Secondary structure and small RNA-seq evidence for dme-mir-2535b

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:21169287-21169387 -	ACGTACATCACTAAGGTAAGTGACTATGCCG-----GGATTGTGGTTAT---TGAACTTAGCG----TCTCCACT--CACGGC-ATTT--CAT------------TCACTTGCAGTACATCACCGCCGAG
droSim1	chrX:12918307-12918407 +	ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTAT---TATACTTAGCG----TCTCCACT--CACGGC-ATTT--CAT------------TCACTTGCAGTACATCACCGCCGAG
droSec1	super_8:3476294-3476394 -	ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTAT---TATACTTAGAG----TCTCCACT--CACGGC-ATTT--CAT------------TCACTTGCAGTACATCACCGCCGAG
droYak2	chrX:20345010-20345110 -	ACGTACATCACCAAGGTAAGTGACAATGCCG-----GGATTGTGGTTAT---TGAAAATACCT----TCTCCACT--CACGGC-ATTA--TAT------------TCACTTGCAGTACATCACCGCCGAG
droEre2	scaffold_4690:17698644-17698744 -	ACGTACATCACCAAGGTAAGTGACAGTGCCG-----GGATTGTGGTTAT---TAAAAATACCT----TCTCCACT--CACGGC-ATTT--CAT------------TCACTTGCAGTACATCACCGCCGAG
droAna3	scaffold_13334:1053972-1054064 +	TCTGGCTACCGATTGGTGAGTTATCG----A-----CATTATCGATTTCTATCGATTT----------------------------CTATCGAGTTAAAAAAATCCCCTTTCCAGATCTGTGTCAAACGC
dp4	chrXL_group1a:9058690-9058790 +	ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGGGATTG------------AACCTCTCATCTCTCACCTCT--CACGGC-ATAT--CAA------------TCACTTGCAGTACATCACCGCCGAG
droPer1	super_15:1452144-1452244 +	ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGGGATTG------------AACCTCTCATCTCTCACCTCT--CACGGC-ATAT--CAA------------TCACTTGCAGTACATCACCGCCGAG
droWil1	Unknown	ACTTACATTACCAAGGTGAGT----------------------------------------------------------------TTT--GTT------------TTTCTTACAGTACATTACATCGGAG
droVir3	Unknown	ACGTGCATTACCAAGGTAAGC-----------------------------------------------CTCTTCT--CACGAC-ATCCCTTAA------------TCCCTTGCAGTACGTTGCCAACGAA
droMoj3	Unknown	ACATGCATAACCAGGGTAAGTGCTCA-GCTG-----CTtTTtTttTttT---tgttTTTTttT-------------------T-tTTT--CGT------------CGCCTTACAGTACATCTCCAAGGAG
droGri2	scaffold_15203:11132616-11132716 +	ACCTACATTACTAAGGTATGT------TCGA-----TGATTTTGGTTTTTTTTGGCTTTACTT----TCACCGTTTACACGACAATTT--CAT------------CCTTTTGCAGTACGTGACCAGTGAG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:21169287-21169387 -	ACGTACATCACTAAGGTAAGTGACTATGCCG-----GGATTGTGGTTATTGAACTTAGCG----TCTCCACTCACGGCATTTCATTCACTTGCAGTACATCACCGCCGAG
droSim1	chrX:12918307-12918407 +	ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTATTATACTTAGCG----TCTCCACTCACGGCATTTCATTCACTTGCAGTACATCACCGCCGAG
droSec1	super_8:3476294-3476394 -	ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTATTATACTTAGAG----TCTCCACTCACGGCATTTCATTCACTTGCAGTACATCACCGCCGAG
droYak2	chrX:20345010-20345110 -	ACGTACATCACCAAGGTAAGTGACAATGCCG-----GGATTGTGGTTATTGAAAATACCT----TCTCCACTCACGGCATTATATTCACTTGCAGTACATCACCGCCGAG
droEre2	scaffold_4690:17698644-17698744 -	ACGTACATCACCAAGGTAAGTGACAGTGCCG-----GGATTGTGGTTATTAAAAATACCT----TCTCCACTCACGGCATTTCATTCACTTGCAGTACATCACCGCCGAG
dp4	chrXL_group1a:9058690-9058790 +	ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGGGATTG---------AACCTCTCATCTCTCACCTCTCACGGCATATCAATCACTTGCAGTACATCACCGCCGAG
droPer1	super_15:1452144-1452244 +	ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGGGATTG---------AACCTCTCATCTCTCACCTCTCACGGCATATCAATCACTTGCAGTACATCACCGCCGAG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTATTATACTTAGCGTCT----CCACTCACGGCATTTCATTCACTTGCAGTACATCACCGCCGAG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.....................................................................ACTCACGGCATTTCATTCACTTGCAGT..............	27	1	5.00	5	5
.....................................................................ACTCACGGCATTTCATTCACTTGCA................	25	1	3.00	3	3
.....................................................................ACTCACGGCATTTCATTCACT....................	21	1	3.00	3	3
.....................................................................ACTCACGGCATTTCATTCACTT...................	22	1	3.00	3	3
.....................................................................ACTCACGGCATTTCATTCACTTGCAG...............	26	1	2.00	2	2
...............GTAAGTGACTATGCCG-----GGATTGTG..................................................................	24	1	1.00	1	1
...............GTAAGTGACTATGCCG-----GGA.......................................................................	19	1	1.00	1	1
.......................................................................TCACGGCATTTCATTCACTTGCAGT..............	25	1	1.00	1	1
...............GTAAGTGACTATGCCG-----GGATTGTGG.................................................................	25	1	1.00	1	1
........................TATGCCG-----GGATTGTGGTTATT............................................................	21	1	1.00	1	1

