Secondary structure and small RNA-seq evidence for dme-mir-989

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:10032841-10033044 - ATT-TTATTTAAGTACAA-------AGATTTTGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACAGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCATG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTACAAG-CAACA------CGAA-GT---GA
droSim1 chr2R:8799008-8799211 - ATT-TTATTTAAGTACAT-------AAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACTGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCATG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTGCAAG-CAACA------CGAA-GT---GA
droSec1 super_1:7540579-7540782 - ATT-TTATTTAAGTACAG-------AAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACTGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCTTG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCCGAAATTGCAAG-CAGCA------CGAA-GT---GA
droYak2 chr2R:9968911-9969114 - TTTTTTATTTAATTACAA-------AGATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACAGGTGACACTGATC---CGGATTTGGTGGTGG-ACCCATTCTC-ATT-----------------------------CCGAGATTAGTTTTATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTTGCAAG-CAACA------TGGA-GT---AA
droEre2 scaffold_4845:15804995-15805201 + ATT-TTATTTAATTACAA-------AGATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACCCAGGTGACACTGATC---CGGATTTGGTAGTCGTACAAATCCTCCATT-----------------------------CCGAGTTAAGTTTCATTCTGCGTCTTTTGAA------TTCGAACAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTTGCAAG-CAACA------TGTA-GGCA-TA
droAna3 scaffold_13266:5886554-5886734 + A--------------CCA-------ACGTTTCGGGAAGTGGCCACTACCTCGCAGTCACGTGATGCC---AAAATGCAACTGACACTGATC---CGGAGATGGT------------CCTCCATC---------C-------------------TTGGGATTAGTGTTAATTTGTGTTTTTTTTA------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTCCTAA-CAACA------AAAA-GT---GA
dp4 chr3:2729279-2729420 - A-------------------------CGTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATC---GGAATGCAA------------------------------------T-----------------------------------------GATCTACGTTAAATTGTGTTTCTT---------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAG-CAACA------GAAATGT---AC
droPer1 super_2:2918784-2918948 - TTG-TAAACCAAGAAGAACCAAACAACGTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATC---GGAATGCAA------------------------------------T-----------------------------------------GATCTACGTTAAATTGTGTTTCTT---------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAG-CAACA------GAAATGT---AC
droWil1 scaffold_180745:1541090-1541255 + TAC-GAGTTCGAGTACAA----TAAATGTTTTGGGAATTGGCCACTACCTCGCAGTCACGTGATGAG---AGA---------------------------------------------------GATGCAAGA------------------------GGACTTTG------TATGCCATTTGCATTTAATATTTCATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGAGCTTTAAAGTCATCA------AGAA-GG---AA
droVir3 scaffold_12875:1889282-1889470 + A---------------------AAAACGATTCGGGAATTGGCCACTACCTCGCAGTCACGTGATCCA---CAAACGCAGC--------------CGGCTCTGGTGCTTG-GGAAA---------AATACAATTTTCTTTTGTTTTCCTGGGCGCCGCA-------ACGTTTTGCGT----TCA--------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTTTGCAG-CCACA------GCGC-GAAGTG-
droMoj3 scaffold_6496:23382296-23382464 - A---------------------AAAACGATTCGGGAATTGGCCACTACCTCGCACTCACGTGATGCACTCAAAACGCCGACGAGGACGT---------------------CCAAATT--CCAT---------TTTCT--CGTTTTCCTC--------------TGTCGTTTTGCGT----TGA--------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGCC-----CCAGCAATCCG----------
droGri2 scaffold_15112:3992495-3992691 + ATG-TAAT-----GAA------AAAGCGTTCCGGGAATTGGCCACTACCTCGCAGTCACGTGATGCC---ACAAGGCGGGC-ACGCCGTGCAACATCCTCTCTTCGTTT-ACACATCTCCTCTT-----------------------------GAGAGGATTGCGTCGTTCCGCCT----TGAA-------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTTTCCCA-CAACA------AGAA-CA---AC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:10032841-10033044 - ATT-TTATTTAAGTACAA-------AGATTTTGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACAGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCATG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTACAAG-CAACA------CGAA-GT---GA
droSim1 chr2R:8799008-8799211 - ATT-TTATTTAAGTACAT-------AAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACTGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCATG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTGCAAG-CAACA------CGAA-GT---GA
droSec1 super_1:7540579-7540782 - ATT-TTATTTAAGTACAG-------AAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACTGGTGACACTGATC---CGGATTTGGTAGTTG-ACAAATCCTCCTTG-----------------------------CCGAGATTAGTTTCATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCCGAAATTGCAAG-CAGCA------CGAA-GT---GA
droYak2 chr2R:9968911-9969114 - TTTTTTATTTAATTACAA-------AGATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACACAGGTGACACTGATC---CGGATTTGGTGGTGG-ACCCATTCTC-ATT-----------------------------CCGAGATTAGTTTTATTTTGCGTCTTTTGAA------TTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTTGCAAG-CAACA------TGGA-GT---AA
droEre2 scaffold_4845:15804995-15805201 + ATT-TTATTTAATTACAA-------AGATGCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAA---AAGACCCAGGTGACACTGATC---CGGATTTGGTAGTCGTACAAATCCTCCATT-----------------------------CCGAGTTAAGTTTCATTCTGCGTCTTTTGAA------TTCGAACAGTTCATGTGATGTGACGTAGTGGAACATACCTGGTGTTGCAAG-CAACA------TGTA-GGCA-TA
