Secondary structure and small RNA-seq evidence for dme-mir-4918

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:4134138-4134222 -	TCGCACATGTCTAAGGTGAG------CAC----GATGGCCACATTTA-----TTGGGCAA----------CCAATGAA-------TT--CCCGCCTGCC---CACAGGTTCACTCG--GTCTGC
droSim1	chr3R:17124439-17124521 +	TCGCACATGTCCAAGGTGAG------CAC----GATGGCCACATTTA-----TTGGGCAA----------CCCATGAA-------TC--C--TCCTGCC---CACAGGTTCACTCG--GTCTGC
droSec1	super_0:17695137-17695219 +	TCGCACATGTCCAAGGTGAG------CAC----GATGGCCACATTTA-----TTGGGCAA----------CCCATGAA-------TC--C--TCCTGCC---CACAGGTTCACTCG--GTCTGC
droYak2	chr3R:8209596-8209678 -	GCGCACATGTCCAAGGTGAG------CAC----GGCGGCCCCA------AA--------ATCAAAGTTCTCTGACCAA-------A-----ATCCCGCC---CACAGGTTCACTCC--GTCTGC
droEre2	scaffold_4770:17439359-17439448 +	GCGCACATGTCCAAGGTGAG------CAC----GATGGCCCCG------AC--------ATCGAAATT--C---TAAATCCCCAATCCAAAATCCCGCC---CACAGGTTCACTCA--GTCTGC
droAna3	scaffold_13340:13231716-13231803 -	GCCCATCTGAACAAGGTAAT------TTG-AAT--TTGTGTTTT-TG-GCC-AGGAGCAA----------TTGATGTA-------TT--TGTTTATGTT---CGAAGGTACACTCT--GTTTGC
dp4	chr2:14657774-14657858 -	GCCCACACGTCCAAGGTAAG------AA-----GCTAGTCGAA------AA--------ATTGAGGCATTTTCACGAA-------AC--A---ATTGTCTGAGGCAGGTTCACTCC--GTCTGC
droPer1	super_0:5758126-5758210 +	GCCCACACGTCCAAGGTAAG------AA-----GCTGGTCGAA------AA--------ATTGAGGCATTTTCACGAA-------AC--A---AATGTCTGAGGCAGGTTCACTCC--GTCTGC
droWil1	scaffold_181089:2794443-2794538 +	GCACATATGTCCAAGGTAAT------CAA-ATT--TAATGTAATTTA-----CCAGACAAGCGTTCCCTTTTTACAAA-------TT--TTCTTTCCCT---GGCAGGTTCACTCG--GTTTGC
droVir3	scaffold_12822:435887-435972 +	CCACACATGTCAAAGGTGGG------TATAAAA--CCATTTAGT-CT-GTC-----------GGTGGCATTTAATTGG-------TT-----TTCTTTT---CGTAGGTGCATTCG--GTGTGC
droMoj3	scaffold_6540:27855886-27855971 -	CAGCAA-TAGCAACAGCAAC------AGC----AATAGCAACAGCAACAGC----AGCAA----------CACCTGCAA------GC--CGCGGCAGCC---CAAAGTCTCGTTCG--CACCGC
droGri2	scaffold_15245:11304334-11304423 -	ATGCACAGCTCCTTAAGCAATATGAACAG----CAGAGCCTGG------GTAGTGATGTA----------CC--TGGAT------CC--C-GGCCCATC---TACACGTTCAGTGGACATCAGC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:4134138-4134222 -	TCGCACATGTCTAAGGTGAGCACGATGGCCACATTTATTGGGCAACCAATGAATTCCCGCCTGCCCACAGGTTCACTCGGTCTGC
droSim1	chr3R:17124439-17124521 +	TCGCACATGTCCAAGGTGAGCACGATGGCCACATTTATTGGGCAACCCATGAAT--CCTCCTGCCCACAGGTTCACTCGGTCTGC
droSec1	super_0:17695137-17695219 +	TCGCACATGTCCAAGGTGAGCACGATGGCCACATTTATTGGGCAACCCATGAAT--CCTCCTGCCCACAGGTTCACTCGGTCTGC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TCGCACATGTCCAAGGTGAGCACGATGGCCACATTTATTGGGCAA-CCCATGAAT--CCTCCTGCCC---ACAGGTTCACTCGGTCTGC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

GCCCACACGTCCAAGGTAAGAA-GCTAGTCGAAAAATTGAGGCATTTTCACGAAA--CA-ATTGTCTGAGGCAGGTTCACTCCGTCTGC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-18.4, p-value=0.009901

droSim1

dG=-14.2, p-value=0.009901	dG=-14.2, p-value=0.009901	dG=-13.7, p-value=0.009901

droSec1

dG=-14.2, p-value=0.009901	dG=-14.2, p-value=0.009901	dG=-13.7, p-value=0.009901

droYak2

dG=-9.6, p-value=0.009901	dG=-8.9, p-value=0.009901

droEre2

dG=-6.3, p-value=0.009901	dG=-6.0, p-value=0.009901	dG=-5.6, p-value=0.009901

droAna3

dG=-6.6, p-value=0.009901	dG=-6.5, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-6.0, p-value=0.009901	dG=-5.7, p-value=0.009901

dp4

dG=-5.3, p-value=0.009901	dG=-5.2, p-value=0.009901	dG=-5.1, p-value=0.009901	dG=-5.0, p-value=0.009901	dG=-4.5, p-value=0.009901	dG=-4.4, p-value=0.009901

droPer1

dG=-6.7, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-5.7, p-value=0.009901

droWil1

dG=-2.74, p-value=0.009901	dG=-2.2, p-value=0.009901	dG=-2.14, p-value=0.009901	dG=-1.9, p-value=0.009901

droVir3

dG=-10.5, p-value=0.009901	dG=-9.9, p-value=0.009901	dG=-9.9, p-value=0.009901

droMoj3

dG=-7.3, p-value=0.009901	dG=-6.9, p-value=0.009901	dG=-6.5, p-value=0.009901	dG=-6.4, p-value=0.009901	dG=-6.3, p-value=0.009901

droGri2

dG=-9.5, p-value=0.009901	dG=-9.3, p-value=0.009901	dG=-9.2, p-value=0.009901	dG=-8.9, p-value=0.009901	dG=-8.8, p-value=0.009901

Generated: 03/07/2013 at 05:34 PM