Secondary structure and small RNA-seq evidence for dme-mir-4910

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:4817801-4817896 - GGGTGAAACAGGCAGGTTTGTATGGAAT---TCCATGAGCTT--------------------------CAAAGTAATGCTTCTAACTCTGTGGTTTTTC-ATA-----TTTCCCAGTGGCAAGAGCACCCA
droSim1 chr2L:4687585-4687681 - GGGTGAAACAGGCAGGTTTGTATGGAAT---TCCAGAAGCTC--------------------------CAAAGTAATCTTTCTAACTCTGCGGGTTTTCTATC-----TTTCCCAGTGGCAAGAGCACCCA
droSec1 super_5:2913658-2913754 - GGGTGAAACAGGCAGGTTTGTATGGAAT---TCCAGGTGTTC--------------------------CAAAGTAATCTTTCTAGCTCTGTGGTTTTTTCATA-----TTTCCCAGTGGCAAGAGCACCCA
droYak2 chr2L:4827662-4827759 - GGGTGAAACAGGCAGGTTTGTTTGGAAC---TCCACAAGAT-------------------------TTCAAGGTATTCCTTCTAACTCTGTGGTTTTTCCACA-----TTTTCCAGTGGGAAAAGCACCCA
droEre2 scaffold_4929:4898740-4898837 - GGGTGAAACAGGCAGGTGTGTATGCAAT---TCCAAAAGGT-------------------------CTCAATGTATTCCTTCTAACTCTGTGGTTTTTCTATA-----TTTCCCAGTGGCAAGAGCACCCA
droAna3 scaffold_12916:9386286-9386375 - GGGCGAGACCGGCAGGTGAGAATACAAT---TCTACAACCCA--------------------------TACCCTTGTTTTCA------TATCATTTTTT-CAA-----TTTTTCAGTGGCAAGAGCACCCA
dp4 chr4_group3:3567830-3567920 - GGGCGAAACAGGAAGGTGAGTGAGAAGCAAAT----------------ATGTATGCCCCAAGAAATCCTAACGA----------------TC--------ATATTTTCCCCTTCAGCGGCAAGAGCACACA
droPer1 super_1:5048029-5048119 - GGGCGAAACAGGAAGGTGAGTGAGAAGCAAAT----------------ATGTATGCCCCAAGAAATCCTAACGA----------------TC--------ATATTTTCCCCTTCAGCGGCAAGAGCACACA
droWil1 scaffold_180772:7924021-7924113 + CGGAGAGACGGGCAGGTAATT----AAA---ACCATAAGGTTACCTTAATGTATATTTAAAGTATTTAT-----------------------G---TACGATA-----TTTTGCAGTGGAAAGAGCACTCA
droVir3 scaffold_13246:521378-521407 + GGGCGAGACGGGC-----------------------------------------------------------------------------------------------------AGCGGGAAGAGCACGCA
droMoj3 scaffold_6500:7585086-7585115 - GGGCGAGACGGGG-----------------------------------------------------------------------------------------------------TCTGGCAAAACGACGCA
droGri2 scaffold_15252:16729554-16729583 - GGGTGAAACTGGC-----------------------------------------------------------------------------------------------------AGTGGGAAGAGCACACA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:4817801-4817896 - GGGTGAAACAGGCAGGTTTGTATGGAATTCCATGAG-CTTCAAAGTAATGCTTCTAACTCTGTGGTTTTT-CATATTTCCCAGTGGCAAGAGCACCCA
droSim1 chr2L:4687585-4687681 - GGGTGAAACAGGCAGGTTTGTATGGAATTCCAGAAG-CTCCAAAGTAATCTTTCTAACTCTGCGGGTTTTCTATCTTTCCCAGTGGCAAGAGCACCCA
droSec1 super_5:2913658-2913754 - GGGTGAAACAGGCAGGTTTGTATGGAATTCCAGGTG-TTCCAAAGTAATCTTTCTAGCTCTGTGGTTTTTTCATATTTCCCAGTGGCAAGAGCACCCA
droYak2 chr2L:4827662-4827759 - GGGTGAAACAGGCAGGTTTGTTTGGAACTCCACAAGATTTCAAGGTATTCCTTCTAACTCTGTGGTTTTTCCACATTTTCCAGTGGGAAAAGCACCCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGGTGAAACAGGCAGGTTTGTATGGA---ATTCCAGAAGCTCCAAAGTAATCTTTCTAACTCTGCGGGTTTTCTATC-----TTTCCCAGTGGCAAGAGCACCCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GGGCGAAACAGGAAGGTGAGTGAGAAGCAAATATGTATGCCCCA-AGAAATCCTAACGA------------TC-ATATTTTCCCCTTCAGCGGCAAGAGCACACASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-15.5 -14.5

droSim1

-10.8 -10.8 -10.8 -10.8 -10.5

droSec1

-11.9 -11.5 -11.1 -11.1 -10.9

droYak2

-14.8 -14.8 -14.4 -14.3 -14.3 -14.1

droEre2

-3.7 -3.5 -3.4 -3.3 -3.1 -3.0

droAna3

-4.3 -3.3

dp4

-3.6 -3.4 -3.2 -3.0 -2.9 -2.9

droPer1

-3.6 -3.4 -3.2 -3.0 -2.9 -2.9

droWil1

-6.4 -6.4 -5.8 -5.7 -5.7

droVir3

0.0

droMoj3

0.0

droGri2

0.0

Generated: 01/05/2013 at 05:19 PM