Secondary structure and small RNA-seq evidence for dme-mir-955

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:3299040-3299166 + TAAGGAACACTTTTTGGCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--ACAA-------------------------------------------------TT
droSim1 chr3L:2834561-2834687 + TAAAGAACACTTTTTGGCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAATCGCATTCAATTTCTGCACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--AAAA-------------------------------------------------TT
droSec1 super_2:3291343-3291466 + TAATAAACACTTTTTGGTC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAATCGCATTCAATTTCTGCAG---AGAGATGGTACGCTTAGAAACAACCTACA--AAAA-------------------------------------------------TT
droYak2 chr3L:3844747-3844864 + TAAAGTAAA---------C--AGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGT---GTGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--ATGA-------------------------------------------------GT
droEre2 scaffold_4784:5981989-5982116 + AAGGAATACACTTTTGTCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGT---GTGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--GCAA-------------------------------------------------GT
droAna3 scaffold_13337:7606422-7606539 + TGAAGGATGTTTTTTGAGA--AGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAAT----TTTTAACCATTCGCATTCAACCTTTGGACGGTAGAGATGGTCAGTGAGAAAGCAACCTA-----------------------------------------------------------
dp4 chr4_group1:2379981-2380081 + AATT----------TAAAA--AAATGAATAAATTCAAATGACAAAAATGTAAATGAATTAA-----------AAAATAAATTCAAATGATAAAAAGTAAA----------TGAATAAAAAAATAAAGTAAAA-------------------------------------------------TT
droPer1 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_180698:10215726-10215851 + ATTCAAATACTTTTGCGTTAAGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTTCGTTTGTTTTCTCTAATGGCATTCAACCTTGGAGCGATAGAGACGGCCAATCGAGAAACAGCCTAAA---------------------------------------------------------
droVir3 scaffold_12758:855562-855687 - TATGTATGGATCTCTCATC--AGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGA---GTTTTTCCTAGTGGCATTCAACCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAAA--CTAA-------------------------------------------------TA
droMoj3 scaffold_6680:1909563-1909732 - TCAGGTATCCAATATG-----GGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGT---GT-TTGGCTAGTCGCATTCAGCCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAAC---TGAAAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAATCATATAGAAATAGTT
droGri2 scaffold_15110:657067-657177 + TAAAG-----------------GTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGA---GT-TTGCCAAGTGGCATTCAGCCCCTGGACGCTAGAGATGGCCAACTGAAAAGCAACCTAAA--AA------------------------------------------------CAATC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:3299040-3299166 + TAAGGAACACTTTTTGGCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT----GTTTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA------------------------------------------------ACAATT
droSim1 chr3L:2834561-2834687 + TAAAGAACACTTTTTGGCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT----GTTTTGCCTAATCGCATTCAATTTCTGCACGGTAGAGATGGTACGCTTAGAAACAACCTAAA------------------------------------------------AAAATT
droSec1 super_2:3291343-3291466 + TAATAAACACTTTTTGGTC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT----GTTTTGCCTAATCGCATTCAATTTCTGCAG---AGAGATGGTACGCTTAGAAACAACCTACA------------------------------------------------AAAATT
droYak2 chr3L:3844747-3844864 + TAAAGTAAA---------C--AGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGT----GTGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA------------------------------------------------ATGAGT
droEre2 scaffold_4784:5981989-5982116 + AAGGAATACACTTTTGTCC--AGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGT----GTGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA------------------------------------------------GCAAGT
droAna3 scaffold_13337:7606422-7606539 + TGAAGGATGTTTTTTGAGA--AGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAAT-----TTTTAACCATTCGCATTCAACCTTTGGACGGTAGAGATGGTCAGTGAGAAAGCAACCTA--------------------------------------------------------
droWil1 scaffold_180698:10215726-10215851 + ATTCAAATACTTTTGCGTTAAGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTT-CGTTTGTTTTCTCTAATGGCATTCAACCTTGGAGCGATAGAGACGGCCAATCGAGAAACAGCCTAAA------------------------------------------------------
droVir3 scaffold_12758:855562-855687 - TATGTATGGATCTCTCATC--AGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGA----GTTTTTCCTAGTGGCATTCAACCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAAA------------------------------------------------CTAATA
droMoj3 scaffold_6680:1909563-1909732 - TCAGGTATCCAATATG-----GGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGT----GT-TTGGCTAGTCGCATTCAGCCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAACTGAAAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAATCATATAGAAATAGTT
droGri2 scaffold_15110:657067-657177 + TAAAG-----------------GTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGA----GT-TTGCCAAGTGGCATTCAGCCCCTGGACGCTAGAGATGGCCAACTGAAAAGCAACCTAAA-----------------------------------------------AACAATC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TAAAGAACACTTTTTGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTGTTTTGCCTAATCGCATTCAATTTCTGCACGGTAGAGATGGTACGCTTAGAAACAACCTAAA--AAAATTSizeHit CountTotal NormTotalGSM343915
Embryo
................................CATCGTGCAGAGGTTTGAGTGTC..........................................................................231395.00395395
................................CATCGTGCAGAGGTTTGAGTGT...........................................................................22184.008484
................................CATCGTGCAGAGGTTTGAGTG............................................................................21160.006060
.................................ATCGTGCAGAGGTTTGAGTGTC..........................................................................22129.002929
.........................................................................CATTCAATTTCTGCACGGTAGA..................................22117.001717
..............TGGCCAGCTAATCAACTCC................................................................................................1918.0088
.................................ATCGTGCAGAGGTTTGAGTGTCC.........................................................................2316.0066
.................................ATCGTGCAGAGGTTTGAGTGT...........................................................................2114.0044
................................CATCGTGCAGAGGTTTGAGT.............................................................................2013.0033
.................................ATCGTGCAGAGGTTTGAGTGTCCTG.......................................................................2512.0022
.............TTGGCCAGCTAATCAACTC.................................................................................................1911.0011
.................................ATCGTGCAGAGGTTTGAGTGTCCT........................................................................2411.0011
..........................................................................ATTCAATTTCTGCACGGTAGA..................................2111.0011
dp4
AA----------TTTAAAAAAATGAATAAATTCAAATGACAAAAATGTAAATGAATTAAA--------AAATAAATTCAAATGATAAAAAGTAAA----------TGAATAAAAAAATAAAGTAAAATTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-21.1,  p-value=0.009901

droSim1

dG=-28.1,  p-value=0.009901 dG=-28.1,  p-value=0.009901 dG=-28.1,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901

droSec1

dG=-20.2,  p-value=0.009901 dG=-20.2,  p-value=0.009901 dG=-20.2,  p-value=0.009901 dG=-19.9,  p-value=0.009901 dG=-19.9,  p-value=0.009901

droYak2

dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901

droEre2

dG=-22.0,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901

droAna3

dG=-26.4,  p-value=0.009901 dG=-26.4,  p-value=0.009901 dG=-26.4,  p-value=0.009901 dG=-26.3,  p-value=0.009901 dG=-26.3,  p-value=0.009901

dp4

dG=-3.4,  p-value=0.009901 dG=-2.9,  p-value=0.009901 dG=-2.7,  p-value=0.009901 dG=-2.7,  p-value=0.009901

droPer1

No secondary structure predictions returned

droWil1

dG=-24.5,  p-value=0.009901 dG=-24.5,  p-value=0.009901 dG=-24.5,  p-value=0.009901

droVir3

dG=-22.0,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901

droMoj3

dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.5,  p-value=0.009901

droGri2

dG=-24.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.6,  p-value=0.009901 dG=-24.2,  p-value=0.009901

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