Secondary structure and small RNA-seq evidence for dme-mir-929

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:121076-121193 +	TGA--C-ATGGCG---GAACCAG-------------TCCTGGTGGAGCTCAAATTGACTCTAGTAGGGAGTCCTTT-AATGAGCGACTCCCTAACGGAGTCAGATTGAGCTGCAAAGGAGCGA-CACAAC-----AGAGGAGC----A
droSim1	chr3R:194547-194664 +	TGG--C-ATGGCG---CAACCAG-------------TCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTTT-AATGAGCGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGA-GACAAC-----AGAGGAGC----A
droSec1	super_6:240419-240536 +	TGA--C-ATGGCG---CAACCAG-------------TCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTTT-AATGAGCGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGA-GACAAC-----AGAGGAGC----A
droYak2	chr3R:481089-481206 +	TGA--A-ATGGCA---AAACCAG-------------TCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTTT-AATGAACGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGA-GACAAC-----ACAGGACC----A
droEre2	scaffold_4770:471031-471148 +	TGA--A-GTGGCG---GAACCAG-------------TCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTTC-CATAAGCGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGA-GACAAC-----ACAGGTGC----A
droAna3	scaffold_13340:11127706-11127842 +	AGC--C-ACCAAC---CAACCAACCAACCAACCACTTCCTGGCGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTAACGAGAGACTCCCTAACGGAGTCAGATTGAATTACAAAGGAGCGA-GACAACGACTACGTGGTGG----C
dp4	chr2:24810831-24810947 -	G-A--A-GT-GCA---CGGCAA-------------TTCCTGCAGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTATTGAGCGACTCCCTAACGGAGTCAGATTGAATTACCAAGGAAC-A-GACAAC-----AGTGGAGC----G
droPer1	super_6:111437-111553 -	G-A--A-GT-GCA---CGG--G-----------ATTTCCTGCAGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTATTGAGCGACTCCCTAACGGAGTCAGATTGAATTACCAAGGAAC-A-GACAAC-----AGTGGAGC----A
droWil1	scaffold_181089:9825565-9825678 -	TGA-------------GAA---------------CTTCCTGCGGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTATATAAGCGACTCCCTAACGGAGTCAGATTGAATTACAAAGGAACAACAACAAC-----AAAAA-GCCACGA
droVir3	scaffold_12822:1418795-1418911 +	AGGCCAAGT-GCGACGCGT--G-----------AATTCCTGCCGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTT-CACGAGCGACTCCCTAACGGAGTCAGATTGAATTACAAAGGACCCA-GACAAC-----GAG----------
droMoj3	scaffold_6540:34020273-34020392 +	ACA--T-AT-ACG---CTACGAG-----------TTTCCTCATGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTTTTTAACGACTCCCTAACGGAGTCAGATTGAATTTCAGAGGACCCA-GACAAC-----GAAGAAGC----G
droGri2	scaffold_15074:2468173-2468294 -	TGA--AAGT-GTGCCCCCG--A-----------ACTTCCTGCTGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTAACGAGCGACTCCCTAACGGAGTCAGATTGAGTTACAAAGGACCAA-GTCAAC-----AATGCCCC----A

