Secondary structure and small RNA-seq evidence for dme-mir-4967

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:5899582-5899719 -	CATAGATATGGC--TAACTATAGCGTTGTCTCTTGCGCAAATTGCATTTTC---------TCTCTGTTAACATGTACACATAATTCCTGTAACAAAGGGCATTT-----GCAA--TGTGTGAGTCAGCAAA--CCGCATCCGCTTCCCGGC-CCCTCCT
droSim1	chr2R:4528976-4529111 -	CGAGGAAATAGC--TAACTATAGCGTTCTCTCTTGCGCAAATTGCATTTTC---------TCTCTGTAAACATGTACACATAATTCCTGTAACAAAGGGCATTT-----GCAA--TGTGTGAGTCAGCAAA--CCGCATCCGCCCC-C--CGCCCTCCC
droSec1	super_1:3512309-3512447 -	CGAGGAAATATCTTTAACTATAGCGTTCTCTCTTGCGCAAATTGCATTTCC---------TCTCTGTAAACATGTACACATAATTCCTGTAACAAAGGGCATTT-----GCAA--TGTGTGAGTCAGCAAA--CCGCATCCGCCCCTC--TGCCCTCCT
droYak2	chr2L:18527608-18527740 -	CGGGAAACTCG-----ACTATAGCGTTCTCTCTTGTTTAAATTGTATTTTC---------TCTCTGTTAAAATGTACACATAATTCCTATTTCAAAGGGCTTTG-----GAAA--AGTGTGAGTCAGCAAA--CCGCATCCGCCCG-A--TTTCTTCCT
droEre2	scaffold_4929:8470755-8470887 +	CGGTAAATTCG-----ACTAAAGCGTTCTCTCTTGCTTAAATTGTATTTTC---------TCTCTGTTAACATGTATACATATTTCCTGTAACAAAGGCCATTG-----GAAA--TGTGTGAGTCAGCAAA--CCGCATCCGCCCC-C--TTTCTTCCT
droAna3	scaffold_13266:17255662-17255760 +	TGCTATA-TATCTGTACCTATA----------------------------------------------TGTATGTACGGGTG-TTTATGTAACAAAAGGCATTTTGGTGGAAA--TGCGTGAGTCAGCGGA--CCGCATTAT-------GC-CCTTTGT
dp4	chr3:6114287-6114365 -	C-------------------------------------------------------------TCCATCCATATGTAC--------TTTATAACAAAGGGCATTT-----GGAATATGTGTGAGTCAGCACATGCCGCATCCGTG-----GC-CCCTTCC
droPer1	super_2:6317550-6317666 -	TTTTGACA--GC-----TTTAAGCGTTCC----------------ATTTCCATTCACGAACCTCCATCCATATGTAC--------TTTATAACAAAGGGCATTT-----GGAATATGTGTGAGTCAGCACATGCCGCATCCGTG-----GC-CCCTTCC
droWil1	scaffold_180700:5327370-5327375 -	CCC---------------------------------------------------------------------------------------------------------------------------------------------------------TTT
droVir3	scaffold_12875:417241-417243 -	CCT------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:5073155-5073192 +	GAGACACTTA-------------------------------------------------------------------------------------ACTCCGTTC-----ACCT--TGTGCGA----------------------------C-TCCCTAA
droGri2	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:5899582-5899719 -	CATAGATATGGC--TAACTATAGCGTTGTCTCTTGCGCAAATTGCATTTTCTCTCTGTTAACATGTACACATAATTCCTGTAACAAAGGGCATTTGCAATGTGTGAGTCAGCAAACCGCATCCGCTTCCCGGCCCCTCCT
droSim1	chr2R:4528976-4529111 -	CGAGGAAATAGC--TAACTATAGCGTTCTCTCTTGCGCAAATTGCATTTTCTCTCTGTAAACATGTACACATAATTCCTGTAACAAAGGGCATTTGCAATGTGTGAGTCAGCAAACCGCATCCGCCCCCC-G-CCCTCCC
droSec1	super_1:3512309-3512447 -	CGAGGAAATATCTTTAACTATAGCGTTCTCTCTTGCGCAAATTGCATTTCCTCTCTGTAAACATGTACACATAATTCCTGTAACAAAGGGCATTTGCAATGTGTGAGTCAGCAAACCGCATCCGCCCCTCTG-CCCTCCT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CGAGGAAATAGCTAACTATAGCGTTCTCTCTTGCGCAAATTGCATTTTCTCTCTGTAAACATGTACACATAATTCCTGTAACAAAGGGCATTTGCAA--TGTGTGAGTCAGCAAA--CCGCATCCGCCCCCCG--CCCTCCC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

C--------------------------------------------------TCCATCCATATGTAC--------TTTATAACAAAGGGCATTTGGAATATGTGTGAGTCAGCACATGCCGCATCCGT-----GGCCCCTTCC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-14.4, p-value=0.009901	dG=-14.4, p-value=0.009901	dG=-13.6, p-value=0.009901	dG=-13.4, p-value=0.009901

droSim1

dG=-12.3, p-value=0.009901	dG=-12.1, p-value=0.009901	dG=-11.4, p-value=0.009901

droSec1

dG=-12.3, p-value=0.009901	dG=-12.1, p-value=0.009901	dG=-11.4, p-value=0.009901

droYak2

dG=-8.6, p-value=0.009901	dG=-8.4, p-value=0.009901

droEre2

dG=-11.9, p-value=0.009901	dG=-10.9, p-value=0.009901

droAna3

dG=-8.0, 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

dp4

dG=-9.8, p-value=0.009901	dG=-9.3, p-value=0.009901	dG=-8.9, p-value=0.009901	dG=-8.8, p-value=0.009901

droPer1

dG=-12.6, p-value=0.009901	dG=-12.4, p-value=0.009901	dG=-12.1, p-value=0.009901	dG=-11.9, p-value=0.009901	dG=-11.7, p-value=0.009901

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

dG=-1.4, p-value=0.009901	dG=-0.4, p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 06:14 PM