Secondary structure and small RNA-seq evidence for dme-mir-286

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:15548912-15549041 -	TTG-G--------GCAC--------T------CC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCAAA-G-A------AA-------GGTT----TCG--ATTAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----TCA--G
droSim1	chr2R:14254346-14254476 -	TTG-G--------GCAC--------T------CC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCCAA-AGA------AA-------GGTT----TCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----TCA--G
droSec1	super_1:13063641-13063770 -	TTG-G--------GCAC--------T------CC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCCAA-T-A------AA-------GGTT----TCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----TCA--G
droYak2	chr2R:13623749-13623876 +	TAG----------GCAC--------T------CC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCAAA-A--------GA-------GGTT----TCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----TCA--G
droEre2	scaffold_4845:9749162-9749292 -	TAG----------GCAC--------T------GC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCAAA-G--------AA-------GGTT----TCG--ATCGA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----ACACTG
droAna3	scaffold_13266:9731344-9731477 +	TTT-A--------GCAT--------C------AG----------AATTTTAAAATTGAATGGCGATTGTCGGTATGGTCGCTTTTTCACA-A-A------AAAATT---GGTT----ACC--AACAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCATCAAGC-----TAA--A
dp4	chr3:12677574-12677700 -	AAA-A--------GAAG--------A------CA----------AATTTTAAAATTAAATGGCGATTGTCGGTTTGGTCGCTTTTTACCA-----------G-------GGTT----CCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAGAATGTTCAACATGG-----CCA--A
droPer1	super_2:8905966-8906092 +	AAA-A--------GAAG--------A------CA----------AATTTTAAAATTAAATGGCGATTGTCGGTTTGGTCGCTTTTTACCA-----------G-------GGTT----CCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAGAATGTTCAACATGG-----CCA--A
droWil1	scaffold_180701:1651730-1651882 -	TAT----------GCAA--------T------TG-AAATT----ACTTTTAAAATTGAATGGCGATTGTCGGTATAGTCTCTTTTTCCAA-A--------AATCTTGTTTGTTTTTGCCA--ATCTAATAAGAAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCAACAAGCAACAACCA--A
droVir3	scaffold_12875:4112084-4112243 +	GTG-----TTCCAGTATTCCAGTGTTTCAATTCCAATATTCCAGTATTTTAAAATTAAATGGCGATTGTCGGTATGGTCGCTTTTTCAAA-C--------AA-------TATA----CCATTATC--TATATAAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCAACGTAT-----ATA--A
droMoj3	scaffold_6496:20936771-20936914 -	TCC-A--------GTGT--------T------CGAAAATTATAAAATTTTAAAATTAAATGGCGATTGTCGGTATGGTCTCTTTTTCAACAT-ATACACCAA-------ACAT----T------C--TATATAAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCAACAATT-----TCA--A
droGri2	scaffold_15112:2108802-2108953 -	TGTGTGTGTT---GCAG--------T-CAAACCCAG----CCAGTATTTTAAAATTAAATGGCGATTGTCGGTATGGTCGCTTTTGAACC-T-AAACTC------T---ATAT----ACA--ATA--TATATAAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCAACATAG-----GCA--T

