Secondary structure and small RNA-seq evidence for dme-mir-4972

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:3636951-3637088 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCG--------------GC---------------------------------------------------------------------------------------TTTACAGATATATATATATATATCGTGTATATATCTGTGCGATCGGG-A-TTGAGACTGAGGTTGGT-----CCGAG-TACTTTTGTGGCCA--TTTACACC
droSim1 chr2L:3596396-3596533 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCAACTCG--------------GC---------------------------------------------------------------------------------------TTTATATATATGTATATATATCGTGTATATATATCTGAGAGATCGGG-A-TTGAGACTGAGGTTGGT-----CCGAG-TACTTTTGTGGCCA--TTTACACC
droSec1 super_5:1737908-1738045 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCG--------------GC---------------------------------------------------------------------------------------TTTATATATATGTATATATATCGTGTATATATATCTGAGAGATCGGG-A-TTGAGACTGAGGTTGGT-----CCGAG-TACTTTTGTGGCCA--TTTACACC
droYak2 chr2L:3630931-3631061 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCAACTCG--------------AC---------------------------------------------------------------------------------------TATATATGTATATATATA-------TATATATATCTGTGAGATCGGG-A-TTGAGACTGAGGTTGGT-----CTCAG-TACTTTTGTGGCCA--TTTACACC
droEre2 scaffold_4929:3675838-3675960 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCA--------------GC---------------------------------------------------------------------------------------TATATATATATGT---------------GTGTATCTGTGGGATCGGG-A-TTGAGACTGAGGTTGGT-----CTTAG-TACTTTTGTGGCCA--TTTGCACC
droAna3 scaffold_12916:5691742-5691836 - CACTTGCAAGGCATAAATCAAAAGCGCCGTAGGCCT-CCGCCACT------------------------------------------------------------------------------------------------------------------------------------------------ATGAGT-C-TGGAGTCTGGTGATGGT-----GGAGT-GCCTTTTGTGGCCA--TTGGCACC
dp4 chr4_group3:5095808-5095886 + CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTT-TGGAGTTTTTTGTGGCACAG-------------------------------------------------------------------------------------TGTGTGT--GTG----------------------------------------------------------------------------------TGTGTG
droPer1 super_1:6587322-6587402 + CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTT-TGGAGTTTTTTGTGGCACAG-------------------------------------------------------------------------------------TGTGTGTATGTG----------------------------------------------------------------------------------TGTGTG
droWil1 scaffold_180708:9512363-9512488 + CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTTCCACCTCT---------ATAT-------AGTATAATGTGTTCCACATACTCGAC---------------------------------------------------------------------------------------------------TTGGG-AGTTGAATTCGAAGTTG-T-----CCATG-T-CTTTTGTGGCCAATTTTACACC
droVir3 scaffold_12963:15108661-15108745 + CACTCGCGTGGCATAAATCAAATGCGTTGCAGGCCG-CCGGCGCT-------CCACGTT-----------------------GCACTCGACTC--------------------------------------------------------------CT-------------------------------------------------------------------C-TA--CTTGCGGCTA--GCAGCTCC
droMoj3 scaffold_6500:18077427-18077576 + CACTTGTGTGGCATAAATCAAATGCGCAGCAGGCCG-CCAGCTGA--------------------CGCTGACCGTGTT----GCACTCGAGTCGAG------------------------TTGAGTGGA---GTCAACTCGCCGCAGCTTTTCATTCGCATATACCCA-----------------------------------------GCCAAGCCAAG-----TGGTCTTTGGGGCCA--TTTACACG
droGri2 scaffold_15126:4287105-4287265 - CACTTGCATGGCATAAATCAAATGCGCCGCGGGCCT-TTGCTACG-----------------------------TGCCACATGCACTCGACTCTCGCCTCTCAACACGACTGACCGAACATTGGCTGGACAAGCCAAGCTGCAG------------------------------------------CAGATCGGGGCATTCCACTCCAAG---------------TGGTCTTTGAGGCCA--TTTGCACG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:3636951-3637088 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCTCGGCTTTACAGATATATATATATATATCGTGT--ATATATCTGTGCGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTTTGTGGCCATTTACACC
droSim1 chr2L:3596396-3596533 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAACTCGGCTTTATA--TATATGTATATATATCGTGTATATATATCTGAGAGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTTTGTGGCCATTTACACC
droSec1 super_5:1737908-1738045 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCTCGGCTTTATA--TATATGTATATATATCGTGTATATATATCTGAGAGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTTTGTGGCCATTTACACC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAACTCGGCTTTATA------------------TATATGTATATATATCGTGTATATATATCTGAGAGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTTTGTGGCCATTTACACCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCTGAGACT-----TTGGAGTTTTTTGTGGCACAGTGTGTGTGTGTGTGTG------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-23.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901

droSim1

dG=-18.9,  p-value=0.009901 dG=-18.6,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.5,  p-value=0.009901

droSec1

dG=-18.9,  p-value=0.009901 dG=-18.6,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.0,  p-value=0.009901 dG=-18.0,  p-value=0.009901

droYak2

dG=-15.4,  p-value=0.009901 dG=-15.2,  p-value=0.009901 dG=-15.0,  p-value=0.009901 dG=-15.0,  p-value=0.009901 dG=-14.8,  p-value=0.009901

droEre2

dG=-11.7,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-11.0,  p-value=0.009901

droAna3

dG=-5.1,  p-value=0.009901 dG=-4.2,  p-value=0.009901 dG=-4.1,  p-value=0.009901

dp4

dG=-6.8,  p-value=0.009901 dG=-5.9,  p-value=0.009901 dG=-4.6,  p-value=0.009901

droPer1

dG=-5.3,  p-value=0.009901 dG=-4.9,  p-value=0.009901 dG=-4.4,  p-value=0.009901 dG=-3.1,  p-value=0.009901

droWil1

dG=-8.8,  p-value=0.009901 dG=-8.6,  p-value=0.009901 dG=-8.3,  p-value=0.009901 dG=-8.0,  p-value=0.009901 dG=-7.9,  p-value=0.009901

droVir3

dG=-3.3,  p-value=0.009901 dG=-3.3,  p-value=0.009901 dG=-2.9,  p-value=0.019802 dG=-2.7,  p-value=0.009901 dG=-2.5,  p-value=0.009901

droMoj3

dG=-20.5,  p-value=0.009901 dG=-19.8,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.5,  p-value=0.009901

droGri2

dG=-22.1,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-21.3,  p-value=0.009901 dG=-21.3,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-20.1,  p-value=0.009901

Generated: 03/07/2013 at 06:18 PM