Secondary structure and small RNA-seq evidence for dme-mir-6-2

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:15548359-15548462 -	TAACCA---------------------TGCCG--TTTTTAACCCAAGGGAACTTCTGCTGCTGATATATTAT-----------TGA-------------AAAA----CTACTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAA
droSim1	chr2R:14253794-14253897 -	TAACCA---------------------TGCCG--TTTTTAACCCCAGGGAACTTCTGCTGCTGATATATTAT-----------TGA-------------AAAA----CTCCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAA
droSec1	super_1:13063092-13063195 -	TAACCA---------------------TGCCG--TTTTTAACCCCAGGGAACTTCTGCTGCTGATATATTAT-----------TGA-------------AAAA----CTCCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAA
droYak2	chr2R:13624327-13624430 +	TAACCA---------------------TACCG--TTTTTAACCGCAGGGAACCTCTGCTGCTGATATATTAT-----------TGA-------------GAAA----CTTCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAA
droEre2	scaffold_4845:9748613-9748715 -	AACCCA---------------------TACCG--TTTTTAACCCCAGGGAACCTCTGCTGCTGATATATTAT-----------TGA--------------AAA----CTCCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAG
droAna3	scaffold_13266:9731948-9732061 +	ATATTA---------------------TTCCG--GTGTTAGCCCCAGGGAACTGTTGCTGCTGATATATTATTCTCCCAAAAA-AA-------------AAAT----CACCTATATCACAGTGGCTGTTCTTTTTGGCTGCACCGACAAG-TTCAC
dp4	chr3:12676931-12677045 -	TCCCCG---------------------TGCCGTGTCCCCAACCGCAGGGAACCGCTGCTGCTGATATATTATCCACCCATCTTTGA---------------CA----TTTCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAG-TCCAA
droPer1	super_2:8906627-8906741 +	TCCCCG---------------------TGCCGTGTCCCCAACCGCAGGGAACCGCTGCTGCTGATATATTATCCACCCATCTTTGA---------------CA----TTTCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAG-TCCAA
droWil1	scaffold_180701:1651131-1651259 -	TTTTTA---------------------AAGTTTTTGTTTAACCGCAGGGAACTGTCGCTGCTGATATAT-----ATATATTATTGTTATATATAATTTAAAAATGATTTTCTATATCACAGTGGCTGTTCTTTTTGGTTTTACGATCATT-TTCAA
droVir3	scaffold_12875:4112748-4112878 +	TAAATATTTGCTGACAAATTTCTTATGTGCTA--TGTTTAACCGCAGGGAACTGCTGCTGCTGATATACTGTATAGATTATATCGA----------------------TTCCATATCACAGTGGCTGTTCTTTTTGGTTGCATCGCAATC-CACAA
droMoj3	scaffold_6496:20936121-20936236 -	TATCCA------GAGA-----------GATTG--CGTTTAACCGCAGGGAACTGCTGCTGCTGATATACTATA----TGTATTTGT---------------CA--GTACTCTATATCACAGTGGCTGTTCTTTTTGGTTGCATCGCAAATAGCCAA
droGri2	scaffold_15112:2108071-2108181 -	TTCACC-------------------AATGCTA--TGTTTAACCACAGGGAACTGCTGCTGCTGATATAC-----AACCATAT-TTA-------------TACA----CGACTATATCACAGTGGCTGTTCTTTTTGGTTGCATCGCCATT-TGCAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:15548359-15548462 -	TAACCA---------------------TGCCG--TTTTTAACCCAAGGGAACTTCTGCTGCTGATATATTAT-----------TGA-------------AAAA----CTACTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAA
droSim1	chr2R:14253794-14253897 -	TAACCA---------------------TGCCG--TTTTTAACCCCAGGGAACTTCTGCTGCTGATATATTAT-----------TGA-------------AAAA----CTCCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAA
droSec1	super_1:13063092-13063195 -	TAACCA---------------------TGCCG--TTTTTAACCCCAGGGAACTTCTGCTGCTGATATATTAT-----------TGA-------------AAAA----CTCCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAA
droYak2	chr2R:13624327-13624430 +	TAACCA---------------------TACCG--TTTTTAACCGCAGGGAACCTCTGCTGCTGATATATTAT-----------TGA-------------GAAA----CTTCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAA
droEre2	scaffold_4845:9748613-9748715 -	AACCCA---------------------TACCG--TTTTTAACCCCAGGGAACCTCTGCTGCTGATATATTAT-----------TGA--------------AAA----CTCCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAT-TCCAG
droAna3	scaffold_13266:9731948-9732061 +	ATATTA---------------------TTCCG--GTGTTAGCCCCAGGGAACTGTTGCTGCTGATATATTATTCTCCCAAAAA-AA-------------AAAT----CACCTATATCACAGTGGCTGTTCTTTTTGGCTGCACCGACAAG-TTCAC
dp4	chr3:12676931-12677045 -	TCCCCG---------------------TGCCGTGTCCCCAACCGCAGGGAACCGCTGCTGCTGATATATTATCCACCCATCTTTGA---------------CA----TTTCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAG-TCCAA
droPer1	super_2:8906627-8906741 +	TCCCCG---------------------TGCCGTGTCCCCAACCGCAGGGAACCGCTGCTGCTGATATATTATCCACCCATCTTTGA---------------CA----TTTCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAG-TCCAA
droWil1	scaffold_180701:1651131-1651259 -	TTTTTA---------------------AAGTTTTTGTTTAACCGCAGGGAACTGTCGCTGCTGATATAT-----ATATATTATTGTTATATATAATTTAAAAATGATTTTCTATATCACAGTGGCTGTTCTTTTTGGTTTTACGATCATT-TTCAA
droVir3	scaffold_12875:4112748-4112878 +	TAAATATTTGCTGACAAATTTCTTATGTGCTA--TGTTTAACCGCAGGGAACTGCTGCTGCTGATATACTGTATAGATTATATCGA----------------------TTCCATATCACAGTGGCTGTTCTTTTTGGTTGCATCGCAATC-CACAA
droMoj3	scaffold_6496:20936121-20936236 -	TATCCA------GAGA-----------GATTG--CGTTTAACCGCAGGGAACTGCTGCTGCTGATATACTATA----TGTATTTGT---------------CA--GTACTCTATATCACAGTGGCTGTTCTTTTTGGTTGCATCGCAAATAGCCAA
droGri2	scaffold_15112:2108071-2108181 -	TTCACC-------------------AATGCTA--TGTTTAACCACAGGGAACTGCTGCTGCTGATATAC-----AACCATAT-TTA-------------TACA----CGACTATATCACAGTGGCTGTTCTTTTTGGTTGCATCGCCATT-TGCAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TAACCATGCCGTTTT--TAACCCCAGGGAACTTCTGCTGCTGATATATTAT-----------TGAAAAACTCCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAATTCCAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
........................AGGGAACTTCTGCTGCTGATATA......................................................................	23	1	37.00	37	37
........................AGGGAACTTCTGCTGCTGATAT.......................................................................	22	1	21.00	21	21
........................AGGGAACTTCTGCTGCTGATA........................................................................	21	1	6.00	6	6
........................AGGGAACTTCTGCTGCTGAT.........................................................................	20	1	2.00	2	2
.......................CAGGGAACTTCTGCTGCTGATAT.......................................................................	23	1	1.00	1	1
...........................................................................TATCACAGTGGCTGTTCTTTT.....................	21	3	0.33	1	1

