Secondary structure and small RNA-seq evidence for dme-mir-303

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:4260197-4260296 -	AAAACC-AAATTGATATCTTGGTTTAGGTTTCAC-AGGAAACTGGTTTAATAACGAAAA----------CTAGTTTCCTCTAAAATCCTAATCAAGACATCATGTGTCGTCG
droSim1	chrX:3275244-3275342 -	AAAACC-AATGTGATCTCTTGCTTTGGCATT-AA-AGGAAGCTAGTTTAATTACGAAAA----------CTAGTTTCCTCTAACGTTTCAAACAATACATCATGTGTCGTCG
droSec1	super_4:2464323-2464421 +	AAAACC-AATGTGATCTCTTGCTTTGGCTTT-AA-AGGAATCTAGTTTGATTACGAAAA----------CTAGTTTCCTCTAAGGTTTTAAACATTACATCATGTGTCGTCG
droYak2	chrX:4177737-4177835 +	GAACTCAAATAATCTGCCTTGCTTAGAATTTTAA-GAGCAAAAAGTTTGTTTACAAAAA----------CTATTTACCCCTAAAATTCTAATCTAGTCAGCATTAT--TTCG
droEre2	scaffold_4690:1630987-1631073 -	GAACCA-AAAAATGTGCTTTGTTTAGAATTTTAGCGAGGAATCATTACAAATATGGATGTGAACTTAAAGTACTCACTGCAAG------------------------AAACG
droAna3	Unknown	----------------------------------------------------------------------------------------------------------------
dp4	Unknown	----------------------------------------------------------------------------------------------------------------
droPer1	Unknown	----------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181150:2098814-2098829 +	AAA------------------------------------------------------------------------------------------------TCATTCGTCAACT
droVir3	Unknown	----------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	----------------------------------------------------------------------------------------------------------------
droGri2	Unknown	----------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:4260197-4260296 -	AAAACCAAATTGATAT--CTTGGTTTAGGTTTCACAGGAAACTGGTTTAATAACGAAAACTAGTTTCCTCTAAAATCCTAATCAAGACATCATGTGTCGTCG
droSim1	chrX:3275244-3275342 -	AAAACCAATGTGATCT--CTTGCTTTGGCATT-AAAGGAAGCTAGTTTAATTACGAAAACTAGTTTCCTCTAACGTTTCAAACAATACATCATGTGTCGTCG
droSec1	super_4:2464323-2464421 +	AAAACCAATGTGATCT--CTTGCTTTGGCTTT-AAAGGAATCTAGTTTGATTACGAAAACTAGTTTCCTCTAAGGTTTTAAACATTACATCATGTGTCGTCG
droYak2	chrX:4177737-4177835 +	GAACTCAA-ATAATCTGCCTTGCTTAGAATTTTAAGAGCAAAAAGTTTGTTTACAAAAACTATTTACCCCTAAAATTCTAATCTAGTCAGCATTAT--TTCG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAAACCAATGTGATCTCTTGCTTTGGCA-TTAAAGGAAGCTAGTTTAATTACGAAAACTAGTTTCCTCTAACGTTTCAAACAATACATCATGTGTCGTCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
......................TTGGCA-TTAAAGGAAGCTAGT........................................................	21	1	1.00	1	1
......................TTGGCA-TTAAAGGAAGCTAGTT.......................................................	22	1	1.00	1	1

dp4

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

Secondary Structure

dm3

dG=-22.3, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.8, p-value=0.009901	dG=-21.5, p-value=0.009901

droSim1

dG=-19.2, p-value=0.009901	dG=-18.6, p-value=0.009901	dG=-18.5, p-value=0.009901	dG=-18.4, p-value=0.009901	dG=-18.3, p-value=0.009901

droSec1

dG=-19.5, p-value=0.009901	dG=-19.4, p-value=0.009901

droYak2

dG=-10.8, p-value=0.009901	dG=-10.3, p-value=0.009901	dG=-10.1, p-value=0.009901

droEre2

dG=-4.4, p-value=0.009901	dG=-3.9, p-value=0.009901	dG=-3.6, p-value=0.009901	dG=-3.5, p-value=0.009901	dG=-3.5, p-value=0.009901

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 05:10 PM