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

-34.9 -34.9 -34.8 -34.8 -34.4 -34.4

droSim1

-27.6 -27.6 -27.6 -27.6 -27.4 -27.4

droSec1

-30.5 -30.3 -30.1 -30.0 -30.0 -29.9

droYak2

-27.3 -27.3 -27.1 -27.1 -26.9 -26.9

droEre2

-25.9 -25.7 -25.5 -25.4 -25.4 -25.3

droAna3

-19.9 -19.5 -19.5 -19.4 -19.2 -19.2

dp4

-21.6 -21.4 -21.3 -21.2 -21.1 -21.1

droPer1

-25.0 -25.0 -24.8 -24.8 -24.5 -24.5

droWil1

-24.2 -24.1 -24.0 -23.9 -23.8 -23.7

droVir3

-40.2 -40.2 -40.2 -39.9 -39.9 -39.9

droMoj3

-37.4 -37.4 -37.4 -37.4 -37.2 -37.2

droGri2

-49.9 -49.9 -49.7 -49.7 -49.7 -49.7

Generated: 01/05/2013 at 05:22 PM