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

-44.2	-43.7	-43.4	-43.3

droSim1

-40.6	-40.1	-39.8

droSec1

-30.3	-30.0	-29.9	-29.8	-29.8	-29.7

droYak2

-43.5	-43.3	-43.3	-43.3	-42.6

droEre2

-31.9	-31.9	-31.4	-31.4	-31.3	-31.1

droAna3

-17.9	-17.5	-17.3	-17.3	-17.3	-17.2

dp4

-36.4	-36.3	-35.7	-35.6

droPer1

-31.8	-31.7	-31.4	-31.3	-31.3	-31.2

droWil1

-18.8	-18.4	-18.4	-18.4	-18.2	-18.1

droVir3

-34.9	-34.7	-34.7	-34.2	-34.2	-34.2

droMoj3

-27.7	-27.7	-27.7	-27.7	-27.7	-27.7

droGri2

-27.9	-27.8	-27.8	-27.5	-27.1	-27.1

Generated: 01/05/2013 at 05:10 PM