Secondary structure and small RNA-seq evidence for dme-mir-2279

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2RHet:1322818-1322960 -	TCCGATGACCCATGGCG----G--GAGAGGATTATGAAAGACAATTTGAAATTAAATATCTGTGT-GTGAAATTATT--------------TAAAAGATTAATTTCACGCGAAGATATTTAT----TTTTACATTTGTCCCTATAATAACCGGGGT----------------------------------------G---------------CCA---ACATACAT
droSim1	chr2R:265657-265782 +	AGGC------------------A--------------------ATTTTCAATTAAATATCTGTGT-GTGGAATTATTAAAAACAATGAGTTCAAAGGTTTAGTTTCACGTAAAGATATTTATTTTG-TTTAAATTT-TCCCTAGAATAACCAGTAT----------------------------------------G---------------CCG---ACATAAA-
droSec1	super_55:122657-122779 +	AAGT------------------A-------------------AACTTAAAATTATAAATATGTGT-GTGAAATTAATAAA--CGGTAAGTTCGAAAGTTTAGTTTCACGCGAAAGTATTTAT----TTTTACATTTGTCCATAGAATAACCGGGGG----------------------------------------G---------------CCA---ACATAAA-
droYak2	chr2h_random:1837227-1837349 -	AAGA------------------C-------------------AACTTAAATTTTTATATCTGTGT-GGGAAATTAAGAAA--CAGTGAGTTCGAAAATTTAGTTTCGTGTAAAGTTATTTAT----TTCTGCATTTGTCCCTAGAATAACCGAGGT----------------------------------------C---------------CCA---ACATAAA-
droEre2	scaffold_4845:21278391-21278511 +	CTCCATAACTCAACTT-ATCTT--AATCGGATTTTGAAGTGGCA---TACCT-CTAAATGTTTGTGGTGCAATTATC--------------TAAAAAACTGCATTCAAATTTAAAAATTTATTTTT-TTTACATTTTTTTGTA-----------------------------------------------------------------------------------
droAna3	scaffold_13334:5190-5293 +	AAAA------------------AA-------TTAGTAAAAAAAATAATAAATAAAAAAAAATATG-GTGGGATTTTT--------------TAAAAGATATTTTTTATATGGCAATTGGT----------------------------------------------------------------AGTTAAATATTAG---------------TCT---TTTTAAGA
dp4	Unknown_group_37:8363-8450 +	GGCAATGAGG--------------------------------------------------------------------------------TAGGAGGGACAATTTTGTAT-----------------------------TCTATAATTATCGTTAGACCTACGCAAAGGATACATTTTACTGCGGG----------T---------------TGT---ATATTTT-
droPer1	super_5473:1216-1318 +	TATA------------------C----------------------------------GTGTGTAA-GTGGAACTATG--------------CAGGGGAATGATTTCACATGAAGAAAGTCGATTCG-CCTGTACC------TATTGCATTCC-TA-----------------------------AGCTGAGGTTT-A---------------AGC---TTTAACAT
droWil1	scaffold_180772:5217896-5218034 +	GCCGTTGACCAGTGGCG----G--CG----------------CCAAAGTGC--ACATATTCTTGT-CAGAGTTAGCTGGATAGTATGTTCCTGAAAATTCAATTA-AAATTGAA-----------------------------AGAGGACTTG--------------------------------TTGCAATGAATTTTTTTTTAATATTTGTCTAGATTTCGACC
droVir3	scaffold_291:1622-1745 -	AAAG------------------AA-------TCATTAGATAAATCTTTAAAATATAGATTTTTTT-TTACCATATTT--------------GTAATGATTTTTGGATTGCGAAATTTTTTAT----TTAAATTGTTAATTATATAATATATTAAAT----------------------------------------A---------------TTT---ATATATAT
droMoj3	scaffold_6473:7010400-7010528 +	AAAGACAAAAAAAAAT-AAAAT--AA----------------AAAAAATAAACAAACAAAAGTGT-GTAA---------------AGAGTGCAATGCCAACAAATCATACGTAGATTTCTAT----ATTTACATATGTACATAAATATATATATGT----------------------------------------A---------------TGC---ACATACAT
droGri2	scaffold_14906:12727535-12727642 +	TGCC------------------GAGAAGGG------------AAAACGAGAATACAATTTTGTTA-TATTATTTAATTTA--TCTTA-TCTTG------------------------------------TCCTTTTATTTGAAAGATAATTTGA------------------------------ATTTGAATAAATT---------------TAT---ATTTGTAT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2RHet:1322818-1322960 -	TCCGATGACCCATGGCGGGAGAGGATTATGAAAGACAATTTGAAATTAAATATCTGTGTGTGAAATTATTTAAAAGATTAATTTCACGCGAAGATATTTATTTTTACATTTGTCCCTATAATAACCGGGGTGCCAACATACAT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

