Secondary structure and small RNA-seq evidence for dme-mir-2496

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:1904318-1904465 + AAGAGCGCAAAATGA--GT--------------------------------GCGCCG----GTGTGCGTGTGTGAGAGGCC--ATCGTAAAAGCCTTGTTTGCGTGCGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGCG-----------------GGGCACTCACACACGCATATTCAGCCGCA--------CATCT--GGGAAAATGGG
droSim1 chrX:1343126-1343273 + AAGAGCGCGAAATGA--GT--------------------------------GCGCCG----GTGTGCGTGTGTGAGAGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCG-----------------GGGCACACACACACGCATATTCAGCCGCA--------CATCT--GGGAAAATGGG
droSec1 super_10:1689518-1689665 + AAGAGCGCAAAATGA--TT--------------------------------GCGCCT----GTGTGCGTGTGTGAGAGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCG-----------------GGGCACTCACACACGCATATTCAGCCGCA--------CATCT--GGGAAAATGGG
droYak2 chrX:6422544-6422691 - AAGAGCGCAAAATGT--GT--------------------------------GCGCCG----GTGTGCGTGTGTGAGAGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATCGGG-----------------GGGCACTCACACACGCACATACAGCCGCA--------CATCT--GGGAAAATGGG
droEre2 scaffold_4644:1874871-1875018 + AAGAGCGCAAAATGT--GT--------------------------------GCGCCG----GTGTGCGTGTGTGAGAGGCC--ATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGGG-----------------GGGCACTTACACACGCACATACAGCCGCA--------CATCT--GGGAAAATGGG
droAna3 scaffold_12929:1897894-1898023 + AAGGGGGAGAGAGCA--GT--------------------------------TTGCAT----GTGTGCGATTTT-----GTG--GTCATAAAAGCTTTGTTTGCGTGTGGAATTTAACTGTTTTCTAGCCGTCTGCGAATTGGG-----------------GGGGGGGGG-------------GGCCATA--------CAAGC--TGGAAAATAGG
dp4 chrXL_group1a:2576130-2576311 + AAGAGGGAGAGATA-----GAGAGAGAGAATAATGGAGTGCTGGTGTATATGTACCTACATATGTACGTGTGGTTGA-GTA--CCCATAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTGTGTTGGG-----------------CGGCACACACACCAGCGCCATTGGCTTTT--------CACAGGGCGAGAAGTAAG
droPer1 super_28:1013167-1013344 + AAGAGGGAGAGATA-----GAGAGAGAGAATAATGGAGTGCTGGTGTATATGTACCT----ATGTACGTGTGGTTGA-GTA--CCCATAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTGTGTTGGG-----------------CGGCACACACACCAGCGCCATTGGCTTTT--------CACAGGGCGAGAAGTAAG
droWil1 scaffold_181096:6994288-6994457 - GAGGCCAAAA-GAGACAGT--------------------------------GCGATA----GAGAG--AGGTAGAGAGAACGTACAGAGAGAG-CTTGTTCTGGTTTGTAACTA-ATTTTCCCCCTCAAATGTAAGCATTTCGAATGCATGTGTGTGTACGTGTAATCACACACGCACACAAATAC-CACGTCATTACGAT---TTCCACATGGC
droVir3 scaffold_12928:6459245-6459266 + G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGTA--------TTTCT--GTGCAAGTGTG
droMoj3 Unknown -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 scaffold_15203:11679615-11679698 + -----------------------------------------------------------------------------------------------TTGTTTTCGCTTTTCATTT---TGTTTTACGATTAACTGTAAACTGCA-----------------G-----CCGGCCAACCATTTTCGAGCCCA-----------CTGGCAAAGAATGGG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:1904318-1904465 + AAGAGCGCAAAATGAGTGCGCCGGTGTGCGTGTGTGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGCGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGCGGGGCACTCACACACGCATATTCAGCCGCACATCTGGGAAAATGGG
droSim1 chrX:1343126-1343273 + AAGAGCGCGAAATGAGTGCGCCGGTGTGCGTGTGTGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGGCACACACACACGCATATTCAGCCGCACATCTGGGAAAATGGG
droSec1 super_10:1689518-1689665 + AAGAGCGCAAAATGATTGCGCCTGTGTGCGTGTGTGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGGCACTCACACACGCATATTCAGCCGCACATCTGGGAAAATGGG
droYak2 chrX:6422544-6422691 - AAGAGCGCAAAATGTGTGCGCCGGTGTGCGTGTGTGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATCGGGGGGCACTCACACACGCACATACAGCCGCACATCTGGGAAAATGGG
droEre2 scaffold_4644:1874871-1875018 + AAGAGCGCAAAATGTGTGCGCCGGTGTGCGTGTGTGAGAGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTCGCCGTCTGCGAATTGGGGGGCACTTACACACGCACATACAGCCGCACATCTGGGAAAATGGG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAGAGCGCGAAATGA-----------------------------GTGCGCCGG----TGTGCGTGTGTGAG-AGGCCATCGTAAAAGCCTTGTTTGCGTGTGGAATTTAACTGTTTTCTTGCCGTCTGCGAATTGCGGGGCACACACACACGCATATTCAGCCGCACATCTGG--GAAAATGGGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AAGAGGGAGAGATAGAGAGAGAGAATAATGGAGTGCTGGTGTATATGTACCTACATATGTACG--TGTGGTTGAGTACCCATAAAAGCCTTGTTTGCGTGCTAGTTTTAACTGTTTTTTCGGTGTTCTTGTGTTGGGCGGCACACACACCAGCGCCATTGGCTTTTCACAGGGCGAGAAGTAAGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-46.3,  p-value=0.009901 dG=-46.1,  p-value=0.009901 dG=-45.7,  p-value=0.009901 dG=-45.5,  p-value=0.009901 dG=-45.4,  p-value=0.009901

droSim1

dG=-38.2,  p-value=0.009901 dG=-38.0,  p-value=0.009901 dG=-37.9,  p-value=0.009901 dG=-37.8,  p-value=0.009901 dG=-37.7,  p-value=0.009901 dG=-36.2,  p-value=0.009901

droSec1

dG=-40.9,  p-value=0.009901 dG=-40.9,  p-value=0.009901 dG=-40.9,  p-value=0.009901 dG=-40.8,  p-value=0.009901 dG=-40.5,  p-value=0.009901

droYak2

dG=-43.0,  p-value=0.009901 dG=-42.9,  p-value=0.009901 dG=-42.8,  p-value=0.009901 dG=-42.2,  p-value=0.009901 dG=-42.1,  p-value=0.009901

droEre2

dG=-40.0,  p-value=0.009901 dG=-39.3,  p-value=0.009901 dG=-39.1,  p-value=0.009901

droAna3

dG=-13.1,  p-value=0.009901 dG=-12.2,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-9.4,  p-value=0.009901

dp4

dG=-22.3,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-16.1,  p-value=0.009901

droPer1

dG=-22.9,  p-value=0.009901 dG=-22.7,  p-value=0.009901 dG=-22.3,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-16.1,  p-value=0.009901

droWil1

dG=-31.6,  p-value=0.009901 dG=-31.6,  p-value=0.009901 dG=-31.6,  p-value=0.009901 dG=-31.6,  p-value=0.009901 dG=-31.1,  p-value=0.009901

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

dG=-3.3,  p-value=0.009901 dG=-3.3,  p-value=0.009901 dG=-3.2,  p-value=0.009901 dG=-3.2,  p-value=0.009901 dG=-3.0,  p-value=0.009901

Generated: 03/07/2013 at 04:59 PM