Secondary structure and small RNA-seq evidence for dme-mir-4954

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:1923021-1923142 -	ATATAAGTGTTCG--------ATTTGGCGCTTGGAATCGATACCCGAGCCATGATAGATTGAAGTCAA-CCCA-ATC----G----------ATC-GC-GGT-TCGAGTGCTCGAGTCTTGTGCGCCGGCATGC-TTGAGAT---GTCCACTA
droSim1	vgb65a08_5.b1:263-385 -	ATATAAGTGTTCG--------ATTTGGCGCTTGGAATCGATACCCGAGCCCTGATAGATTGAAGTCAA-CCCA-ATC----G----------ATC-GC-GGT-TCGGGTGCTCGAGTCCTGTGCGCCGGCATGC-TTGAGAT---GTCCACTA
droSec1	super_10:1708076-1708197 -	ATATAAGTGTTCG--------ATTTGGCGCTTGGAATCGACACCCGTGCCCTGATAGATTGAAGTCAA-CCCA-ATC----G----------ATC-GC-GGT-TCGGGTGCTCGAGTCTTGTGCGCCGGCATGC-TTGAGAT---GTCCACTA
droYak2	chrX:6403257-6403382 +	ACATAAAAGTTCA--------ATTTGGCGCTTGGAATCGTAACTCGAGCCCTCAAAGATTGAAGTCAAATGCA-ATC----G----------ATCCGG-GGTGTCGAGTGCTCGATTCTGGTGCGCCGGCATGCTTTGAGAT---GTCCACTA
droEre2	scaffold_4644:1895276-1895400 -	ATATAAGTGTTCG--------ATTTGGCGCTTGGAATCGAACCTCGAGCCCTGACAGATTGAAGTCAA-CCCAAAAC----G----------ATC-CCGGGG-TCGAGTGTTCGAGTCCGGTGCGCCGGCATGCTTTGAGTT---GTCCACTA
droAna3	scaffold_12929:1917028-1917098 -	ATATCCTTGACTT-------------------------CATAA-GGAACAATGA---------------------------------------TC-AT--GT--------------TAAGGTTCTCAGGCATGTCTCGAGATTATATCGAATC
dp4	chrXL_group1a:2597066-2597203 -	ATATAAATACATACTGCATAGTGTAGCAGAATGGACTCGGAACTCGATCCATGCATGCCACATGCCACATGCC-ACATGTCGCAGAGGGGGCAGC-GT-GGC-TCGAGTGCCAGAGTCCGGCGAG-------GC-ATGAGAC---TACTTACC
droPer1	super_28:1034311-1034357 -	A--------------------------------------------------------------------------------------------GC-GT-GGC-TCGAGTGCCAGAGTCCGGCGAG-------GC-ATGAGAC---TACTTACC
droWil1	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6473:2911987-2912050 +	ATATATGTGTGTG--------TGTTTGTGTATTGTATTTAGATTTGAGCTATAAAATGTTTAATAAAA-CTCA--------------------------------------------------------------------------------
droGri2	Unknown	---------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:1923021-1923142 -	ATATAAGTGTTCGATTTGGCGCTTGGAATCGATACCCGAGCCATGATAGATTGAAGTCAACCC-AATCGATC-GC-GGT-TCGAGTGCTCGAGTCTTGTGCGCCGGCATGCT-TGAGATGTCCACTA
droSim1	vgb65a08_5.b1:263-385 -	ATATAAGTGTTCGATTTGGCGCTTGGAATCGATACCCGAGCCCTGATAGATTGAAGTCAACCC-AATCGATC-GC-GGT-TCGGGTGCTCGAGTCCTGTGCGCCGGCATGCT-TGAGATGTCCACTA
droSec1	super_10:1708076-1708197 -	ATATAAGTGTTCGATTTGGCGCTTGGAATCGACACCCGTGCCCTGATAGATTGAAGTCAACCC-AATCGATC-GC-GGT-TCGGGTGCTCGAGTCTTGTGCGCCGGCATGCT-TGAGATGTCCACTA
droYak2	chrX:6403257-6403382 +	ACATAAAAGTTCAATTTGGCGCTTGGAATCGTAACTCGAGCCCTCAAAGATTGAAGTCAAATGCAATCGATCCGG-GGTGTCGAGTGCTCGATTCTGGTGCGCCGGCATGCTTTGAGATGTCCACTA
droEre2	scaffold_4644:1895276-1895400 -	ATATAAGTGTTCGATTTGGCGCTTGGAATCGAACCTCGAGCCCTGACAGATTGAAGTCAACCCAAAACGATC-CCGGGG-TCGAGTGTTCGAGTCCGGTGCGCCGGCATGCTTTGAGTTGTCCACTA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATATAAGTGT--------TCGATTTGGCGCTTGGAATCGATACCCGAGCCCTGATAGATTGAAGTCAACC--CAATCG-------------ATCGCGGTTCGGGTGCTCGAGTCCTGTGCGCCGGCATGCTTGAGATGTCCACTA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................ATACCCGAGCCCTGATAGATTG....................................................................................	22	1	1.00	1	1

dp4

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

Secondary Structure

dm3

dG=-24.3, p-value=0.009901	dG=-23.6, p-value=0.009901

droSim1

dG=-30.5, p-value=0.009901	dG=-29.8, p-value=0.009901

droSec1

dG=-28.7, p-value=0.009901	dG=-28.0, p-value=0.009901

droYak2

dG=-23.3, p-value=0.009901	dG=-23.1, p-value=0.009901	dG=-23.0, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.7, p-value=0.009901

droEre2

dG=-26.3, p-value=0.009901	dG=-25.7, p-value=0.009901

droAna3

dG=0.0, p-value=0.009901	dG=0.1, p-value=0.009901	dG=0.2, p-value=0.009901	dG=0.9, p-value=0.009901

dp4

dG=-40.4, p-value=0.009901	dG=-39.7, p-value=0.009901	dG=-39.5, p-value=0.009901

droPer1

dG=-6.2, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-5.4, p-value=0.009901

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

dG=-2.9, p-value=0.009901	dG=-2.3, p-value=0.009901	dG=-2.2, p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 05:55 PM