Secondary structure and small RNA-seq evidence for dme-mir-4953

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:18599846-18599969 +	CGTAAGAATA-------------TTG-------CACTAAAGTTCACAGGCGACCATGA-AT---GTTAATAAAG----A--------ATAT---------------------TTACCAATAAAGTTTTATTTTTTATTGAAGGTCATGGACATCCTTGAACCGATTTTGCAACATG-----CATGT
droSim1	chr3R:18412164-18412275 +	CGTAAAAATA-------------TTG-------CACGAAAGTTCGCAGGCGACCATGA-AT---GTTAATAAAG----A--------ATAT---------------------TTACCAATAAAGTTTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACG--------------------GTGT
droSec1	super_0:18960705-18960813 +	CGTAAAAATA-------------TTG-------CACGAAAGTTCGCAGGCGACCATGA-AT---GTTAATAAAG----A--------ATAT---------------------TTACCAATAAAGTTTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACG--------------------GTGT
droYak2	chr3R:19450585-19450700 +	TGCTCAAATT-------------TTG-------CACGAAAGTTCGATGGCGACCATGA-AT---GCGAATGAAG----A--------ATAT---------------------TTACCATTAGTGTTTTGCTCATTATTGAAGGTCATGGACATCCTTGA-----TTTTGCAAAATG--------TT
droEre2	scaffold_4820:9473651-9473779 -	CGCTAAAATA-------------TGG-------CACGAAAGTTCACTGGCGACCATGA-AT---GTTAATAAAG----A--------ATAT---------------------TTACCATAAAGATATGTTTTTTTATTGAAGGTCATGGACATCCTTGAACCGATTTTGCAATATGTTCTACGTGT
droAna3	scaffold_13340:12717426-12717507 -	GGGGAAAAAA-------------TGA-------AAAGAA-----ACAAATGACCTTAGTAGGTCAGTGACTAAATTTTTGCCCATAA----GT-----------------------------GATTTAATCGTATATCAA----------------------------------------------
dp4	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12822:414561-414651 -	TGCAAGCAAA-------------TTT-------TGCCTAAGTTCTGA------------------CTAATAACT----A--------ATGT---------------------ATGTACTTAATGTTATTGTGATAAATTAATGTTATTTGTAACCAA------------------------AATGT
droMoj3	scaffold_6540:33042485-33042630 -	CGTAGTTTGACCACATAGAGACATCAAGTCTAAGAGGAAAACTCA--------TTTGG-AC---ACTGATTAAAAATCAGTCCCGAT----GAGAGCGAT------------AT---ATTAACATTAATTTTCTTATTGCATTTTACGTATATTTTTTTTTTGCTTTTAACA---------TACAT
droGri2	scaffold_15074:3394740-3394844 +	GTATGATACA-------------------------TTAAAGTTCTCCATAATCAATTT-GT---GT-------------------------GTGTGTGTGTCATCGACAAATTTACCATCTTAACTACACTTATTTTCAAAAT-------------------A-TTTCACATA--------TATTT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:18599846-18599969 +	CGTAAGAATATTGCACTAAAGTTCACAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGT-TTTATTTTTTATTGAAGGTCATGGACATCCTTGAACCGATTTTGCAACATG-----CATGT
droSim1	chr3R:18412164-18412275 +	CGTAAAAATATTGCACGAAAGTTCGCAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGT-TTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACGG--------------------TGT
droSec1	super_0:18960705-18960813 +	CGTAAAAATATTGCACGAAAGTTCGCAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGT-TTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACGG--------------------TGT
droYak2	chr3R:19450585-19450700 +	TGCTCAAATTTTGCACGAAAGTTCGATGGCGACCATGAATGCGAATGAAGAATATTTACCATTAGTGT-TTTGCTCATTATTGAAGGTCATGGACATCCTTGA-----TTTTGCAAAATGT--------T
droEre2	scaffold_4820:9473651-9473779 -	CGCTAAAATATGGCACGAAAGTTCACTGGCGACCATGAATGTTAATAAAGAATATTTACCAT-AAAGATATGTTTTTTTATTGAAGGTCATGGACATCCTTGAACCGATTTTGCAATATGTTCTACGTGT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CGTAAAAATATTGCACGAAAGTTCGCAGGCGACCATGAATGTTAATAAAGAATATTTACCAATAAAGTTTTGTTTTTTATTAAAGGTCATGGACATCCTTGAACGG---------------TGT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

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

Secondary Structure

dm3

-24.9	-24.5

droSim1

-24.3	-23.9

droSec1

-24.3	-23.9

droYak2

-17.2	-17.1	-17.0	-16.9	-16.9	-16.8

droEre2

-21.7	-21.5	-21.1	-20.9	-20.9	-20.7

droAna3

-10.2	-9.8	-9.6	-9.6	-9.4	-9.2

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

-6.9

droMoj3

-18.2	-18.1	-17.9	-17.7	-17.6	-17.4

droGri2

-6.3	-6.2	-5.7	-5.7	-5.6	-5.5

Generated: 01/05/2013 at 05:23 PM