Secondary structure and small RNA-seq evidence for dme-mir-276b

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:10312870-10312998 +	GACCA-------TC-----GAAC-GA--AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCTATATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCAGCATA--------TAGTTAAAA
droSim1	chr3L:9702897-9703022 +	GACCA-------TC-----GAAC-G---AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCT--ATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATA--------TAGTTGAAA
droSec1	super_0:2526747-2526871 +	GACCA--------C-----GAAC-G---AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCT--ATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATA--------TAGTTGAAA
droYak2	chr3L:10302128-10302256 +	GACAA-------CA-----GAAA-GAACAAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCT--ATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATA--------AAGTTAAAA
droEre2	scaffold_4784:10306167-10306292 +	GACAA-------CC-----GAAT-A---AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCT--ATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATA--------AAGTTGAAA
droAna3	scaffold_13337:15233368-15233487 +	ATTT------------------CTG---AAGAAACCGAAGCCTATTTGCCATCAGCGAGGTATAGAGTTCCTACGTGCCA--CTTAAACTAGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCATCATG--------A-----AAG
dp4	chrXR_group6:8706029-8706135 +	ATCTA---------------------------AAGCGAAGCCTCTTTACCATCAGCGAGGTATAGAGTTCCTACGTGCCG-TATC-CAA-AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCCATCAAC--------------------
droPer1	super_27:1146104-1146210 +	ATCTA---------------------------AAGCGAAGCCTCTTTACCATCAGCGAGGTATAGAGTTCCTACGTGCCG-TATC-CAA-AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCCATCAAC--------------------
droWil1	scaffold_181024:290398-290516 -	AACAA--------------ATTT-G---AAATAAACGAAGCCTATTTACCATAAGCGAGGTATAGAGTTCCTACGTGCAA--ATTGCAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGAACAACAA-----------------A
droVir3	scaffold_13049:16093198-16093326 +	TATCT--------T---AAGATTTA---AAGATACCGAAGTCTATATACCATCAGCGAGGTATAGAGTTCCTACGTGCAA--ATTGCAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAGCAA-----------GAAAAGA
droMoj3	scaffold_6680:20678203-20678343 -	GACCAAGTGAAACAGAG--ATTGTA---AAGATAACGAAGTCTATATACCATCAGCGAGGTATAGAGTTCCTACGTGCAA--ATTGCAATAGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAACAAA--------ACGAATAAA
droGri2	scaffold_15110:12572308-12572448 -	AAATC-------TC---AAAACCGA---AAGATAACGAAGTCTATTTACCATTAGCGAGGTATAGAGTTCCTACGTGCAA--ATTGCAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAGCATTGATCAAAACAATTAAGT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:10312870-10312998 +	GACCA-------TC-----GAAC-GA--AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCTATATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCAGCATA--------TAGTTAAAA
droSim1	chr3L:9702897-9703022 +	GACCA-------TC-----GAAC-G---AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCT--ATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATA--------TAGTTGAAA
droSec1	super_0:2526747-2526871 +	GACCA--------C-----GAAC-G---AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCT--ATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATA--------TAGTTGAAA
droYak2	chr3L:10302128-10302256 +	GACAA-------CA-----GAAA-GAACAAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCT--ATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATA--------AAGTTAAAA
droEre2	scaffold_4784:10306167-10306292 +	GACAA-------CC-----GAAT-A---AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCT--ATT-C---AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATA--------AAGTTGAAA
droAna3	scaffold_13337:15233368-15233487 +	ATTT------------------CTG---AAGAAACCGAAGCCTATTTGCCATCAGCGAGGTATAGAGTTCCTACGTGCCA--CTTAAACTAGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCATCATG--------A-----AAG
dp4	chrXR_group6:8706029-8706135 +	ATCTA---------------------------AAGCGAAGCCTCTTTACCATCAGCGAGGTATAGAGTTCCTACGTGCCG-TATC-CAA-AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCCATCAAC--------------------
droPer1	super_27:1146104-1146210 +	ATCTA---------------------------AAGCGAAGCCTCTTTACCATCAGCGAGGTATAGAGTTCCTACGTGCCG-TATC-CAA-AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCCATCAAC--------------------
droWil1	scaffold_181024:290398-290516 -	AACAA--------------ATTT-G---AAATAAACGAAGCCTATTTACCATAAGCGAGGTATAGAGTTCCTACGTGCAA--ATTGCAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGAACAACAA-----------------A
droVir3	scaffold_13049:16093198-16093326 +	TATCT--------T---AAGATTTA---AAGATACCGAAGTCTATATACCATCAGCGAGGTATAGAGTTCCTACGTGCAA--ATTGCAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAGCAA-----------GAAAAGA
droMoj3	scaffold_6680:20678203-20678343 -	GACCAAGTGAAACAGAG--ATTGTA---AAGATAACGAAGTCTATATACCATCAGCGAGGTATAGAGTTCCTACGTGCAA--ATTGCAATAGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAACAAA--------ACGAATAAA
droGri2	scaffold_15110:12572308-12572448 -	AAATC-------TC---AAAACCGA---AAGATAACGAAGTCTATTTACCATTAGCGAGGTATAGAGTTCCTACGTGCAA--ATTGCAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAGCATTGATCAAAACAATTAAGT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GACCATCGAACGAAA-AAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCC--TATTC--AGTCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATCATATAGTTGAAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
..............................................................................TAGGAACTTAATACCGTGCT.................................	20	2	0.50	1	1

