Secondary structure and small RNA-seq evidence for dme-mir-2494

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:12444473-12444619 +	GGC--AACCTGCCACTGTCCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATT------------G-GGAAT-----------------AACCTTCAAAAGCTGCAACTT-AAATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC
droSim1	chr3R:9022585-9022731 -	GGC--AACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATT------------G-GGAAT-----------------AACCTTCAAAAGCTGCAACTT-AAATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC
droSec1	super_12:1702814-1702963 -	GGC--ATCCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCATAGT-----A---A--ATGGAAT-----------------AACCTTCAAAATCTGCAACTT-AAATATTCCCAGTAATGTCCGCTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC
droYak2	chr3R:11948210-11948356 -	GGC--GACCTGCCACTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCACCAGATT------------G-GGATT-----------------AACCTTCAAAAGCTGCAGCTT-AACTATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGATGGCTGGGTGGACAA--CCTATTCGGACC
droEre2	scaffold_4770:9192977-9193123 -	GGC--AACCTGCCCCTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCAACAGATT------------G-GGAGT-----------------AACCGTCAAAAGCTACAACTT-CAATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGCTGGATAGACAA--CCTATTCGGACC
droAna3	scaffold_13340:7435217-7435360 -	GGC--AGCCTGCCAGTCAGCATTTATCGGCCTTCCATAAGTAAGTACTATATACG------------T-CCTGC-----------------TGTCTTATAAAATTGTTATTT----TTTTTCTAGTAATTGCCACATATAAGGAGCCATTAGTTGGATGGGTGGATAA--CCTTTATGGACC
dp4	chr2:5294042-5294203 -	GGC--GACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCC----TTAGAT---G--AT-GCAAGGCCTTGGATGGAACTG-----AAACATTGTGTAACAT-GACTCTCCACAGTCGTGCCCACCTACCAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC
droPer1	super_19:1006170-1006331 -	GGC--GACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCC----TTAGAT---G--AT-GCAAGGCCTTGGATGGAACTG-----AAACATTGTGTAACAT-GACTCTCCACAGTCGTGCCCACCTACAAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC
droWil1	scaffold_181108:4575766-4575914 -	GGC--AATCTACCAATCTGTATTTTTCGCCCTGGTGTCAGTAAGTCCTCAAAATT------------C------------AACTTGTAACT-----ATAGCTGTTAAATTTTCTCCTTATTATAGTTATTGCCACCGCCAAGGAGCCAGTTTCGGGTTGGATTGACAA--TTTATATGGACC
droVir3	scaffold_13047:18500357-18500519 -	ACAAAAAGCTGCCCATTATCGTCACAAGGCCTTCCATCGGTATGTAGGTCC----CGCT-A---A--CT-GGTTGGGCTTGACAAGTAACC-----ATATTTATTTTTTTTT-TTGTTCGCCCAGTGACGGCGGCCATACACGAGCCCATGCCCGGATGGATTGAGGG--CGTGAACGGACC
droMoj3	scaffold_6496:22335084-22335230 -	GCC--GGTCTGCCGGCAGCCATAGTTAGGCCATCCATAGGTGAGTC----GAAGTATAAATCTAATTG-AG-AA-----------------GGCCCTAACTGACTGCTATT----------ACAGTATACGGTACACTGGAGCACCCCATGAAGGGCTGGGTGGGCAATGCCAACTCGGGTC
droGri2	scaffold_15074:333824-333971 -	AGC--GGTTTGCCCATAAGCATCTTTCGCCCGGGTGTCAGTAAGTTCGTCGAATCATTAAGATCA----------------GTAAGAA---GATGTTCTCAGTCT-----------CCATTTCAGTTATTGGCAGCTACAAGGACCCCCTCCCGGGCTGGGTTGACAA--TCTATATGGTCC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:12444473-12444619 +	GGCAACCTGCCACTGTCCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATT---GGGAATAACCTTCAAAAGCTGCAACTTAAATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAACCTATTCGGACC
droSim1	chr3R:9022585-9022731 -	GGCAACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATT---GGGAATAACCTTCAAAAGCTGCAACTTAAATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAACCTATTCGGACC
droSec1	super_12:1702814-1702963 -	GGCATCCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCATAGTAAATGGAATAACCTTCAAAATCTGCAACTTAAATATTCCCAGTAATGTCCGCTTACAAGGAGCCCCTGGTTGGATGGGTGGACAACCTATTCGGACC
droYak2	chr3R:11948210-11948356 -	GGCGACCTGCCACTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCACCAGATT---GGGATTAACCTTCAAAAGCTGCAGCTTAACTATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGATGGCTGGGTGGACAACCTATTCGGACC
droEre2	scaffold_4770:9192977-9193123 -	GGCAACCTGCCCCTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCAACAGATT---GGGAGTAACCGTCAAAAGCTACAACTTCAATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGCTGGATAGACAACCTATTCGGACC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGCAACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGT---GCACCAGATTGGGAATAACCTTCAAAAG------------CTGCAACTTAAATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAACCTATTCGGACC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.....................................................................................................TCCCAGTAATGTCCACTTACAAG......................................	23	1	2.00	2	2
.....................................GTAAGT---GCACCAGATTGGGAA.....................................................................................................	21	1	1.00	1	1
.....................................GTAAGT---GCACCAGATTGGG.......................................................................................................	19	1	1.00	1	1
.....................................GTAAGT---GCACCAGATTGGGAAT....................................................................................................	22	1	1.00	1	1

dp4

GGCGACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCTTAGATGATGCAAGGCCTTGGATGGAACTGAAACATTGTGTAACATGACTCTCCACAGTCGTGCCCACCTACCAGGAGCCCGTCGTTGGTTGGACTGACAATCTGTACGGGCC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-20.3, p-value=0.009901

droSim1

dG=-20.3, p-value=0.009901

droSec1

dG=-10.0, p-value=0.009901	dG=-9.7, p-value=0.009901	dG=-9.6, p-value=0.009901	dG=-9.5, p-value=0.009901	dG=-9.4, p-value=0.009901

droYak2

dG=-19.2, p-value=0.009901	dG=-19.0, p-value=0.009901	dG=-19.0, p-value=0.009901	dG=-19.0, p-value=0.009901

droEre2

dG=-19.9, p-value=0.009901

droAna3

dG=-3.1, p-value=0.009901	dG=-3.0, p-value=0.009901	dG=-2.8, p-value=0.009901	dG=-2.7, p-value=0.009901	dG=-2.6, p-value=0.009901

dp4

dG=-14.5, p-value=0.009901	dG=-13.7, p-value=0.009901	dG=-13.7, p-value=0.009901	dG=-13.7, p-value=0.009901	dG=-13.5, p-value=0.009901	dG=-12.4, p-value=0.009901

droPer1

dG=-14.5, p-value=0.009901	dG=-13.7, p-value=0.009901	dG=-13.7, p-value=0.009901	dG=-13.7, p-value=0.009901	dG=-13.7, p-value=0.009901	dG=-12.4, p-value=0.009901

droWil1

dG=-5.2, p-value=0.009901	dG=-5.1, p-value=0.009901	dG=-5.0, p-value=0.009901	dG=-4.9, p-value=0.009901	dG=-4.9, p-value=0.009901

droVir3

dG=-24.8, p-value=0.009901	dG=-24.1, p-value=0.009901	dG=-24.1, p-value=0.009901

droMoj3

dG=-6.8, p-value=0.009901	dG=-6.4, p-value=0.009901	dG=-6.2, p-value=0.009901

droGri2

dG=-6.2, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-6.1, p-value=0.009901

Generated: 03/07/2013 at 04:57 PM