--------------------------------AGGCAATTTTCAATTAAATATCTGTGTGTGGAATTATTAAAAACAATGAGTTCAAAGGTTTAGTTTCACGTAAAGATATTTATTTTGTTTAAATTTTCCCTAGAATAACCAGTATGCCGACATAAA---------------------------------------------------------------------	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

GGCAATGA----------------GGTAGGAGGGACAATTTTGTATTCTATAATTATCGTT------------------------------------------------------------------------------------AGACCTACGCAAAGGATACATTTTACTGCGGGTTGTATATTTT---------------------------------------	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-23.8, p-value=0.009901	dG=-23.5, p-value=0.009901	dG=-23.3, p-value=0.009901	dG=-23.0, p-value=0.009901	dG=-23.0, p-value=0.009901

droSim1

dG=-16.6, p-value=0.009901	dG=-16.4, p-value=0.009901	dG=-16.3, p-value=0.009901	dG=-16.1, p-value=0.009901	dG=-16.1, p-value=0.009901

droSec1

dG=-18.8, p-value=0.009901	dG=-18.7, p-value=0.009901	dG=-18.2, p-value=0.009901	dG=-18.2, p-value=0.009901	dG=-18.1, p-value=0.009901

droYak2

dG=-8.8, p-value=0.009901	dG=-8.2, p-value=0.009901	dG=-8.0, p-value=0.009901	dG=-8.0, p-value=0.009901	dG=-7.9, p-value=0.009901

droEre2

dG=-6.8, p-value=0.009901	dG=-6.6, p-value=0.009901	dG=-6.4, p-value=0.009901	dG=-6.4, p-value=0.009901	dG=-6.3, p-value=0.009901

droAna3

dG=-3.1, p-value=0.009901	dG=-2.7, p-value=0.009901	dG=-2.4, p-value=0.009901	dG=-2.4, p-value=0.009901	dG=-2.1, p-value=0.009901

dp4

dG=0.0, p-value=1.0	dG=0.5, p-value=1.0	dG=0.7, p-value=1.0

droPer1

dG=-15.1, p-value=0.009901	dG=-15.1, p-value=0.009901	dG=-15.1, p-value=0.009901	dG=-14.7, p-value=0.009901	dG=-14.7, p-value=0.009901

droWil1

dG=-8.5, p-value=0.009901	dG=-8.0, p-value=0.009901	dG=-7.6, p-value=0.009901	dG=-7.6, p-value=0.009901	dG=-7.5, p-value=0.009901	dG=-6.7, p-value=0.009901

droVir3

dG=-4.7, p-value=0.009901	dG=-4.0, p-value=0.009901	dG=-3.7, p-value=0.009901

droMoj3

dG=-6.7, p-value=0.009901	dG=-5.8, p-value=0.009901	dG=-3.6, p-value=0.009901

droGri2

dG=-2.1, p-value=0.009901	dG=-1.6, p-value=0.009901	dG=-1.6, p-value=0.009901	dG=-1.4, p-value=0.009901	dG=-1.4, p-value=0.009901

Generated: 03/07/2013 at 04:53 PM