Secondary structure and small RNA-seq evidence for dme-mir-4959

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19063148-19063296 - TGCTCATGGCCCTGATGTCCGGTTTGAACCTTCTGTGCCGGCTGGCCATGATTTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGTTGCGTTTCATGACCAAACGGCATGTGAAGCGTGCCCTGCGGGACCTGACCATCGGC
droSim1 chrX:14724057-14724205 - TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droSec1 super_8:1352288-1352436 - TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droYak2 chrX:17654811-17654959 - TACTGATGGCCCTGATGTCTGGCCTAAATCTCCTCTGCCGGCTGGCCATGATCTGCAGCGGGTATCTTCGGGAGCAGATGATACGCAGCCAGTTGCGGTTCATGACCAAGCGGCATGTGAAGCGCGCCCTGCGCGACCTCACCATCGGC
droEre2 scaffold_4690:9326382-9326530 - TGCTGATGGCCCTGATTTCCGGCCTGAACCTCCTCTGCCGGCTGGCCATGATCTGCAGCAGGTATCTACGGGAGCAGATGATCCGCAGCCAGCTGCGGTTCATGTCCAAGCGGCATGTGAAGCGCGCCCTACGGGACCTCACCATCGGC
droAna3 scaffold_12903:667658-667806 + TCCTGATGGCCCTGATGTCCGGCCTGAATTTGGTCTGTCGCGTGGCGATGATTATCAGCAAGACCCTAAGAGAGCAGATGATCCGGAGCCAGTTGAGGTTCATGAAGAAGCGGCATGTCCAGAGGGCGCTGAGGGATCTGACGATCGGG
dp4 chrXL_group1e:10756223-10756371 - TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTGCGCGACCTCACCATCGGG
droPer1 super_14:190427-190575 - TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTTCGCGACCTCACCATCGGG
droWil1 scaffold_181096:8247011-8247159 - TGCTGATGGCCATCATGTCGGGCCTCAATCTACTCTGTCGCCTGGCCATGATGCTGAGCAAGAGTGTGCGTGAGCAAATGATTCGCAGTCAATTGCGTTTTATGCCCAAACGGCATATCCAACGAGCTCTCAGGGATCTAACCATTGGC
droVir3 scaffold_12726:998444-998592 - TGCTGATGGCCTTCATGTCCGGCCTGAACCTGCTCTGCCGTCTGGCCATGATGCTCAGCCGGACGCTGCGTGAGCTGATGATACGCAGCCAATTGCGCTTCATGACCAAGCAGCATGTACAGCGCGTTTTCCGGGATCTAACCATCGGT
droMoj3 scaffold_6473:9166585-9166733 + TGCTGATGGCCTTCATGTCCGGCCTGAATCTGCTCTGTCGCCTGGCCATGATGCTCAGCCGGACGCTGCGCGAGCTGATGATACGCAGCCAATTGCGCTATATGACCAAACAGCATGTGCAGCACGTCTTCAGGGATCTGACCATCGGC
droGri2 scaffold_14853:5433396-5433544 - TCCTCATGGCGATCATCGCTGGCCTAAATCTGCTCTGTCGCCTAACCATGATGGTCAGCCGGACGCTGCGCGAACTGATGATTCGCAGCCAGTTGCGATTCATGACCAAAGAGCATGTGCAGCGCATCTTTAGCCATTTAACCATCGGC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19063148-19063296 - TGCTCATGGCCCTGATGTCCGGTTTGAACCTTCTGTGCCGGCTGGCCATGATTTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGTTGCGTTTCATGACCAAACGGCATGTGAAGCGTGCCCTGCGGGACCTGACCATCGGC
droSim1 chrX:14724057-14724205 - TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droSec1 super_8:1352288-1352436 - TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTATCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGC
droYak2 chrX:17654811-17654959 - TACTGATGGCCCTGATGTCTGGCCTAAATCTCCTCTGCCGGCTGGCCATGATCTGCAGCGGGTATCTTCGGGAGCAGATGATACGCAGCCAGTTGCGGTTCATGACCAAGCGGCATGTGAAGCGCGCCCTGCGCGACCTCACCATCGGC
droEre2 scaffold_4690:9326382-9326530 - TGCTGATGGCCCTGATTTCCGGCCTGAACCTCCTCTGCCGGCTGGCCATGATCTGCAGCAGGTATCTACGGGAGCAGATGATCCGCAGCCAGCTGCGGTTCATGTCCAAGCGGCATGTGAAGCGCGCCCTACGGGACCTCACCATCGGC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TGCTCATGGCCCTGATGTCCGGCTTGAACCTTCTGTGCCGGCTGGCCATGATCTGCAGCAGGTACCTCCGAGAGCAGATGATACGCAGCCAGCTGCGTTTCATGACCAAGCGGCATGTGAAGCGTGCCCTGCGTGACCTGACCATCGGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TCCTGATAGCCATCATATCCGGCGTGAATATCCTCTTCCGGCTGGCCATGCTGTCCATCAAGAGTCTGCGCGAGAAGATGATCCGCAGCCAGCTGTCCTTCATGACCAAACGACATGTGCAGCGGGCCCTGCGCGACCTCACCATCGGGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-30.4,  p-value=0.009901 dG=-30.2,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.6,  p-value=0.009901 dG=-29.5,  p-value=0.009901

droSim1

dG=-32.1,  p-value=0.009901 dG=-31.8,  p-value=0.009901 dG=-31.1,  p-value=0.009901 dG=-30.9,  p-value=0.009901

droSec1

dG=-32.5,  p-value=0.009901 dG=-32.3,  p-value=0.009901 dG=-32.1,  p-value=0.009901 dG=-31.8,  p-value=0.009901 dG=-31.8,  p-value=0.009901

droYak2

dG=-37.0,  p-value=0.009901

droEre2

dG=-37.9,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-36.9,  p-value=0.009901 dG=-36.9,  p-value=0.009901

droAna3

dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-17.5,  p-value=0.009901

dp4

dG=-19.3,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-19.0,  p-value=0.009901

droPer1

dG=-19.3,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.1,  p-value=0.009901 dG=-19.0,  p-value=0.009901 dG=-19.0,  p-value=0.009901

droWil1

dG=-21.8,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-21.0,  p-value=0.009901

droVir3

dG=-28.8,  p-value=0.009901 dG=-28.8,  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=-27.6,  p-value=0.009901

droMoj3

dG=-21.1,  p-value=0.009901 dG=-20.4,  p-value=0.009901 dG=-20.2,  p-value=0.009901 dG=-18.6,  p-value=0.009901

droGri2

dG=-19.6,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-18.8,  p-value=0.009901 dG=-17.4,  p-value=0.009901

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