dp4

ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGG---------GATTGAACCTCTCATCTCTCACCTCTCACGGCATATCAATCACTTGCAGTACATCACCGCCGAG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.....................................................................TCTCACGGCATATCAATCACTTGCA................	25	1	47.00	47	28	19
.....................................................................TCTCACGGCATATCAATCACTTGCAG...............	26	1	31.00	31	19	12
.....................................................................TCTCACGGCATATCAATCACTT...................	22	1	21.00	21	1	20
.....................................................................TCTCACGGCATATCAATCACT....................	21	1	13.00	13	1	12
.....................................................................TCTCACGGCATATCAATCACTTGC.................	24	1	11.00	11	4	7
.....................................................................TCTCACGGCATATCAATCACTTG..................	23	1	5.00	5	1	4
.....................................................................TCTCACGGCATATCAATCACTTGCAGT..............	27	1	5.00	5	1	4
.......................................................................TCACGGCATATCAATCACTTGCA................	23	1	2.00	2	2	0
...............GTAAGTGGCTATGCCGCGACGG---------G...............................................................	23	1	2.00	2	1	1
.................AAGTGGCTATGCCGCGACGG---------GA..............................................................	22	1	1.00	1	1	0
.........................................................................ACGGCATATCAATCACTTGCAG...............	22	1	1.00	1	1	0

Secondary Structure

dm3

-22.6	-22.6	-22.3	-22.1	-22.1	-21.8

droSim1

-22.6	-22.3	-22.1	-22.0	-21.8	-21.8

droSec1

-24.3	-23.8

droYak2

-23.0	-22.5	-22.5	-22.0	-22.0

droEre2

-23.0	-22.5	-22.3

droAna3

-9.0	-8.7

dp4

-23.1	-23.1	-23.0	-22.4	-22.2	-22.2

droPer1

-23.1	-23.1	-23.0	-22.4	-22.2	-22.2

droWil1

-2.8

droVir3

-0.8	0.0	0.1

droMoj3

-3.89	-3.64

droGri2

-8.3	-8.0	-7.5

Generated: 01/05/2013 at 05:11 PM