Secondary structure and small RNA-seq evidence for dme-mir-4965

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:16500125-16500242 +	GTATTCGCAGTAC-AAGCACAAGGTGATCGATGGGAGATGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCAC--ACACTCACTCA--------------------------CCCAGGTTTCATCCATACAAATGTGTTTG
droSim1	chrX_random:4339044-4339160 +	GTATTCGCAATAC-AAGCACAAGGTGATCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCAC--ACACTCACTCA--------------------------CCCA-GTTTCATCCATGCAAATGTGTTTG
droSec1	super_17:323461-323577 +	GTATTCGCAATAC-AAGCACAAGGTGATCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCAC--ACACTCACTCA--------------------------CCCA-GTTTCATCCATGCAAATGTGTTTG
droYak2	chrX:10606276-10606397 +	GAATTTAGAATAA-AAACAAAAGGTGATCGATGGGAGCTGACCTTGAGCCTGAGCTGAGATGATGAAGTAGATCGATCACAC-AC--TCACTCACTCA--------------------------CTCA-GTTTCATCCATGCAAATTTGTTTG
droEre2	scaffold_4690:6858711-6858812 +	CCC-----AATAA-AACCAAAAGGTGATCGATGGGAGCTGA----G--CCTGA--AGTGATGATGAAGTAAATCGATCACA-------CACTCACT------------------------------CA-GATTCATCCATGCAAATTTGTTTG
droAna3	scaffold_13337:17013621-17013746 +	GAAATCTCAGCAGCAAGCTCAG-CGGATCG---GGTGTTGG----A--GGTGG--TCTGCCATTGACGAAGAGCAACAGCACCAA--TTCCTTCC---AGGAGCATAGCGCTCCCAAGC----------GTCGTCCCAGTATGGGTGCCTTGG
dp4	chrXL_group1a:8134511-8134553 -	ACT------------------------------------------------------------------------------CCAC--ACACACACACA--------------------------CACA---GACAGACATATAAAGGA-CATG
droPer1	super_5:779941-779973 +	ACACTCGCACTCC-C---ACAAGAAGAGCAGCAGTAG--------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180698:6476640-6476654 +	ATTT------------------------------------------------------------------------------------------------------------------------------------------GAATGTGTGTG
droVir3	scaffold_13042:4246856-4246902 -	CAC-----------------------------------------------------------------------------AC-ACACACACACACATG--------------------------TACAGCTTTCACTCATGCATATTTGTT--
droMoj3	scaffold_6500:26586811-26586907 +	GCATTTGCACTG------------------CTCGAAAATGA----GCAATTGC--AAAGATCATTG-----------CACA---A--TACATTGC---AGAGAAATACTGCACAAAATAATTTAGTTA-ATTT------------TAAGTTGA
droGri2	scaffold_15245:5234538-5234618 -	GCAAAATGAACAC-----AAAAACTGTTG------------------------------------------------CATACCAC--ACACTAACTG--T--AAATATCA--------------CATTTTTATTATTCTTATAATTATTAATA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:16500125-16500242 +	GTATTCGCAGTACAAGCACAAGGTGATCGATGGGAGATGAGCGCCTGATGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCAGGTTTCATCCATACAAATGTGTTTG
droSim1	chrX_random:4339044-4339160 +	GTATTCGCAATACAAGCACAAGGTGATCGATGGGAGCTGAGCGCCTGATGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCA-GTTTCATCCATGCAAATGTGTTTG
droSec1	super_17:323461-323577 +	GTATTCGCAATACAAGCACAAGGTGATCGATGGGAGCTGAGCGCCTGATGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCA-GTTTCATCCATGCAAATGTGTTTG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GTATTCGCAATACAAGCACAAGGTGATCGATGGGAGCTGAGCGCCTGATGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCAG-TTTCATCCATGCAAATGTGTTTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

-----------------------------------------------------------------------ACTCCACACACACACACACACAG---ACAGACATATAAAGGA-CATG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-19.8, p-value=0.009901	dG=-19.4, p-value=0.009901

droSim1

dG=-18.4, p-value=0.009901	dG=-18.2, p-value=0.009901	dG=-18.0, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.8, p-value=0.009901

droSec1

dG=-18.4, p-value=0.009901	dG=-18.2, p-value=0.009901	dG=-18.0, p-value=0.009901	dG=-17.8, p-value=0.009901	dG=-17.8, p-value=0.009901

droYak2

dG=-16.8, p-value=0.009901	dG=-16.4, p-value=0.009901	dG=-16.1, p-value=0.009901	dG=-16.0, p-value=0.009901	dG=-15.9, p-value=0.009901

droEre2

dG=-12.5, p-value=0.009901	dG=-12.2, p-value=0.009901	dG=-12.1, p-value=0.009901	dG=-12.1, p-value=0.009901	dG=-12.1, p-value=0.009901

droAna3

dG=-22.1, p-value=0.009901	dG=-21.4, p-value=0.009901	dG=-21.3, p-value=0.009901	dG=-21.3, p-value=0.009901	dG=-21.1, p-value=0.009901	dG=-16.6, p-value=0.009901

dp4

dG=0.0, p-value=1.0

droPer1

dG=0.0, p-value=1.0

droWil1

No secondary structure predictions returned

droVir3

dG=0.0, p-value=1.0	dG=0.9, p-value=1.0	dG=1.0, p-value=1.0

droMoj3

dG=-9.8, p-value=0.009901	dG=-9.4, p-value=0.009901	dG=-9.3, p-value=0.009901	dG=-9.1, p-value=0.009901	dG=-9.0, p-value=0.009901

droGri2

dG=0.0, p-value=1.0

Generated: 03/07/2013 at 06:13 PM