Secondary structure and small RNA-seq evidence for dme-mir-311

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:16471367-16471480 - TGAAAA-----------------A-TCG---AAATTTCTAGATCATTTTTCGGA--CGGTATATGGGTTAATATTTCAT------------TTGTCGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GAATT-------AACATC-----------------------------------GAA---AAG
droSim1 chr2R:15132667-15132782 - TGAAAA-----------------A-TCG---AAATTTCTAGATAATTTTTCGGA--CGGTATATGAGTCAATATTTTCT----------TTTTTTCGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GAATT-------AGCATC-----------------------------------GAA---AAA
droSec1 super_1:14025591-14025696 - GAAA------------------------------TTTCTAGATAATTTTTCGGA--CGGTATATGAGTCAATGTTTTCT------------TTTTCGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GAATT-------AGCATC-----------------------------------GAA---AAA
droYak2 chr2R:12724807-12724923 + TTTAAA-----------------AA-TATCTCACTTTCTAGATAGTTTTGCGGA--CGGTATCTGCGTCAATATTTCCT------------TGTTAGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GGACT-------TGCATC-----------------------------------GAA---AAG
droEre2 scaffold_4845:10616532-10616644 - TTGAAA-----------------C-CCC---TA-ACCCTAGATAGTTTTTCGGA--CGGTATCTGCGTCAATATTTCCT------------TGTTAGAATATATTGCACATTCACCGGCCTGAAAATATCA-A--GGACT-------TACATC-----------------------------------AAA---AAG
droAna3 scaffold_13266:4132915-4133034 + AGAGAA-----------------A-TAT---TTGTTGCCAGATTATCTTCAGGA--CGGTATTTGTGTCAATATGGATA-------------TTTCAAACATATTGCACTTATACCGGCCTGATGATCTCC-G--GCGCTCGTCATCTGTGAC-----------------------------------TAA---AAG
dp4 chr3:8679876-8679985 + CATCGA-----------------GC-TGCTTTGATTTGTA-----------GGC--CGTGGTTCTTGCAAATACGGATT---------------CATAACGTATTGCACTAGCCCCGGTCCAAAAAACAAT-A--GCAA-CGCC---GGCAAC-----------------------------------AGCAAAGTA
droPer1 gnl|ti|732560583:591-697 + CATCGA-----------------GC-TGCTTTGATTTGTA-----------GGC--CGTGGTTCTTGCAAATACGAATT---------------CATAACGTATTGCACTAGCCCCGGTCCAAAAAACAAT-A--GCAA-CGCC---GGCAAC-----------------------------------AGC---AAA
droWil1 scaffold_180700:3453290-3453392 + TAAT-------------------------------TTATA-----------GGCTTCGGGGT-TGTTGCAAAATGGTTTATTCT-----AATAACTCCCCATATTGCACCTTTTCCGGCCTCTAAATTAACTTTTG-----------AACATCCCG--------------------------------GGT---GGG
droVir3 scaffold_12875:13668876-13669002 - GAAAAA-----------------C-TAG-TGCGTCCGCATGACCATTTTAAGGA--CGGTATTTGTGACAATATGTGCAG-TTAAATCAATTTGTTTAGCATATTGCACATCTCCCGGCCTAAAAATGAAC-C--GTGCT-------CTCTTC-----------------------------------GAT---ATA
droMoj3 scaffold_6496:9090405-9090568 - AAACGAAAAATGTCAAATTTTCAGC-TG---------------CGTTTGCAGGA--CGGTATTTGTGACAATATGAATTATTGAAATCAATTTATTCAGCATATTGCACATCTCCCGGCCTATAAAACAGT-T--GTGA-GCCC---GTCGAT---TTAAATGATTTGTGTATTTAAAATAAATTTTCACC-----A
droGri2 scaffold_15245:17564385-17564474 + AAAT-------------------------------TTGCAGTTCGTGTTTAG------T-----------GTTTTTTCC------------CGCTTAAGCATCTTGCAAATTATATGGCTTGCAGTTATCT-G--CATTA-------ACCATT-----------------------------------TTC---AGG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:16471367-16471480 - TGAAAA-----------------A-TCG---AAATTTCTAGATCATTTTTCGGA--CGGTATATGGGTTAATATTTCATT------------TGTCGAATATATTGCACATTCACCGGCCTGAAAAT-----ATCAAGAATT-------A-----------------------------------ACATCGAAAAG
droSim1 chr2R:15132667-15132782 - TGAAAA-----------------A-TCG---AAATTTCTAGATAATTTTTCGGA--CGGTATATGAGTCAATATTTTCTT----------TTTTTCGAATATATTGCACATTCACCGGCCTGAAAAT-----ATCAAGAATT-------A-----------------------------------GCATCGAAAAA
droSec1 super_1:14025591-14025696 - GAA------------------------------ATTTCTAGATAATTTTTCGGA--CGGTATATGAGTCAATGTTTTCTT------------TTTCGAATATATTGCACATTCACCGGCCTGAAAAT-----ATCAAGAATT-------A-----------------------------------GCATCGAAAAA
droYak2 chr2R:12724807-12724923 + TTTAAA-----------------AA-TATCTCACTTTCTAGATAGTTTTGCGGA--CGGTATCTGCGTCAATATTTCCTT------------GTTAGAATATATTGCACATTCACCGGCCTGAAAAT-----ATCAAGGACT-------T-----------------------------------GCATCGAAAAG
droEre2 scaffold_4845:10616532-10616644 - TTGAAA-----------------C-CCC---TA-ACCCTAGATAGTTTTTCGGA--CGGTATCTGCGTCAATATTTCCTT------------GTTAGAATATATTGCACATTCACCGGCCTGAAAAT-----ATCAAGGACT-------T-----------------------------------ACATCAAAAAG
droAna3 scaffold_13266:4132915-4133034 + AGAGAA-----------------A-TAT---TTGTTGCCAGATTATCTTCAGGA--CGGTATTTGTGTCAATATGGATAT-------------TTCAAACATATTGCACTTATACCGGCCTGATGAT-----CTCCGGCGCTCGTCATCT-----------------------------------GTGACTAAAAG
dp4 chr3:8679876-8679985 + CATCGA-----------------GC-TGCTTTGATTTG-----------TAGGC--CGTGGTTCTTGCAAATACGGATT---------------CATAACGTATTGCACTAGCCCCGGTCCAAAAAACAAT-AGCAACGC-C-------GGCA--------------------------------ACAGCAAAGTA
droPer1 gnl|ti|732560583:591-697 + CATCGA-----------------GC-TGCTTTGATTTG-----------TAGGC--CGTGGTTCTTGCAAATACGAATT---------------CATAACGTATTGCACTAGCCCCGGTCCAAAAAACAAT-AGCAAC-GCC-------G-----------------------------------GCAACAGCAAA
droWil1 scaffold_180700:3453290-3453392 + TAATTT-------------------------------A-----------TAGGCTTCGGGGT-TGTTGCAAAATGGTTTATTCTA-----ATAACTCCCCATATTGCACCTTTTCCGGCCTCTAAATTAACTTTTGAACA---------------------------------------------TCCCGGGTGGG
droVir3 scaffold_12875:13668876-13669002 - GAAAAA-----------------C-TAG-TGCGTCCGCATGACCATTTTAAGGA--CGGTATTTGTGACAATATGTGCAG-TTAAATCAATTTGTTTAGCATATTGCACATCTCCCGGCCTAAAAAT-----GAACCGTGCT-------C-----------------------------------TCTTCGATATA
droMoj3 scaffold_6496:9090405-9090568 - AAACGAAAAATGTCAAATTTTCAGC-TG---------------CGTTTGCAGGA--CGGTATTTGTGACAATATGAATTATTGAAATCAATTTATTCAGCATATTGCACATCTCCCGGCCTATAAAACAGT-TGTGAGCC-C-------GTCGATTTAAATGATTTGTGTATTTAAAATAAATTTTCACC-----A

