Secondary structure and small RNA-seq evidence for dme-mir-4916

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:9130478-9130566 - AAGTACTCAAGATAAG--TGGGT-GTTCTTG--GAAATTCGCC-TCGATCGGTAGCTAAA---------------------------------TTTCTGATTACTCCTAAAAGCCT-TTTGGATTGAGC
droSim1 chrX:7292594-7292672 - A---------GATAAG--TGGGT-GTTCTTG--GAAATTCGCC-TCGATCGGTA-CTAAA---------------------------------TTTCTGATTACTCCTAAAAGCCT-TTTGGATTGAGC
droSec1 super_68:18213-18301 - AAGTACTCAAGATAAG--TGGGT-GTTCTTG--GAAATTCGCC-TCGATCGGTAGCTAAA---------------------------------TTTCTGATTACTCCTAAAAGCCT-TTTGGATTGAGC
droYak2 chrX:17726636-17726725 - AAGTTCTCAAGATAAG--TGGGT-GTTCTTG--GAAATTCGCCTTCGATCGGTTGCTAAA---------------------------------TTTCTGATTACCCCTAAAAGCCT-TTTGGATTGAGC
droEre2 scaffold_4690:5984818-5984906 + AAGTTCTCAAGATAAG--TGGGT-GTTCTTG--GAAATTCGCC-TCGTTCGGTAGCTAAA---------------------------------TTTCTAATTACTCCCAAAAGCCT-TTTGGATTGAGC
droAna3 scaffold_13047:993021-993104 - AAAACCTGAGAATAAG--TGGGTAGTTCCGAGCGAAAGACTCC-TCCATCTTAA---------------------------------------CATCCATTT--CCCGTTCAGCCT-TTTGGATTGAGC
dp4 chrXL_group1e:1170761-1170857 + AGCTGCTCAAGATAAG--TGGGT----TCCG--CAGATACGTTTTTCCTCTGCAG-----------------------ACTCGAGAGTCTCTTTTTTTGGCTTTCGCCCACAGCCT-TTTGGATAGAGC
droPer1 super_30:24276-24372 - AGCTGCTCAAGATAAG--TGGGT----TCCG--CAGATTCGTGTTTCCCCTACAG-----------------------ACTCGTGAGTCTCTTTTTTTGGCTTTCGCCCACAGCCT-TTTGGATAGAGC
droWil1 scaffold_181096:7487008-7487059 + TTGATTACTACAT--------------------------------------------TGATTTCAACTTTCA---------------------T-----------TTGATAAGCCT-TTTGGATTGAGC
droVir3 scaffold_13052:1731753-1731829 + AAAATTTAAATAAATA--TATGT-GTAATTT--GAATACTGCC-TCGATGGTTAGCTACG---------------------------------TTTTTTA------------TTCT-TATGTACCTCTT
droMoj3 scaffold_6498:2397368-2397459 + TAATATTTGAAATTAGGCTTATT-GTTATTAA-TAAAGCCTCA-TTTTTCTGCA-CTTGG---------------------------------CTTTAAATTATTTTTCAAAATTTGGAGATATTGAGC
droGri2 scaffold_15203:7061820-7061918 + AAGAGCTTAAGATAAG--TATGT-GTTCCGT--GTGATAAAAG--GAATCTTCAG----A------------CAGCGAACT-GA---TCGCC-TTACTGAATCCG-CTTGCAGTCT-TTTGGATTGAGC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:9130478-9130566 - AAGTACTCAAGATAAGTGGGTGTTCTTGGAAATTCGCC-TCGATCGGTAGCTAAATTTCTGATTACTCCTAAAAGCCTTTTGGATTGAGC
droSim1 chrX:7292594-7292672 - A---------GATAAGTGGGTGTTCTTGGAAATTCGCC-TCGATCGGTA-CTAAATTTCTGATTACTCCTAAAAGCCTTTTGGATTGAGC
droSec1 super_68:18213-18301 - AAGTACTCAAGATAAGTGGGTGTTCTTGGAAATTCGCC-TCGATCGGTAGCTAAATTTCTGATTACTCCTAAAAGCCTTTTGGATTGAGC
droYak2 chrX:17726636-17726725 - AAGTTCTCAAGATAAGTGGGTGTTCTTGGAAATTCGCCTTCGATCGGTTGCTAAATTTCTGATTACCCCTAAAAGCCTTTTGGATTGAGC
droEre2 scaffold_4690:5984818-5984906 + AAGTTCTCAAGATAAGTGGGTGTTCTTGGAAATTCGCC-TCGTTCGGTAGCTAAATTTCTAATTACTCCCAAAAGCCTTTTGGATTGAGC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
A---------GATAAGTGGGTGTTCTTGGAAATTCGCCTC-GATCGGTA-----------CTAAATTTCTGATTACTCCTAAAAGCCTTTTGGATTGAGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AGCTGCTCAAGATAAGTGGGTTC---CGCAGATACGTTTTTCCTCTGCAGACTCGAGAGTCTCTTTTTTTGGCTTTCGCCCACAGCCTTTTGGATAGAGCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-12.9,  p-value=0.009901

droSim1

dG=-13.5,  p-value=0.009901 dG=-12.5,  p-value=0.009901

droSec1

dG=-12.9,  p-value=0.009901

droYak2

dG=-12.4,  p-value=0.009901 dG=-12.4,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-12.0,  p-value=0.009901 dG=-12.0,  p-value=0.009901

droEre2

dG=-16.1,  p-value=0.009901

droAna3

dG=-7.6,  p-value=0.009901 dG=-7.0,  p-value=0.009901

dp4

dG=-22.5,  p-value=0.009901 dG=-21.6,  p-value=0.009901

droPer1

dG=-16.1,  p-value=0.009901

droWil1

dG=0.0,  p-value=1.0 dG=0.4,  p-value=1.0

droVir3

dG=-3.0,  p-value=0.009901 dG=-3.0,  p-value=0.009901 dG=-2.4,  p-value=0.009901 dG=-2.3,  p-value=0.009901 dG=-2.1,  p-value=0.009901

droMoj3

dG=-7.5,  p-value=0.009901 dG=-7.2,  p-value=0.009901 dG=-6.9,  p-value=0.009901

droGri2

dG=-12.1,  p-value=0.009901 dG=-11.6,  p-value=0.009901 dG=-11.4,  p-value=0.009901 dG=-11.4,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-11.0,  p-value=0.009901

Generated: 03/07/2013 at 05:33 PM