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:15548912-15549041 -	TTG-G--------GCAC--------T------CC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCAAA-G-A------AA-------GGTT----TCG--ATTAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----TCA--G
droSim1	chr2R:14254346-14254476 -	TTG-G--------GCAC--------T------CC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCCAA-AGA------AA-------GGTT----TCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----TCA--G
droSec1	super_1:13063641-13063770 -	TTG-G--------GCAC--------T------CC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCCAA-T-A------AA-------GGTT----TCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----TCA--G
droYak2	chr2R:13623749-13623876 +	TAG----------GCAC--------T------CC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCAAA-A--------GA-------GGTT----TCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----TCA--G
droEre2	scaffold_4845:9749162-9749292 -	TAG----------GCAC--------T------GC----------AGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCAAA-G--------AA-------GGTT----TCG--ATCGA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGC-----ACACTG
droAna3	scaffold_13266:9731344-9731477 +	TTT-A--------GCAT--------C------AG----------AATTTTAAAATTGAATGGCGATTGTCGGTATGGTCGCTTTTTCACA-A-A------AAAATT---GGTT----ACC--AACAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCATCAAGC-----TAA--A
dp4	chr3:12677574-12677700 -	AAA-A--------GAAG--------A------CA----------AATTTTAAAATTAAATGGCGATTGTCGGTTTGGTCGCTTTTTACCA-----------G-------GGTT----CCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAGAATGTTCAACATGG-----CCA--A
droPer1	super_2:8905966-8906092 +	AAA-A--------GAAG--------A------CA----------AATTTTAAAATTAAATGGCGATTGTCGGTTTGGTCGCTTTTTACCA-----------G-------GGTT----CCG--ATCAA---GCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAGAATGTTCAACATGG-----CCA--A
droWil1	scaffold_180701:1651730-1651882 -	TAT----------GCAA--------T------TG-AAATT----ACTTTTAAAATTGAATGGCGATTGTCGGTATAGTCTCTTTTTCCAA-A--------AATCTTGTTTGTTTTTGCCA--ATCTAATAAGAAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCAACAAGCAACAACCA--A
droVir3	scaffold_12875:4112084-4112243 +	GTG-----TTCCAGTATTCCAGTGTTTCAATTCCAATATTCCAGTATTTTAAAATTAAATGGCGATTGTCGGTATGGTCGCTTTTTCAAA-C--------AA-------TATA----CCATTATC--TATATAAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCAACGTAT-----ATA--A
droMoj3	scaffold_6496:20936771-20936914 -	TCC-A--------GTGT--------T------CGAAAATTATAAAATTTTAAAATTAAATGGCGATTGTCGGTATGGTCTCTTTTTCAACAT-ATACACCAA-------ACAT----T------C--TATATAAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCAACAATT-----TCA--A
droGri2	scaffold_15112:2108802-2108953 -	TGTGTGTGTT---GCAG--------T-CAAACCCAG----CCAGTATTTTAAAATTAAATGGCGATTGTCGGTATGGTCGCTTTTGAACC-T-AAACTC------T---ATAT----ACA--ATA--TATATAAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATGTTCAACATAG-----GCA--T

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TTGGGCACTCCAGTTTTAAAATTGAATGGCGAATGTCGGTATGGTCTCTTTTTCCAAAGAAAGGTTTCGATCAAGCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAAAATATTCAACATGCTCAG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................................................................TGACTAGACCGAACACTCGTGCT............................	23	1	169942.00	169942	169942
................................................................................TGACTAGACCGAACACTCGTGC.............................	22	1	7816.00	7816	7816
................................................................................TGACTAGACCGAACACTCGTG..............................	21	1	439.00	439	439
................................................................................TGACTAGACCGAACACTCGTGCTA...........................	24	1	90.00	90	90
.................................................................................GACTAGACCGAACACTCGTGCT............................	22	1	79.00	79	79
................................................................................TGACTAGACCGAACACTCGTGCTAT..........................	25	1	77.00	77	77
................................................................................TGACTAGACCGAACACTCGT...............................	20	1	75.00	75	75
....................................................................................TAGACCGAACACTCGTGCT............................	19	1	35.00	35	35
..................................................................................ACTAGACCGAACACTCGTGCT............................	21	1	30.00	30	30
...................................................................................CTAGACCGAACACTCGTGCT............................	20	1	19.00	19	19
.........................ATGGCGAATGTCGGTATGGTC.....................................................................................	21	1	13.00	13	13
...........................GGCGAATGTCGGTATGGTCTCT..................................................................................	22	1	10.00	10	10
.....................................................................................AGACCGAACACTCGTGCT............................	18	1	7.00	7	7