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TGAAAAATCGA---AATTTCTAGATAATTTTTCGGACGGTATATGAGTCAATATTTTCTTTTTTTCGAATATATTGCACATTCACCGGCCTGAAA----ATATCAAGA--ATTAGCATCGAAAAASizeHit CountTotal NormTotalGSM343915
Embryo
.......................................................................TATTGCACATTCACCGGCCTGA................................2215438.0054385438
.......................................................................TATTGCACATTCACCGGCCTG.................................211644.00644644
.......................................................................TATTGCACATTCACCGGCCTGAA...............................231321.00321321
................................CGGACGGTATATGAGTCAATATT......................................................................23181.008181
........................................................................ATTGCACATTCACCGGCCTGA................................21173.007373
.......................................................................TATTGCACATTCACCGGCCTGAAA----..........................24169.006969
................................CGGACGGTATATGAGTCAATAT.......................................................................22123.002323
.......................................................................TATTGCACATTCACCGGCCT..................................20118.001818
........................................................................ATTGCACATTCACCGGCCTG.................................20111.001111
.......................................................................TATTGCACATTCACCGGCCTGAAA----A.........................2517.0077
........................................................................ATTGCACATTCACCGGCCTGAA...............................2216.0066
..........................................................................TGCACATTCACCGGCCTGA................................1913.0033
................................CGGACGGTATATGAGTCAATA........................................................................2113.0033
...........................................................................GCACATTCACCGGCCTGA................................1813.0033
.....................................................................TATATTGCACATTCACCGGCCT..................................2212.0022
.....................................................................TATATTGCACATTCACCGGCCTGA................................2412.0022
........................................................................ATTGCACATTCACCGGCCTGAAA----A.........................2411.0011
.......................................................................TATTGCACATTCACCGGC....................................1811.0011
.........................................................................TTGCACATTCACCGGCCTGA................................2011.0011
...............................TCGGACGGTATATGAGTCA...........................................................................1911.0011
......................................................................ATATTGCACATTCACCGGCCTGA................................2311.0011
.........................................................................TTGCACATTCACCGGCCTG.................................1911.0011
dp4
CATCGAGCTGCTTTGATTTGTAGGCCGTGGTTCTTGCAA-ATACGGATTCAT---------------AACGTATTGCACTAGCCCCGGTCCAAAAAACAATAGCAACGCCGGCAACAGCAAAGTASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.......................................................................TATTGCACTAGCCCCGGTCCA.................................211149.0014910940
.......................................................................TATTGCACTAGCCCCGGTCCAA................................22146.00463610
.......................................................................TATTGCACTAGCCCCGGTCC..................................20143.0043349
.......................................................................TATTGCACTAGCCCCGGTC...................................19120.0020218
.......................................................................TATTGCACTAGCCCCGGTCCAAA...............................2317.00770
.....................AGGCCGTGGTTCTTGCAA-ATACG................................................................................2314.00404
.......................................................................TATTGCACTAGCCCCGGTCCAAAA..............................2414.00440
.....................AGGCCGTGGTTCTTGCAA-ATA..................................................................................2111.00101
........................................................................ATTGCACTAGCCCCGGTCCA.................................2011.00101