droAna3 scaffold_13266:5886554-5886734 + A--------------CCA-------ACGTTTCGGGAAGTGGCCACTACCTCGCAGTCACGTGATGCC---AAAATGCAACTGACACTGATC---CGGAGATGGT------------CCTCCATC---------C-------------------TTGGGATTAGTGTTAATTTGTGTTTTTTTTA------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTCCTAA-CAACA------AAAA-GT---GA
dp4 chr3:2729279-2729420 - A-------------------------CGTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATC---GGAATGCAA------------------------------------T-----------------------------------------GATCTACGTTAAATTGTGTTTCTT---------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAG-CAACA------GAAATGT---AC
droPer1 super_2:2918784-2918948 - TTG-TAAACCAAGAAGAACCAAACAACGTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATC---GGAATGCAA------------------------------------T-----------------------------------------GATCTACGTTAAATTGTGTTTCTT---------TTTGAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAG-CAACA------GAAATGT---AC
droWil1 scaffold_180745:1541090-1541255 + TAC-GAGTTCGAGTACAA----TAAATGTTTTGGGAATTGGCCACTACCTCGCAGTCACGTGATGAG---AGA---------------------------------------------------GATGCAAGA------------------------GGACTTTG------TATGCCATTTGCATTTAATATTTCATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGAGCTTTAAAGTCATCA------AGAA-GG---AA
droVir3 scaffold_12875:1889282-1889470 + A---------------------AAAACGATTCGGGAATTGGCCACTACCTCGCAGTCACGTGATCCA---CAAACGCAGC--------------CGGCTCTGGTGCTTG-GGAAA---------AATACAATTTTCTTTTGTTTTCCTGGGCGCCGCA-------ACGTTTTGCGT----TCA--------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTTTGCAG-CCACA------GCGC-GAAGTG-
droMoj3 scaffold_6496:23382296-23382464 - A---------------------AAAACGATTCGGGAATTGGCCACTACCTCGCACTCACGTGATGCACTCAAAACGCCGACGAGGACGT---------------------CCAAATT--CCAT---------TTTCT--CGTTTTCCTC--------------TGTCGTTTTGCGT----TGA--------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGCC-----CCAGCAATCCG----------
droGri2 scaffold_15112:3992495-3992691 + ATG-TAAT-----GAA------AAAGCGTTCCGGGAATTGGCCACTACCTCGCAGTCACGTGATGCC---ACAAGGCGGGC-ACGCCGTGCAACATCCTCTCTTCGTTT-ACACATCTCCTCTT-----------------------------GAGAGGATTGCGTCGTTCCGCCT----TGAA-------TTTCATATTTCATGTGATGTGACGTAGTGGAACATTCCTGACGTTTCCCA-CAACA------AGAA-CA---AC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATTTTATTTAAGTACATAAATTCCGGGAATCGGCCACTACCTTGCAGTCACGTGATGAAAAGACACTGGTGACACTGATCCGGATTTGGTAGTTGACAAATCCTCCATGCCGAGATTAGTTTCATTTTGCGTCTTTTGAATTCGAATAGTTCATGTGATGTGACGTAGTGGAACATACCTGAAATTGCAAGCAACACGAA-GTGASizeHit CountTotal NormTotalGSM343915
Embryo
.........................................................................................................................................................TGTGATGTGACGTAGTGGAAC...............................21110.001010
.........................................................................................................................................................TGTGATGTGACGTAGTGGAACA..............................2219.0099
.........................................................................................................................................................TGTGATGTGACGTAGTGGAA................................2013.0033
dp4
AC-----------------GTTGCGGGAATGGGCCACTACCTCGCAGTCACGTGATATCGGAATG--------------------------------CAATGATCTACGTTAAATTGTGTTTCTTTTT---------------GAATAGTTCATGTGATGTGACGTAGTGGAACATTCCTGGCGTTGTCAGCAACAGAAATGTACSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.........................................................................................................................................................TGTGATGTGACGTAGTGGAACA..............................221245.0024568177
.........................................................................................................................................................TGTGATGTGACGTAGTGGAAC...............................211187.0018729158
.........................................................................................................................................................TGTGATGTGACGTAGTGGAA................................20170.0070961
.........................................................................................................................................................TGTGATGTGACGTAGTGGA.................................1919.00909
........................................................................................................................................................ATGTGATGTGACGTAGTGGAA................................2114.00431
........................................................................................................................................................ATGTGATGTGACGTAGTGGAAC...............................2213.00321
.........................................................................................................................................................TGTGATGTGACGTAGTGGAACAT.............................2311.00101
..........................................................................................................................................................GTGATGTGACGTAGTGGAACA..............................2111.00110

