Secondary structure and small RNA-seq evidence for dme-mir-137

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:11952744-11952864 - TTACGATGGCGT------------CGC--------------------------------CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGAAA--TCC-AAATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATAAAA---------------------------------AGAG
droSim1 chr2R:10688339-10688459 - TTACGATGGCGT------------CGC--------------------------------CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGAAA--TCC-AAATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATCAAA---------------------------------AGCG
droSec1 super_1:9448872-9448992 - TTACGATGGCGT------------CGC--------------------------------CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGAAA--TCC-AAATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATCAAA---------------------------------AGCG
droYak2 chr2R:17032219-17032325 + CC---------------------------------------------------------CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGACA--TCC--AATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATTAAA---------------------------------AAAG
droEre2 scaffold_4845:13905048-13905167 + TTACGGTGGCGA--------------------------------------------CTCCAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGACA--TCC--AATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATCAAA---------------------------------GGGG
droAna3 scaffold_13266:15447223-15447345 + TTAAAGTGGCAA-------------------------------------------CCTGGAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACGTGAAA--TGCGAAATGTTATTGCTTGAGAATACACGTAGTTCAGAGAGATTTGTTCAGCAATCGAA---------------------------------GTGG
dp4 chr3:16385856-16386036 - TTAAGATGACAG------------CGACGG-----CCAAGGCAATGCCGACGGCGACTAGAATCTTCAACGGCCACGTGTATACTCATAGCTATAACCTGATA--TCC-GAATGTTATTGCTTGAGAATACACGTAGTTTAACAAGATTCGTTCAGCAATCAAACTGAAACGGAAAGTGTCTGTGAAAGGTGTCCTTAAAG
droPer1 super_4:376928-377074 + TTAAGATGACAG------------CGACGGCCACGCCACGGCAATGCCGACGGCGACTAGAATCTTCAACGGCCACGTGTATACTCATAGCTATAACCTGATA--TCC-GAATGTTATTGCTTGAGAATACACGTAGTTTAACAAGATTCGTTCAGCAATCA---------------------------------------
droWil1 scaffold_181141:1110993-1111093 - TT----------------------------------------------------------------TAATGGCCACGTGTATTCTTATAGCTGTAACCTGTTA--TACAAAATGTTATTGCTTGAGAATACACGTAGTTAA-CTAGATTCGTTCAACGGGTCAA---------------------------------ACAA
droVir3 scaffold_10468:1951-2100 - GTACGTCGGAGCAGACACGACAGCGG---------ACACAACAAT-----TGGAAATTGGAATCTGAAATGGCCACGTGTATGCTCGTAGCTATAACCTGTACAATC--AAATGTTATTGCTTGAGAATACACGTAGTTAA-CAAGATTCTCTCAACGATCCAA----------------------------------TAA
droMoj3 scaffold_6496:10610032-10610171 + CAACGGA-GTGT------------GGA---------CAC---AAT-----TGGAAATTGGAATCGGCAATGGCCACGTGTATGCTCGTAGCTATAACTGGTACAATC--AAATGTTATTGCTTGAGAATACACGTAGTTAG-CCAGATTCGCCCAACATGGCAATGGCA----------------------------ACAT
droGri2 scaffold_15245:16918481-16918602 - GGAGATTGGAAA-------------------------------------------ATTAAAATCTGAAATGGCCACGTGTATGCTCGTAGCTATAACCTGAACAATC--AAATGTTATTGCTTGAGAATACACGTAGTTAA-CAAGATTGCCTCAACGACTCCA---------------------------------ATAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:11952744-11952864 - TTACGATGGCGT------------CGC--------------------------------CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGAAA--TCC-AAATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATAAAA---------------------------------AGAG
droSim1 chr2R:10688339-10688459 - TTACGATGGCGT------------CGC--------------------------------CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGAAA--TCC-AAATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATCAAA---------------------------------AGCG
droSec1 super_1:9448872-9448992 - TTACGATGGCGT------------CGC--------------------------------CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGAAA--TCC-AAATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATCAAA---------------------------------AGCG
droYak2 chr2R:17032219-17032325 + CC---------------------------------------------------------CAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGACA--TCC--AATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATTAAA---------------------------------AAAG
droEre2 scaffold_4845:13905048-13905167 + TTACGGTGGCGA--------------------------------------------CTCCAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGACA--TCC--AATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATCAAA---------------------------------GGGG
