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

Secondary Structure

dm3

-39.9	-39.9

droSim1

-40.1	-39.7

droSec1

-40.1	-39.7

droYak2

-40.1	-39.7

droEre2

-40.1	-39.7

droAna3

-41.4	-40.5

dp4

-38.7	-38.7	-38.6	-38.6	-38.1	-38.1

droPer1

-38.7	-38.7	-38.6	-38.6	-38.1	-38.1

droWil1

-43.9	-43.5

droVir3

-40.2	-39.8

droMoj3

-40.7	-40.3

droGri2

-41.0	-40.6

Generated: 01/05/2013 at 05:12 PM