Secondary structure and small RNA-seq evidence for dme-mir-4960

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:463920-464051 + TGGAGTGACCAGCACAACACAAGGCCTGCCGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGAAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGG-G------ACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT
droSim1 chrX_random:776904-777034 + CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGGAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGGGG------CCT-T-GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droSec1 super_10:310837-310968 + CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGGAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGGG-------GCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droYak2 chrX:383437-383616 + TGCAATGCCCACCACAACACAAGGCCTGATGCCCGAGAAT-CGGTTTATTTCCTCCTCT------------------T-------------------------------------------------------------------------------CCGCAGGCCCAGGAGTCCGGCAGTC----------------GAGCAGTCGAGCTGTTCACCCGGTCAGTCCTT-GGTCCTTGGTCCTTGGGCCTTGGGCTTTCGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droEre2 scaffold_4644:409107-409303 + TGCAATGACCCTCACCACACAAGGCCCGATGCCCGGGAAT-CGGTTTATTTCCTCTTCT------------------T-------------------------------------------------------------------------------CCGCAGGCCCAGGAGTCCGGCAGTCCGACAGTCCAGCAGTCCGGCAGTCGAGTTGTCGAGTAGTCCAGTCATGAGGGGCTGGGGCCTTGGGCCTTGGGCTTACGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droAna3 scaffold_12929:357992-358198 + TGGAATGACC---ACAGCAGAAGGCCTTCTGCCAA-GACTTGGGTGTAGATATGAGTGTGTGTGGGTGTGGGTGTGTTTT--GGCCAGAATATGGTGGGTGATTGTGCAGGGAGGCGTGGCAGATGGGGG-GGCG-------GAGGATGAAGAAGAAGCAGTAGCAGAGGAG--------------------------------------------------------------------G------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
dp4 chrXL_group1e:196231-196421 + TGGAATGACC---ACGGCACAAGGCCT--TG-CCAAGACT-TGTTTTATTTTTTGCTGA------------------TTTGGGGGCAGGAACT-GTAGGTGCCT--GCCGCGCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAG---GACGCAGGAGGCTT-------------CGCAGGA----------------GAG--------------------------------------AA------CTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCAT
droPer1 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_180777:2769923-2769983 + CAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGATTGACG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droVir3 scaffold_12970:10710181-10710231 + G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droMoj3 scaffold_6473:10704148-10704209 - GGGG--------------------------------GGCTTGGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droGri2 scaffold_14853:6069294-6069344 - G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:463920-464051 + TGGAGTGACCAGCACAACACAAGGCCTGCCGCCCAAGAAACGCAAGCCCAGAAGTCCGGCAGTCGAGAATCACGAGGGACTGGGACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT
droSim1 chrX_random:776904-777034 + CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAAACGCAAGCCCAGGAGTCCGGCAGTCGAGAATCACGAGGGACTGGGGCCTTG-GCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droSec1 super_10:310837-310968 + CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAAACGCAAGCCCAGGAGTCCGGCAGTCGAGAATCACGAGGGACTGGGGCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGGAGTGACCAGCACATCACAAGGCCT------------------------------------------------------GGTGCCCAAGAAACGCAAGCC----------------------CAGGAGTCC-GGCAGTCGAGAATCACGAGGGACTGGGGCCTT-GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TGGAATGACC---ACGGCACAAGGCCTTGCCAAGACTTGTTTTATTTTTTGCTGATTTGGGGGCAGGAACTGTAGGTGCCTGCCGCGCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAGGACGCAGGAGGCTTCGCAGGAGAGAA---------------CTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCATSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-26.4,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-25.5,  p-value=0.009901

droSim1

dG=-22.3,  p-value=0.009901 dG=-22.3,  p-value=0.009901 dG=-22.3,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901

droSec1

dG=-29.4,  p-value=0.009901 dG=-28.9,  p-value=0.009901 dG=-28.9,  p-value=0.009901 dG=-28.8,  p-value=0.009901 dG=-28.8,  p-value=0.009901

droYak2

dG=-40.4,  p-value=0.009901 dG=-39.8,  p-value=0.009901 dG=-39.8,  p-value=0.009901 dG=-39.6,  p-value=0.009901 dG=-36.7,  p-value=0.009901

droEre2

dG=-49.3,  p-value=0.009901 dG=-48.7,  p-value=0.009901 dG=-48.5,  p-value=0.009901 dG=-48.4,  p-value=0.009901 dG=-48.3,  p-value=0.009901

droAna3

dG=-28.4,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.3,  p-value=0.009901 dG=-28.2,  p-value=0.009901 dG=-28.0,  p-value=0.009901

dp4

dG=-41.0,  p-value=0.009901 dG=-40.9,  p-value=0.009901 dG=-40.7,  p-value=0.009901 dG=-40.7,  p-value=0.009901 dG=-40.6,  p-value=0.009901

droPer1

No secondary structure predictions returned

droWil1

dG=-8.1,  p-value=0.009901 dG=-8.1,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.2,  p-value=0.009901 dG=-7.2,  p-value=0.009901

droVir3

dG=-2.1,  p-value=0.009901 dG=-1.2,  p-value=0.009901 dG=-1.2,  p-value=0.009901

droMoj3

dG=-4.0,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.7,  p-value=0.009901 dG=-3.5,  p-value=0.009901 dG=-3.5,  p-value=0.009901

droGri2

dG=-2.1,  p-value=0.019802 dG=-1.2,  p-value=0.009901 dG=-1.2,  p-value=0.009901

Generated: 03/07/2013 at 06:10 PM