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

Legend:maturestarmismatch

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---ACAGGTTCACTCGGTCTGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GCCCACACGTCCAAGGTAAGAA-GCTAGTCGAAAAATTGAGGCATTTTCACGAAA--CA-ATTGTCTGAGGCAGGTTCACTCCGTCTGCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-18.4

droSim1

-14.2 -14.2 -13.7

droSec1

-14.2 -14.2 -13.7

droYak2

-9.6 -8.9

droEre2

-6.3 -6.0 -5.6

droAna3

-6.6 -6.5 -6.1 -6.0 -5.7 -5.6

dp4

-5.3 -5.2 -5.1 -5.0 -4.5 -4.4

droPer1

-6.7 -6.1 -6.1 -5.7

droWil1

-2.74 -2.2 -2.14 -1.9

droVir3

-10.5 -9.9 -9.9

droMoj3

-7.3 -6.9 -6.5 -6.4 -6.3 -6.3

droGri2

-9.5 -9.3 -9.2 -8.9 -8.8 -8.7

Generated: 01/05/2013 at 05:20 PM