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:121076-121193 +	TGA--C-ATGGCG---GAACCAG-------------TCCTGGTGGAGCTCAAATTGACTCTAGTAGGGAGTCCTTT-AATGAGCGACTCCCTAACGGAGTCAGATTGAGCTGCAAAGGAGCGA-CACAAC-----AGAGGAGC----A
droSim1	chr3R:194547-194664 +	TGG--C-ATGGCG---CAACCAG-------------TCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTTT-AATGAGCGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGA-GACAAC-----AGAGGAGC----A
droSec1	super_6:240419-240536 +	TGA--C-ATGGCG---CAACCAG-------------TCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTTT-AATGAGCGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGA-GACAAC-----AGAGGAGC----A
droYak2	chr3R:481089-481206 +	TGA--A-ATGGCA---AAACCAG-------------TCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTTT-AATGAACGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGA-GACAAC-----ACAGGACC----A
droEre2	scaffold_4770:471031-471148 +	TGA--A-GTGGCG---GAACCAG-------------TCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTTC-CATAAGCGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGA-GACAAC-----ACAGGTGC----A
droAna3	scaffold_13340:11127706-11127842 +	AGC--C-ACCAAC---CAACCAACCAACCAACCACTTCCTGGCGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTAACGAGAGACTCCCTAACGGAGTCAGATTGAATTACAAAGGAGCGA-GACAACGACTACGTGGTGG----C
dp4	chr2:24810831-24810947 -	G-A--A-GT-GCA---CGGCAA-------------TTCCTGCAGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTATTGAGCGACTCCCTAACGGAGTCAGATTGAATTACCAAGGAAC-A-GACAAC-----AGTGGAGC----G
droPer1	super_6:111437-111553 -	G-A--A-GT-GCA---CGG--G-----------ATTTCCTGCAGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTATTGAGCGACTCCCTAACGGAGTCAGATTGAATTACCAAGGAAC-A-GACAAC-----AGTGGAGC----A
droWil1	scaffold_181089:9825565-9825678 -	TGA-------------GAA---------------CTTCCTGCGGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTATATAAGCGACTCCCTAACGGAGTCAGATTGAATTACAAAGGAACAACAACAAC-----AAAAA-GCCACGA
droVir3	scaffold_12822:1418795-1418911 +	AGGCCAAGT-GCGACGCGT--G-----------AATTCCTGCCGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTT-CACGAGCGACTCCCTAACGGAGTCAGATTGAATTACAAAGGACCCA-GACAAC-----GAG----------
droMoj3	scaffold_6540:34020273-34020392 +	ACA--T-AT-ACG---CTACGAG-----------TTTCCTCATGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTTTTTAACGACTCCCTAACGGAGTCAGATTGAATTTCAGAGGACCCA-GACAAC-----GAAGAAGC----G
droGri2	scaffold_15074:2468173-2468294 -	TGA--AAGT-GTGCCCCCG--A-----------ACTTCCTGCTGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTAACGAGCGACTCCCTAACGGAGTCAGATTGAGTTACAAAGGACCAA-GTCAAC-----AATGCCCC----A

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGGCATGGCGCAACCAGTCCTGGTGAAGCTCAAATTGACTCTAGTAGGGAGTCCTT-TAATGAGCGACTCCCTAACGGAGTCAGATTGAGCTACAAAGGAGCGAGACAACAGAGGAGCA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............................AAATTGACTCTAGTAGGGAGT...................................................................	21	2	416.00	832	832
...................................................................CTCCCTAACGGAGTCAGATTG...............................	21	2	6.50	13	13
....................................................................TCCCTAACGGAGTCAGATTGAG.............................	22	2	1.00	2	2
...............................AAATTGACTCTAGTAGGGA.....................................................................	19	2	0.50	1	1
...................................................................CTCCCTAACGGAGTCAGATTGAG.............................	23	2	0.50	1	1
....................................................................TCCCTAACGGAGTCAGATTGA..............................	21	2	0.50	1	1
...............................AAATTGACTCTAGTAGGGAG....................................................................	20	2	0.50	1	1

dp4

--GAAGTGCACGGCAATTCCTGCAGCAGTTCAAATTGACTCTAGTAGGGAGTCCTTTTATTGAGCGACTCCCTAACGGAGTCAGATTGAATTACCAAGGAAC-AGACAACAGTGGAGCG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...............................AAATTGACTCTAGTAGGGAGTC..................................................................	22	2	2233.50	4467	0	4467
...................................................................CTCCCTAACGGAGTCAGATTG...............................	21	2	842.50	1685	0	1685
...............................AAATTGACTCTAGTAGGGAGT...................................................................	21	2	443.50	887	887	0
...............................AAATTGACTCTAGTAGGGAG....................................................................	20	2	363.50	727	10	717
...............................AAATTGACTCTAGTAGGG......................................................................	18	2	10.00	20	0	20
................................AATTGACTCTAGTAGGGAG....................................................................	19	2	9.50	19	0	19
...................................................................CTCCCTAACGGAGTCAGATTGA..............................	22	2	7.00	14	14	0
......................................................................CCTAACGGAGTCAGATTG...............................	18	2	2.00	4	0	4
.................................ATTGACTCTAGTAGGGAG....................................................................	18	2	1.50	3	0	3
................................AATTGACTCTAGTAGGGA.....................................................................	18	2	1.50	3	0	3

Secondary Structure

dm3

-49.5

droSim1

-46.9

droSec1

-46.9

droYak2

-43.8	-43.2	-42.9

droEre2

-45.6	-45.1

droAna3

-39.6	-39.1	-38.8	-38.7

dp4

-40.9	-40.1	-39.9

droPer1

-40.7	-39.9	-39.9

droWil1

-40.3	-39.5	-39.5

droVir3

-39.1	-38.3	-38.1

droMoj3

-41.9	-41.1

droGri2

-37.7	-36.9

Generated: 01/05/2013 at 05:30 PM