dp4

AAAAGAAGACAAATTTTAAAATTAAATGGCGATTGTCGGTTTGGTCGCTTTTTAC-CA---GGGTTCCGATCAAGCGAAGTGACTAGACCGAACACTCGTGCTATAATTTTAGAATGTTCAACATGGCCAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................................................................TGACTAGACCGAACACTCGTGCT............................	23	1	77398.00	77398	77397	1
................................................................................TGACTAGACCGAACACTCGTGC.............................	22	1	29785.00	29785	29785	0
................................................................................TGACTAGACCGAACACTCGTG..............................	21	1	6677.00	6677	6677	0
................................................................................TGACTAGACCGAACACTCGT...............................	20	1	754.00	754	754	0
................................................................................TGACTAGACCGAACACTCGTGCTA...........................	24	1	108.00	108	108	0
...........................GGCGATTGTCGGTTTGGTCGCT..................................................................................	22	1	68.00	68	68	0
................................................................................TGACTAGACCGAACACTCG................................	19	1	45.00	45	45	0
.................................................................................GACTAGACCGAACACTCGTGCT............................	22	1	37.00	37	37	0
...........................GGCGATTGTCGGTTTGGTCGC...................................................................................	21	1	25.00	25	25	0
....................................................................................TAGACCGAACACTCGTGC.............................	18	1	17.00	17	17	0
...................................................................................CTAGACCGAACACTCGTGC.............................	19	1	16.00	16	16	0
.................................................................................GACTAGACCGAACACTCGTGC.............................	21	1	15.00	15	15	0
...........................GGCGATTGTCGGTTTGGTCG....................................................................................	20	1	13.00	13	12	1
....................................................................................TAGACCGAACACTCGTGCT............................	19	1	12.00	12	12	0
..................................................................................ACTAGACCGAACACTCGTGCT............................	21	1	12.00	12	12	0
..................................................................................ACTAGACCGAACACTCGTGC.............................	20	1	10.00	10	10	0

Secondary Structure

dm3

dG=-21.1, p-value=0.009901	dG=-21.1, p-value=0.009901	dG=-21.0, p-value=0.009901	dG=-21.0, p-value=0.009901	dG=-20.9, p-value=0.009901

droSim1

dG=-21.7, p-value=0.009901	dG=-21.7, p-value=0.009901	dG=-21.6, p-value=0.009901	dG=-21.6, p-value=0.009901	dG=-21.5, p-value=0.009901

droSec1

dG=-20.1, p-value=0.009901	dG=-20.1, p-value=0.009901	dG=-20.1, p-value=0.009901	dG=-20.1, p-value=0.009901	dG=-20.0, p-value=0.009901

droYak2

dG=-20.8, p-value=0.009901	dG=-20.8, p-value=0.009901	dG=-20.7, p-value=0.009901	dG=-20.7, p-value=0.009901	dG=-20.6, p-value=0.009901

droEre2

dG=-22.1, p-value=0.009901	dG=-22.1, p-value=0.009901	dG=-22.0, p-value=0.009901	dG=-22.0, p-value=0.009901	dG=-21.9, p-value=0.009901

droAna3

dG=-24.2, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.0, p-value=0.009901

dp4

dG=-28.4, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-28.2, p-value=0.009901

droPer1

dG=-28.4, p-value=0.009901	dG=-28.4, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-28.3, p-value=0.009901	dG=-28.2, p-value=0.009901

droWil1

dG=-23.2, p-value=0.009901	dG=-23.2, p-value=0.009901	dG=-23.1, p-value=0.009901	dG=-23.1, p-value=0.009901	dG=-23.0, p-value=0.009901

droVir3

dG=-23.9, p-value=0.009901	dG=-23.9, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.7, p-value=0.009901

droMoj3

dG=-19.6, p-value=0.009901	dG=-19.6, p-value=0.009901	dG=-19.5, p-value=0.009901	dG=-19.5, p-value=0.009901	dG=-19.4, p-value=0.009901

droGri2

dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.4, p-value=0.009901	dG=-23.3, p-value=0.009901

Generated: 03/07/2013 at 05:06 PM