droAna3 scaffold_13266:15447223-15447345 + TTAAAGTGGCAA-------------------------------------------CCTGGAATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACGTGAAA--TGCGAAATGTTATTGCTTGAGAATACACGTAGTTCAGAGAGATTTGTTCAGCAATCGAA---------------------------------GTGG
dp4 chr3:16385856-16386036 - TTAAGATGACAG------------CGACGG-----CCAAGGCAATGCCGACGGCGACTAGAATCTTCAACGGCCACGTGTATACTCATAGCTATAACCTGATA--TCC-GAATGTTATTGCTTGAGAATACACGTAGTTTAACAAGATTCGTTCAGCAATCAAACTGAAACGGAAAGTGTCTGTGAAAGGTGTCCTTAAAG
droPer1 super_4:376928-377074 + TTAAGATGACAG------------CGACGGCCACGCCACGGCAATGCCGACGGCGACTAGAATCTTCAACGGCCACGTGTATACTCATAGCTATAACCTGATA--TCC-GAATGTTATTGCTTGAGAATACACGTAGTTTAACAAGATTCGTTCAGCAATCA---------------------------------------
droWil1 scaffold_181141:1110993-1111093 - TT----------------------------------------------------------------TAATGGCCACGTGTATTCTTATAGCTGTAACCTGTTA--TACAAAATGTTATTGCTTGAGAATACACGTAGTTAA-CTAGATTCGTTCAACGGGTCAA---------------------------------ACAA
droVir3 scaffold_10468:1951-2100 - GTACGTCGGAGCAGACACGACAGCGG---------ACACAACAAT-----TGGAAATTGGAATCTGAAATGGCCACGTGTATGCTCGTAGCTATAACCTGTACAATC--AAATGTTATTGCTTGAGAATACACGTAGTTAA-CAAGATTCTCTCAACGATCCAA----------------------------------TAA
droMoj3 scaffold_6496:10610032-10610171 + CAACGGA-GTGT------------GGA---------CAC---AAT-----TGGAAATTGGAATCGGCAATGGCCACGTGTATGCTCGTAGCTATAACTGGTACAATC--AAATGTTATTGCTTGAGAATACACGTAGTTAG-CCAGATTCGCCCAACATGGCAATGGCA----------------------------ACAT
droGri2 scaffold_15245:16918481-16918602 - GGAGATTGGAAA-------------------------------------------ATTAAAATCTGAAATGGCCACGTGTATGCTCGTAGCTATAACCTGAACAATC--AAATGTTATTGCTTGAGAATACACGTAGTTAA-CAAGATTGCCTCAACGACTCCA---------------------------------ATAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTACGATGGCGTCGCC---------------------------AATCTCCAATGGCCACGTGTATGCTCGTAGCTATAACCTGAAATCCAAATGTTATTGCTTGAGAATACACGTAGTTCACCGAGATTTGTTCAGCAATCAAA---------------------------------AGCGSizeHit CountTotal NormTotalGSM343915
Embryo
...............................................................................................TATTGCTTGAGAATACACGTAG................................................................221240.00240240
...............................................................................................TATTGCTTGAGAATACACGTAGT...............................................................2319.0099
...............................................................................................TATTGCTTGAGAATACACGTA.................................................................2119.0099
.........................................................ACGTGTATGCTCGTAGCTATAAC.....................................................................................................2318.0088
.........................................................ACGTGTATGCTCGTAGCTATA.......................................................................................................2112.0022
..............................................................................................TTATTGCTTGAGAATACACGTA.................................................................2211.0011
dp4
TTAAGATGACAGCGACGGCCAAGGCAATGCCGACGGCGACTAGAATCTTCAACGGCCACGTGTATACTCATAGCTATAACCTGATATCCGAATGTTATTGCTTGAGAATACACGTAGTTTAACAAGATTCGTTCAGCAATCAAACTGAAACGGAAAGTGTCTGTGAAAGGTGTCCTTAAAGSizeHit CountTotal NormTotalGSM343916
Embryo
GSM444067
Head
...............................................................................................TATTGCTTGAGAATACACGTAG................................................................2211204.001204437767
...............................................................................................TATTGCTTGAGAATACACGTA.................................................................211139.0013914125
.........................................................ACGTGTATACTCATAGCTATAAC.....................................................................................................23187.0087825
...............................................................................................TATTGCTTGAGAATACACGT..................................................................20161.0061160
...............................................................................................TATTGCTTGAGAATACACGTAGT...............................................................23127.00271116