dp4

TCCCCGTGCCGTGTCCCCAACCGCAGGGAACCGCTGCTGCTGATATATTATCCACCCATCTTTG--ACATTTCTATATCACAGTGGCTGTTCTTTTTGGTTGCACGGCCAAGTCCAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
........................AGGGAACCGCTGCTGCTGATATA......................................................................	23	1	27.00	27	27	0
...............................................TTATCCACCCATCTTTG--ACATTTCT...........................................	25	1	3.00	3	3	0
...............................................TTATCCACCCATCTTTG--ACATTTCTA..........................................	26	1	1.00	1	1	0
........................AGGGAACCGCTGCTGCTGATA........................................................................	21	1	1.00	1	1	0
........................AGGGAACCGCTGCTGCTGAT.........................................................................	20	1	1.00	1	1	0
........................AGGGAACCGCTGCTGCTGATAT.......................................................................	22	1	1.00	1	1	0

Secondary Structure

dm3

-24.7	-24.6	-24.5	-24.3	-24.2	-24.1

droSim1

-22.8	-22.4	-22.1	-21.9

droSec1

-22.8	-22.4	-22.1	-21.9

droYak2

-23.5	-23.5	-23.1	-23.1	-23.1	-22.8

droEre2

-21.9	-21.5	-21.0

droAna3

-25.4	-25.0

dp4

-28.7	-28.6	-28.0

droPer1

-28.7	-28.6	-28.0

droWil1

-31.0	-30.4	-30.3	-30.3	-30.2

droVir3

-26.8	-26.4	-26.2	-26.2	-26.0	-25.9

droMoj3

-29.5	-29.2	-29.1	-28.8	-28.6

droGri2

-28.0	-27.6	-27.1

Generated: 01/05/2013 at 05:29 PM