Secondary structure and small RNA-seq evidence for dme-mir-2281

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:10222106-10222238 -	TCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGAGCAGTACACGTA---TTATCTGCAG------CTGCAGATGCAAATGTATATGTATCTGTATCTG------TATCT--GCAGTAT-TGC-----AGTA-------TCGCTGCTTTATTCATATCCATG-------AGACGCGTCGCG
droSim1	chr3R:11233896-11234028 +	GCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGAGCAGTACTCGTA---TTATCTGCAG------CTGCAGATGCAAATGTATATGTATCTGTATCTG------TATCT--GCAGTAT-TGC-----AGTA-------TCGCTGCTTTATTCGTATCCATG-------TGACGCGTCGCG
droSec1	super_0:11818438-11818570 +	GCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGAGCAGTACTCGTA---TTATCTGCAG------CTGCAGATGCAAATGTATATGTATCTGTATCTG------TATCT--GCAGTAT-TGC-----AGTA-------TCGTTGCTTTATTCGTATCCATG-------TGACGCGTCGCG
droYak2	chr3R:16218838-16218961 +	TCCAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGAGCTGC------G---TTATCTGCAG------CTGCAGATGCAAATGTATCTGTATCTT--TCAG------TAT-T--GCAATGT-TGC-----AGTA-------TCTTTGCTTTATTCGTATCCGTG-------TGACGCGTCGCG
droEre2	scaffold_4770:9756449-9756546 -	TCCAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGAGCAT----C--G---TTATCTGCAG------CTGCAGATGCAAATGTA------------TCTG------TATCT--GCAGTAC-GGC-----------------------------TGTATCCGTG-------TGACGCGGCGCG
droAna3	scaffold_13117:2846333-2846460 -	GTA----------------------------------------------------------------------------------------TCTCGAGATGCATCTGTAAGAGTATCTGCAT------CTGCAAATGTATCTGTATCTGTATCTGTATCTG------TATCT--GTATCTG-TGC-----AAGACTTGCCACCTCTCCTTTTCTCCTTTTCCTG-------AGCAAATGTCGC
dp4	chrXR_group8:8158458-8158593 +	GCTAGTG-------------------------------------------------------------------------CCCACTACTGCCTTTGGCATGTATCTGTATCTGTACCCGTATCCGTATCCGTATCCGTTACTGTATCTGTATCTGTATCTG------TAGCT--GCTCTGAATGC-----AGTA-------TATA---TTTCATCAAATTTTTG-------TA----CTCGCA
droPer1	super_0:4124990-4125137 +	GTAGGGGATCAGGCATGGCCAGGGGCAGCGGCAACGGCAGGGGCAGGGGCAGGGGCAGCTTTTCCAGGCT-------GTGCATCCTACGGATGGCAGGCTGTAC----------------------------------AACCGTATCGGCAGCCGTATCGG------TATCG--G---------------------------------------TGTATCTGTG-------TGACGCGTCGCG
droWil1	scaffold_181089:10073219-10073346 +	CCTGGTAGAGAACGT-----------------------TGGGG--GAGGGGGGGGTTAGTTTTCCAGGCTCGCTGCAAAACATCCTACGATGTGAAAATTGT------G---A---------------------------AGG------------CTACTGAAA--GCG-GT--GCAATGC-GAG-----------------------------GAGAGCGACG-------CAATGCGACGCG
droVir3	scaffold_12928:2113057-2113188 +	GTATCTATATCTGTA----------------------------------------------------------------------TATG------TATCTGT------ATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTG------TATCT--GTAT------C-----TATAT------TTGCTT----CTTTAAATCCGCCTCTTTCGAGACATTTATCC
droMoj3	scaffold_6654:2537235-2537365 +	TTCAGTGAATCTGTATCTGTATCTGTATCTGTATCTG----------------------------------------------------------------------------TATCTGTAT------CTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCG--TATCTGT-ATC-----------------TGTATCTGTATCTGTATCTG----------TATTTGTATCT
droGri2	scaffold_14830:2155779-2155908 -	GCGA-TG-------------------------------------------------------------------------TATCT--CGTATCTCGGCGAGTACGTCGC---------GCAT------CCGTATCTGCAAATGTATCTCTATCTATAGCTG------TATCTGAGCAATGTATGTAGTATAGTA-------TCTGTTGTT--GGGGTTTTCATA-------TTGCTTGTGCTG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:10222106-10222238 -	TCCAGTGCATCCTACGGATGTCGAGCAGTACACGTATTATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCAGTATTGCAGTATCGCTGCTTTATTCATATCCATGAGACGCGTCGCG
droSim1	chr3R:11233896-11234028 +	GCCAGTGCATCCTACGGATGTCGAGCAGTACTCGTATTATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCAGTATTGCAGTATCGCTGCTTTATTCGTATCCATGTGACGCGTCGCG
droSec1	super_0:11818438-11818570 +	GCCAGTGCATCCTACGGATGTCGAGCAGTACTCGTATTATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCAGTATTGCAGTATCGTTGCTTTATTCGTATCCATGTGACGCGTCGCG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GCCAGTGCATCCTACGGATGTCGAGC------AGTACTCGTAT---TATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCA-GTATTGCAGTATCGCTGCTTTATTCGTATCCATGTGACGCGTCGCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

GCTAGTGCCCACTACTGCCTTTGGCATGTATCTGTATCTGTACCCGTATCCGTATCCGTATCCGTTACTGTATCTGTATCTGTATCTGTAGCTGCTCTGAATGCAGTATATA---TTTCATCAAATTTTTGTAC----TCGCA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................................................................ATCTGTATCTGTATCTGT......................................................	18	1	1.00	1	0	1
.......................................................................ATCTGTATCTGTATCTGTA.....................................................	19	1	1.00	1	0	1
......................................................................TATCTGTATCTGTATCTGTA.....................................................	20	1	1.00	1	0	1

Secondary Structure

dm3

-38.0	-37.3	-37.1

droSim1

-39.6	-39.3	-38.9	-38.9	-38.7	-38.6

droSec1

-37.7	-37.4	-37.0	-36.9	-36.8	-36.7

droYak2

-32.6	-32.6	-32.1	-32.1	-32.1	-32.1

droEre2

-32.5

droAna3

-16.7	-16.7	-16.7	-16.7	-16.3	-16.3

dp4

-14.3	-14.2	-14.1	-13.9	-13.9	-13.9

droPer1

-14.7	-14.5	-13.9	-13.9	-13.9

droWil1

-7.5	-7.4	-7.0	-7.0	-6.9

droVir3

-5.2	-5.2	-5.0	-4.3

droMoj3

-4.5	-3.7

droGri2

-19.4	-19.0	-18.8	-18.7	-18.7	-18.7

Generated: 01/05/2013 at 05:09 PM