Secondary structure and small RNA-seq evidence for dme-mir-14

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:5441252-5441344 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droSim1	chr2R:4072822-4072914 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droSec1	super_1:3055916-3056008 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droYak2	chr2L:18072267-18072359 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droEre2	scaffold_4929:8915902-8915994 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droAna3	scaffold_13266:183955-184047 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
dp4	chr3:15883112-15883203 +	ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droPer1	super_4:878748-878839 -	ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droWil1	scaffold_180700:3302349-3302441 +	ACGTACTGCAACCTATGTGGGAGCGAGACGAGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droVir3	scaffold_10324:225313-225405 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droMoj3	scaffold_6496:2042842-2042934 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGATTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droGri2	scaffold_15245:15401666-15401758 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:5441252-5441344 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droSim1	chr2R:4072822-4072914 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droSec1	super_1:3055916-3056008 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droYak2	chr2L:18072267-18072359 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droEre2	scaffold_4929:8915902-8915994 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droAna3	scaffold_13266:183955-184047 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
dp4	chr3:15883112-15883203 +	ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droPer1	super_4:878748-878839 -	ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droWil1	scaffold_180700:3302349-3302441 +	ACGTACTGCAACCTATGTGGGAGCGAGACGAGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droVir3	scaffold_10324:225313-225405 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droMoj3	scaffold_6496:2042842-2042934 +	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGATTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA
droGri2	scaffold_15245:15401666-15401758 -	ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTTATATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACGTACTGCAACCTATGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................................TCAGTCTTTTTCTCTCTCCTA.................	21	2	1436.50	2873	2873
.........................................................AGTCTTTTTCTCTCTCCTAT................	20	2	103.00	206	206
..................GGGAGCGAGACGGGGACTCAC......................................................	21	2	18.50	37	37
........................................................CAGTCTTTTTCTCTCTCCTATA...............	22	2	10.50	21	21
.......................................................TCAGTCTTTTTCTCTCTCC...................	19	2	8.00	16	16
...........................................................TCTTTTTCTCTCTCCTAT................	18	2	6.00	12	12
.................TGGGAGCGAGACGGGGACTCAC......................................................	22	2	3.50	7	7
.........................................................AGTCTTTTTCTCTCTCCTATA...............	21	2	2.50	5	5

dp4

ACGTACTGCATTC-ATGTGGGAGCGAGACGGGGACTCACTGTGCTTTTGAAGTAGTCAGTCTTTTTCTCTCTCCTATACAAATTGCGGGCGTA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................................................TCAGTCTTTTTCTCTCTCCTAT................	22	2	17802.50	35605	18647	16958
.......................................................TCAGTCTTTTTCTCTCTCCTA.................	21	2	2349.50	4699	0	4699
.......................................................TCAGTCTTTTTCTCTCTCCT..................	20	2	2287.50	4575	0	4575
.........................................................AGTCTTTTTCTCTCTCCTAT................	20	2	267.00	534	304	230
.......................................................TCAGTCTTTTTCTCTCTCCTATA...............	23	2	186.50	373	209	164
.......................................................TCAGTCTTTTTCTCTCTCC...................	19	2	44.50	89	0	89
.........................................................AGTCTTTTTCTCTCTCCT..................	18	2	26.50	53	0	53
..................GGGAGCGAGACGGGGACTCACT.....................................................	22	2	24.50	49	0	49
..................GGGAGCGAGACGGGGACTCAC......................................................	21	2	22.00	44	34	10
........................................................CAGTCTTTTTCTCTCTCCTA.................	20	2	8.50	17	17	0
........................................................CAGTCTTTTTCTCTCTCCT..................	19	2	7.00	14	2	12
..................GGGAGCGAGACGGGGACT.........................................................	18	2	7.00	14	0	14
........................................................CAGTCTTTTTCTCTCTCCTATA...............	22	2	5.00	10	7	3
.......................................................TCAGTCTTTTTCTCTCTC....................	18	2	4.00	8	8	0
..................GGGAGCGAGACGGGGACTCA.......................................................	20	2	3.50	7	6	1
...................GGAGCGAGACGGGGACTCACT.....................................................	21	2	3.00	6	0	6
.................TGGGAGCGAGACGGGGAC..........................................................	18	2	2.50	5	0	5
.........................................................AGTCTTTTTCTCTCTCCTATA...............	21	2	2.50	5	5	0
.................TGGGAGCGAGACGGGGACTCAC......................................................	22	2	1.50	3	1	2

Secondary Structure

dm3

-27.5	-27.1

droSim1

-27.5	-27.1

droSec1

-27.5	-27.1

droYak2

-27.5	-27.1

droEre2

-27.5	-27.1

droAna3

-27.5	-27.1

dp4

-25.8	-25.4	-25.3	-25.2	-24.9	-24.8

droPer1

-25.8	-25.4	-25.3	-25.2	-24.9	-24.8

droWil1

-28.4	-28.0

droVir3

-27.5	-27.1

droMoj3

-27.2	-26.8	-26.3	-26.3

droGri2

-27.5	-27.1

Generated: 01/05/2013 at 05:08 PM