Secondary structure and small RNA-seq evidence for dme-mir-4944

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:6338711-6338870 - AGA-TG-CCCAGACAGCAAAAGT----------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTTTTCTGCTT--CT--GCCGCTGAGCAAGTTTTAAATATTACCGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGACTACGTACATAAATATCTTGGCAAGTGT----------------------TT
droSim1 chr3R:15041591-15041748 + AGA-TG-CCCAGACAGCAAAAGT----------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT--CTGCTC--CT--GCCGCCTAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT----------------------TT
droSec1 super_0:15602732-15602889 + AGA-TA-CCCAGACAGCAAAAGC----------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT-TCTGCTC--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG--AAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT----------------------TT
droYak2 chr3R:10367066-10367225 - AGA-TG-CCCAGACAGCAAAAGT----------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTTCGCTGCTC--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT----------------------TT
droEre2 scaffold_4770:15270440-15270598 + AGA-TG-CCCAGACAGCAAAAGT----------------------------------------------------------------------------------------------------------------------------------AACTT-TCGTAATCGAAAAAGTTTCGCTTTTTT-GCTGCTT--CT--GCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGG------------------------------AAG-AAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGT----------------------TT
droAna3 scaffold_13340:761260-761417 + AGA-TGGCCCAGACAGCAAAAGT----------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTCGT------TTTTTTCCATC-CCGAACAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTTCGGA------------------------------GAG-GAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGCCAAATGT----------------------TT
dp4 chr2:7128424-7128589 + AGA-TG-G-CAGACGGCCCAAGG----------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTTTTCGC---TTTTTT--CTCAGTGGCCAAGTTTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAGA------------------------------AAGAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGGCAAATGT----------------------AC
droPer1 super_0:982713-982880 + AGA-TG-G-CAGACGGCCCAAGG----------------------------------------------------------------------------------------------------------------------------------AACTT-TGGTAATCGAAAAAGTTTCGCTTTTTT-TTTGCTTTTTT--CTCAGTGGCCAAGTTTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAGA------------------------------AATAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGGCAAATGT----------------------AC
droWil1 scaffold_181108:125373-125548 - AGA-TG-GG------GCAAAAGTATGTCGACTGAGGAAAACC-GGA--------------------------------------------------------------GAG----------------------CA------------------AACTTGTAGTAATCGAAAAAGTTTCGGTTTGTT------------------GTAGCCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGAA--G---------------------------AGAAAAAGTTATAATTATGCCGTAAGTACATAAATAACACGGCAAATGTGAC--------TT---T-----TT
droVir3 scaffold_13047:1304900-1305088 - AGAA----TAAGAAAGAA-----ATG-----TTAGGACGGCT-GGA--------------------------------------------------------------CAG----------------------GATTCAGTTTTGTTGCTGCTTACTG-CGGTAATCGAAAAAGTTTTGTT-----------------------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCTG--------------------------GAA-AAAAGTTATAATTATGGCGTAAGTACATAAATAACGCTGCAAATGTGCC------GCTTTTCT-----TT
droMoj3 scaffold_6540:5375448-5375637 - GGAATA-ATAAGAAAGAA-----ATG--------------CT-GGA--------------------------------------------------------------GAGGCACAGGCACAGTCTGGCTTGAGATTCAGTT----TGCTGCTTACGG-CGGTAATCGAAAAAGTTTT----------CTGTT-----------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCTG--------------------------GAA-AAAAGTTATAATTGTGGCGTAAGTACATAAATAACGCTGCAAATGC------------------------
droGri2 scaffold_14906:4949937-4950239 + AGAA----TAAGAAAGAA-----ATG-----TAAGCAACGCTCGGACAGATACAGATACAGAGACAGAGCCAGAGACAGAGCCAGAGACGGACACCGAAACTGAAACTGAGGCACA-GCACAG---GACTTGAGATACAGTTTTGTTGCTG----CTG-CGGTAATCGAAAAAGTTTGGTT-----------------------GTAGCCAAGTTTTAAATATTAACGCTTACTT-------ACAGCTGCAGAGCAGAGCTAAGCAGAAAAAAAAAATAAATAAAA-GAAAGTTATAATTATGGCGTAAGTACATAAATAACGCTGCAAATGTGCCAGAGTGGGGTTGGTAGGAGTT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:6338711-6338870 - AGATGCCCAGACAGCAAAAGTAACTTTCGTAATCGAAAAAGTTTCGCTTTTTTTTCTGCTTCTGCCGCTGAGCAAGTTTTAAATATTACCGCTTAGTTACAGCTGCAGGAAGAAAAGTTATAATTATGGACTACGTACATAAATATCTTGGCAAGTGTTT
droSim1 chr3R:15041591-15041748 + AGATGCCCAGACAGCAAAAGTAACTTTCGTAATCGAAAAAGTTTCGCTTTTTT--CTGCTCCTGCCGCCTAGCAAGTTTTAAATATTAACGCTTAGTTACAGCTGCAGGAAGAAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGTTT
droSec1 super_0:15602732-15602889 + AGATACCCAGACAGCAAAAGCAACTTTCGTAATCGAAAAAGTTTCGCTTTTTT-TCTGCTCCTGCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTTACAGCTGCAGGAAGA-AAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGTTT
droYak2 chr3R:10367066-10367225 - AGATGCCCAGACAGCAAAAGTAACTTTCGTAATCGAAAAAGTTTCGCTTTTTTCGCTGCTCCTGCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTTACAGCTGCAGGAAGAAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGTTT
droEre2 scaffold_4770:15270440-15270598 + AGATGCCCAGACAGCAAAAGTAACTTTCGTAATCGAAAAAGTTTCGCTTTTTT-GCTGCTTCTGCCGCCGAGCAAGTTTTAAATATTAACGCTTAGTTACAGCTGCAGGAAGAAAAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGTTT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AGATGCCCAGACAGCAAAAGTAACTTTCGTAATCGAAAAAGTTTCGCTTTTTT--CTGCTCCTGCCGCCTAGCAAGTTTTAAATATTAACGCTTAGTT-------ACAGCTGCAGGAAGAA-AAGTTATAATTATGGGCTAAGTACATAAATAACTTGGCAAGTGTTTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AGATGG-CAGACGGCCCAAGGAACTTTGGTAATCGAAAAAGTTTCGCTTTTTTCGCTT-TTTTCTCAGTGGCCAAGTTTTAAATATTAACGCTTAGTTACTCCGTACAGCTGCAGAAAGAAAAAGTTATAATTATGGCCTAAGTACATAAATAACTCGGCAAATGTACSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-24.9,  p-value=0.009901 dG=-24.8,  p-value=0.009901 dG=-24.4,  p-value=0.009901 dG=-24.0,  p-value=0.009901 dG=-23.9,  p-value=0.009901

