	81	0
..........................GGATGCATTTTGTGCAGTTATG...............................................................	22	1	20.00	20	20	0
.....................................................................CACTGGGCAAAGTGTGTCTCA.....................	21	1	18.00	18	18	0
......................................................................ACTGGGCAAAGTGTGTCTCAGG...................	22	1	15.00	15	15	0
....................................................................TCACTGGGCAAAGTGTGTCTCAG....................	23	1	5.00	5	5	0
.......................................................................CTGGGCAAAGTGTGTCTCA.....................	19	1	4.00	4	4	0
.......TACCGAGGCAACGATCCTG.....................................................................................	19	1	4.00	4	4	0
......................................................................ACTGGGCAAAGTGTGTCTC......................	19	1	4.00	4	4	0
.......................................................................CTGGGCAAAGTGTGTCTCAGGA..................	22	1	3.00	3	3	0
....................................................................TCACTGGGCAAAGTGTGTC........................	19	1	3.00	3	2	1
.........................GGGATGCATTTTGTGCAGTTATG...............................................................	23	1	3.00	3	3	0
........................TGGGATGCATTTTGTGCAGTTA.................................................................	22	1	3.00	3	3	0
........................TGGGATGCATTTTGTGCAGTT..................................................................	21	1	2.00	2	2	0
......................................................................ACTGGGCAAAGTGTGTCT.......................	18	1	2.00	2	2	0
..................................................................CATCACTGGGCAAAGTGTGTCT.......................	22	1	1.00	1	1	0
.....GATACCGAGGCAACGATCCTG.....................................................................................	21	1	1.00	1	1	0
........ACCGAGGCAACGATCCTG.....................................................................................	18	1	1.00	1	1	0

Secondary Structure

dm3

dG=-24.6, p-value=0.009901	dG=-24.0, p-value=0.009901

droSim1

dG=-24.6, p-value=0.009901	dG=-24.0, p-value=0.009901

droSec1

dG=-24.6, p-value=0.009901	dG=-24.0, p-value=0.009901

droYak2

dG=-24.6, p-value=0.009901	dG=-24.0, p-value=0.009901

droEre2

dG=-24.6, p-value=0.009901	dG=-24.0, p-value=0.009901

droAna3

dG=-32.3, p-value=0.009901	dG=-31.3, p-value=0.009901

dp4

dG=-33.3, p-value=0.009901	dG=-32.4, p-value=0.009901	dG=-32.3, p-value=0.009901

droPer1

dG=-33.3, p-value=0.009901	dG=-32.4, p-value=0.009901	dG=-32.3, p-value=0.009901

droWil1

dG=-25.9, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.2, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.9, p-value=0.009901

droVir3

dG=-27.0, p-value=0.009901	dG=-26.7, p-value=0.009901

droMoj3

dG=-26.7, p-value=0.009901	dG=-26.5, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.2, p-value=0.009901

droGri2

dG=-22.7, p-value=0.009901	dG=-22.7, p-value=0.009901	dG=-22.6, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-22.4, p-value=0.009901

Generated: 03/07/2013 at 05:10 PM