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

-52.8 -52.5 -52.3 -52.2 -52.0 -51.9

droSim1

-44.7 -44.4 -44.4 -44.3 -44.2 -44.1

droSec1

-47.8 -47.8 -47.8 -47.7 -47.4 -47.2

droYak2

-49.8 -49.7 -49.6 -49.6 -49.5 -49.4

droEre2

-46.8 -46.6 -46.1 -45.9 -45.9

droAna3

-21.5 -21.4 -20.6 -20.5

dp4

-43.2 -43.0 -42.8 -42.8 -42.6 -42.5

droPer1

-43.1 -42.9 -42.7 -42.7 -42.5 -42.4

droWil1

-34.5 -34.5 -34.4 -34.4 -33.8 -33.8

droVir3

0.0

droMoj3

No secondary structure predictions returned

droGri2

-4.9 -4.9 -4.8 -4.5 -4.4 -4.4

Generated: 01/05/2013 at 05:10 PM