dp4

ATCT------------AAAGCGAAGCCTCTTTACCATCAGCGAGGTATAGAGTTCCTACGTGCC-GTATCCAAAGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCCATCAAC------------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................................................................TAGGAACTTAATACCGTGCTCT...............................	22	2	5401.50	10803	344	10459
.......................................GCGAGGTATAGAGTTCCTACG.......................................................................	21	4	38.50	154	154	0
......................................AGCGAGGTATAGAGTTCCTACGT......................................................................	23	4	36.50	146	8	138
......................................AGCGAGGTATAGAGTTCCTAC........................................................................	21	4	7.75	31	31	0
........................................CGAGGTATAGAGTTCCTACG.......................................................................	20	4	0.75	3	1	2
.......................................GCGAGGTATAGAGTTCCT..........................................................................	18	4	0.50	2	0	2
.....................................CAGCGAGGTATAGAGTTCCTACG.......................................................................	23	4	0.50	2	2	0
...............................................................................AGGAACTTAATACCGTGCTCT...............................	21	2	0.50	1	0	1

Secondary Structure

dm3

dG=-33.4, p-value=0.009901	dG=-33.4, p-value=0.009901

droSim1

dG=-33.6, p-value=0.009901	dG=-33.2, p-value=0.009901

droSec1

dG=-33.6, p-value=0.009901	dG=-33.2, p-value=0.009901

droYak2

dG=-33.6, p-value=0.009901	dG=-33.2, p-value=0.009901

droEre2

dG=-33.6, p-value=0.009901	dG=-33.2, p-value=0.009901

droAna3

dG=-34.4, p-value=0.009901

dp4

dG=-33.4, p-value=0.009901	dG=-33.4, p-value=0.009901

droPer1

dG=-33.4, p-value=0.009901	dG=-33.4, p-value=0.009901

droWil1

dG=-36.4, p-value=0.009901	dG=-36.0, p-value=0.009901

droVir3

dG=-35.9, p-value=0.009901	dG=-35.5, p-value=0.009901

droMoj3

dG=-35.9, p-value=0.009901	dG=-35.5, p-value=0.009901

droGri2

dG=-36.2, p-value=0.009901	dG=-35.8, p-value=0.009901

Generated: 03/07/2013 at 05:00 PM