Secondary Structure

dm3

dG=-50.7,  p-value=0.009901 dG=-50.7,  p-value=0.009901 dG=-50.7,  p-value=0.009901 dG=-50.7,  p-value=0.009901 dG=-50.7,  p-value=0.009901

droSim1

dG=-48.6,  p-value=0.009901 dG=-48.6,  p-value=0.009901 dG=-48.2,  p-value=0.009901 dG=-48.2,  p-value=0.009901 dG=-48.2,  p-value=0.009901

droSec1

dG=-48.2,  p-value=0.009901 dG=-48.2,  p-value=0.009901 dG=-47.9,  p-value=0.009901 dG=-47.8,  p-value=0.009901 dG=-47.8,  p-value=0.009901

droYak2

dG=-51.9,  p-value=0.009901 dG=-51.9,  p-value=0.009901 dG=-51.9,  p-value=0.009901 dG=-51.6,  p-value=0.009901 dG=-51.6,  p-value=0.009901

droEre2

dG=-48.0,  p-value=0.009901 dG=-48.0,  p-value=0.009901 dG=-48.0,  p-value=0.009901 dG=-48.0,  p-value=0.009901 dG=-47.6,  p-value=0.009901

droAna3

dG=-59.7,  p-value=0.009901 dG=-59.7,  p-value=0.009901 dG=-59.4,  p-value=0.009901 dG=-59.4,  p-value=0.009901 dG=-59.3,  p-value=0.009901

dp4

dG=-40.6,  p-value=0.009901 dG=-40.4,  p-value=0.009901 dG=-40.2,  p-value=0.009901 dG=-40.0,  p-value=0.009901 dG=-39.9,  p-value=0.009901

droPer1

dG=-40.6,  p-value=0.009901 dG=-40.4,  p-value=0.009901 dG=-40.2,  p-value=0.009901 dG=-40.0,  p-value=0.009901 dG=-39.9,  p-value=0.009901

droWil1

dG=-41.1,  p-value=0.009901 dG=-40.8,  p-value=0.009901 dG=-40.7,  p-value=0.009901 dG=-40.4,  p-value=0.009901 dG=-40.3,  p-value=0.009901

droVir3

dG=-56.4,  p-value=0.009901 dG=-56.0,  p-value=0.009901 dG=-55.6,  p-value=0.009901 dG=-55.5,  p-value=0.009901 dG=-55.5,  p-value=0.009901

droMoj3

dG=-45.0,  p-value=0.009901 dG=-44.8,  p-value=0.009901 dG=-44.7,  p-value=0.009901 dG=-44.6,  p-value=0.009901 dG=-44.5,  p-value=0.009901

droGri2

dG=-60.4,  p-value=0.009901 dG=-60.3,  p-value=0.009901 dG=-60.2,  p-value=0.009901 dG=-60.1,  p-value=0.009901 dG=-60.0,  p-value=0.009901

Generated: 03/07/2013 at 07:25 PM