droSim1

dG=-20.7,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.3,  p-value=0.009901 dG=-20.1,  p-value=0.009901

droSec1

dG=-20.1,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.2,  p-value=0.009901 dG=-19.2,  p-value=0.009901

droYak2

dG=-19.2,  p-value=0.009901 dG=-18.8,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-18.3,  p-value=0.009901

droEre2

dG=-18.7,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-17.8,  p-value=0.009901 dG=-17.8,  p-value=0.009901

droAna3

dG=-12.8,  p-value=0.009901 dG=-12.4,  p-value=0.009901 dG=-12.4,  p-value=0.009901 dG=-12.1,  p-value=0.009901 dG=-12.1,  p-value=0.009901

dp4

dG=-13.2,  p-value=0.009901 dG=-13.0,  p-value=0.009901 dG=-12.3,  p-value=0.009901

droPer1

dG=-13.7,  p-value=0.009901 dG=-13.5,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-13.1,  p-value=0.009901

droWil1

dG=-12.1,  p-value=0.009901 dG=-11.9,  p-value=0.009901

droVir3

dG=-9.1,  p-value=0.009901 dG=-8.4,  p-value=0.009901

droMoj3

dG=-9.1,  p-value=0.009901 dG=-8.7,  p-value=0.009901 dG=-8.5,  p-value=0.009901 dG=-8.5,  p-value=0.009901 dG=-8.4,  p-value=0.009901

droGri2

dG=-12.2,  p-value=0.009901 dG=-12.0,  p-value=0.009901 dG=-11.3,  p-value=0.009901 dG=-9.0,  p-value=0.009901

Generated: 03/07/2013 at 05:41 PM