................................................................................................ATTGCTTGAGAATACACGTAGT...............................................................22119.0019514
................................................................................................ATTGCTTGAGAATACACGTA.................................................................20114.0014014
........................................................CACGTGTATACTCATAGCTATAA......................................................................................................23110.001082
................................................................................................ATTGCTTGAGAATACACGTAG................................................................2117.00725
................................................................................................ATTGCTTGAGAATACACGT..................................................................1917.00707
.........................................................ACGTGTATACTCATAGCTATAA......................................................................................................2215.00541
.........................................................ACGTGTATACTCATAGCTATA.......................................................................................................2115.00532
........................................................CACGTGTATACTCATAGCTATA.......................................................................................................2214.00440
...............................................................................................TATTGCTTGAGAATACACG...................................................................1913.00303
.................................................................................................TTGCTTGAGAATACACGTAG................................................................2012.00202
..............................................................................................TTATTGCTTGAGAATACACGT..................................................................2112.00202
.................................................................................................TTGCTTGAGAATACACGTAGTT..............................................................2212.00211
.................................................................................................TTGCTTGAGAATACACGTAGT...............................................................2111.00101
.........................................................ACGTGTATACTCATAGCTAT........................................................................................................2011.00101
...................................................................................................GCTTGAGAATACACGTAG................................................................1811.00110
................................................................................................ATTGCTTGAGAATACACGTAGTT..............................................................2311.00101
.........................................................ACGTGTATACTCATAGCTA.........................................................................................................1911.00110

Secondary Structure

dm3

dG=-22.5,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droSim1

dG=-22.5,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droSec1

dG=-22.5,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droYak2

dG=-22.5,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droEre2

dG=-22.5,  p-value=0.009901 dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901

droAna3

dG=-25.4,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.0,  p-value=0.009901 dG=-24.7,  p-value=0.009901 dG=-24.6,  p-value=0.009901

dp4

dG=-22.0,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-21.2,  p-value=0.009901

droPer1

dG=-22.0,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-21.2,  p-value=0.009901

droWil1

dG=-25.6,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.2,  p-value=0.009901

droVir3

dG=-23.8,  p-value=0.009901 dG=-23.4,  p-value=0.009901 dG=-23.0,  p-value=0.009901

droMoj3

dG=-23.9,  p-value=0.009901 dG=-23.7,  p-value=0.009901 dG=-23.5,  p-value=0.009901 dG=-23.3,  p-value=0.009901 dG=-23.1,  p-value=0.009901

droGri2

dG=-24.7,  p-value=0.009901 dG=-24.3,  p-value=0.009901 dG=-23.9,  p-value=0.009901 dG=-23.7,  p-value=0.009901

Generated: 03/07/2013 at 04:51 PM