Secondary Structure

dm3

dG=-16.2,  p-value=0.009901 dG=-15.9,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.3,  p-value=0.009901 dG=-15.2,  p-value=0.009901

droSim1

dG=-18.3,  p-value=0.009901 dG=-17.6,  p-value=0.009901 dG=-17.6,  p-value=0.009901 dG=-17.3,  p-value=0.009901 dG=-17.3,  p-value=0.009901

droSec1

dG=-18.4,  p-value=0.009901 dG=-17.7,  p-value=0.009901 dG=-17.7,  p-value=0.009901 dG=-17.4,  p-value=0.009901

droYak2

dG=-11.5,  p-value=0.009901 dG=-11.2,  p-value=0.009901 dG=-11.2,  p-value=0.009901 dG=-11.1,  p-value=0.009901 dG=-11.0,  p-value=0.009901

droEre2

dG=-14.4,  p-value=0.009901 dG=-14.1,  p-value=0.009901 dG=-14.0,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.7,  p-value=0.009901

droAna3

dG=-29.0,  p-value=0.009901

dp4

dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.4,  p-value=0.009901 dG=-21.0,  p-value=0.009901 dG=-21.0,  p-value=0.009901

droPer1

dG=-20.0,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-20.0,  p-value=0.009901 dG=-19.6,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droWil1

dG=-16.1,  p-value=0.009901 dG=-15.6,  p-value=0.009901 dG=-15.3,  p-value=0.009901

droVir3

dG=-21.2,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-21.2,  p-value=0.009901 dG=-21.1,  p-value=0.009901 dG=-20.9,  p-value=0.009901

droMoj3

dG=-20.0,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.5,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-19.2,  p-value=0.009901

droGri2

dG=-7.8,  p-value=0.009901 dG=-7.8,  p-value=0.009901 dG=-7.4,  p-value=0.009901 dG=-7.4,  p-value=0.009901 dG=-7.2,  p-value=0.009901 dG=-4.7,  p-value=0.009901

Generated: 03/07/2013 at 05:16 PM