Secondary structure and small RNA-seq evidence for dme-mir-3643

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:13653883-13653980 - GAATCCAAGCTGAACGTGAGTTT-A--TCTAAATATG-CCCATTTATCAATAG-TCATAC----------TTATTTA-----T-------GC-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droSim1 chr2R:12393703-12393800 - GAGTCCAAGCTGAACGTGGGTTT-A--TCTAGATACG-CCCATTTATCATTGG-TCATAC----------TTATTTA-----T-------GT-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droSec1 super_1:11152590-11152687 - GAGTCCAAGCTGAACGTGGGTTT-A--TCTATTTACG-CCCATTTATCATTGG-TCATAC----------TTATTTA-----T-------GT-TCCTTTA--ACGCCTTGCAGAGCTTCGAAAAAGAC
droYak2 chr2R:15527673-15527770 + GAATCCAAGCTGAACGTGGGTTC-A--TCTAGATACT-TCCATATATCAAAAG-CCGTAC----------TTATTTA-----T-------GT-TATTTAA--ACTGCTTGCAGAGCTTCGAAAAAGAC
droEre2 scaffold_4845:7883019-7883116 - GAATCCAAGCTGAACGTGGGTTT-T--TCTAGATACG-CCCATTTATCAATGG-CCCTAC----------TTATTTA-----T-------GC-ATTTTAA--ACTCCTTGCAGAGCTTCGAAAAAGAC
droAna3 scaffold_13266:10531972-10532067 + GAATCCAAGCTGAACGTTAGTTACT--TGTGCA-A---CTCGT------------CCAATCGGTTC-AATAACTAGA-----T-------CC-TCCTTTACATCTCCTTGTAGGGCTTCGAGAAGGAC
dp4 chr3:16466931-16467019 - GAATCCAAGCTGAACGTAAGTGC-TTAGCAA---ATG-TTCACTGAACCTTGAAT----------------CATTGCCTTTG------------------TTCTCGGTTCCAGAGCTTCGAAAAGGAC
droPer1 super_4:295271-295359 + GAATCCAAGCTGAACGTAAGTGC-TTAGCAA---ATG-TTCACTGAACCTTGAAT----------------CATTGCCTTTG------------------TTCTCGGTTCCAGAGCTTCGAAAAGGAC
droWil1 scaffold_181141:4609865-4609965 + GAATCAAAATTGAATGTAAGCTG---------A-AAA------------TTTAATTT---ATATTTTGTTTTCTCCTATTTACATACCACGTGTCCTTCA--CTCAATTACAGAGCTTCGAAAAGGAT
droVir3 scaffold_12875:16919908-16919994 - GAATCCAAACTAAATGTGAGTAT-C--TCCTAA-TCGCCTCAT------------CCAAT----------TCATTTT-----T-------GA-CCCTTTG--CCTACTTTTAGAACTTTGAAAAAGAC
droMoj3 scaffold_6496:11084070-11084155 + GAATCTAAACTAAATGTAGGTAT-A--GTAA---TAG-ATGAGTTTTTCTTTTAT----------------TTTAACC-----------------TTTGG--CCCGCTTGCAGAACTTTGAGAAGGAC
droGri2 scaffold_15245:16459236-16459327 - GAATCCAAACTAAATGTGAGATACC--TCTAAA-ACAAATCAT------------AA---AGATTTTGATGTATTGAGATTA------------------TGTACATTTGCAGAACTTTGAGAAAGAC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:13653883-13653980 - GAATCCAAGCTGAACGTGAGTTT-A--TCTAAATATG-CCCATTTATCAATAG-TCATAC----------TTATTTA-----T-------GC-TCCTTTA--ACTCCTTGCAGAGCTTCGAAAAAGAC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GAGTCCAAGCTGAACGTGGGT--TTATCTAGATACGCCCATTTATCATTG-GTCATACTTATTTATGTTCCTTTAACTC---CTTGCAGAGCTTCGAAAAAGACSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GAATCCAAGCTGAACGTAAGTGCTTAGC---AAATGTTCACTGAACCTTGAATCAT---T--------GCCTTTG-TTCTCGGTTCCAGAGCTTCGAAAAGGACSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-5.4 -4.8 -4.5 -4.5

droSim1

-9.6 -8.6

droSec1

-9.7 -8.9 -8.8

droYak2

-4.9 -4.4 -4.3 -4.3 -4.2 -4.1

droEre2

-8.8 -8.8 -8.6 -8.5 -8.4 -8.2

droAna3

-7.9 -7.8 -7.5 -7.4 -7.2 -7.1

dp4

-10.3 -9.5 -9.4 -9.3

droPer1

-10.3 -9.5 -9.4 -9.3

droWil1

-4.8 -4.7 -4.7 -4.6 -4.1 -4.0

droVir3

-2.3 -2.1 -1.5 -1.3 -1.3

droMoj3

-7.5 -7.2 -7.1 -6.8 -6.6 -6.5

droGri2

-6.4 -5.8 -5.5

Generated: 01/05/2013 at 05:18 PM