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

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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

dG=-17.7, p-value=0.009901	dG=-17.7, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.4, p-value=0.009901

droSim1

dG=-17.7, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.4, p-value=0.009901	dG=-17.4, p-value=0.009901	dG=-17.3, p-value=0.009901

droSec1

dG=-19.4, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.1, p-value=0.009901	dG=-18.9, p-value=0.009901	dG=-18.8, p-value=0.009901

droYak2

dG=-18.1, p-value=0.009901	dG=-18.0, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.6, p-value=0.009901	dG=-17.5, p-value=0.009901

droEre2

dG=-18.4, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.0, p-value=0.009901	dG=-18.0, p-value=0.009901	dG=-17.9, p-value=0.009901

droAna3

dG=-9.0, p-value=0.009901	dG=-8.7, p-value=0.009901

dp4

dG=-18.2, p-value=0.009901	dG=-18.2, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901

droPer1

dG=-18.2, p-value=0.009901	dG=-18.2, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901	dG=-18.1, p-value=0.009901

droWil1

dG=0.0, p-value=1.0	dG=0.8, p-value=1.0

droVir3

dG=0.0, p-value=1.0	dG=0.1, p-value=1.0

droMoj3

dG=-1.4, p-value=0.019802	dG=-0.8, p-value=0.019802	dG=-0.8, p-value=0.009901	dG=-0.7, p-value=0.009901	dG=-0.6, p-value=0.009901

droGri2

dG=-7.5, p-value=0.009901

Generated: 03/07/2013 at 04:59 PM