Secondary structure and small RNA-seq evidence for dme-mir-962

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:5641283-5641404 + GAATTCA---ACTACTT---CG-----AT-GGGGC-ACTCAGGCTATAAGGTAGAGAAATTGATGCTGTCTACACTAT--------------T----CAGACTTCAGTTTCATTACCTTTCAATTTGTTTGCCCC-CA--TGCAACAGTGA------------------------------------------TA-----G---------------------------------TA
droSim1 chr2L:5434368-5434488 + GAATCT-ACAACTACCT---CG-----AT-GGGGC-GCTCAGGCTATAAGGTAGAGAAATTGATGTTGTCTACACTAT--------------T----CAGACTTCAGTTTCATTGCCTTTCAATTTGTTTGCCCC-CC--TGCAACAGTGA------------------------------------------TA-----------------------------------------
droSec1 super_5:3719023-3719143 + GAATCT-ACAACTACCT---CG-----AT-GGGGC-ATTCAGGCTATAAGGTAGAGAAATTGATGTTGTCTACACTAT--------------T----CAGACTTCAGTTTCATTGCCTTTCAATTTGTTTGCCCC-CA--TGCAACAGTGG------------------------------------------TA-----------------------------------------
droYak2 chr2L:13551914-13552032 - GAATCCA---ACCAACT---TC-----AT-GGGGC-ACACAAGCTATAAGGTAGAGAAATTGTTGTCTTCCACACTAT--------------T----CAGACATCAGTTTAACTATCTTTCAATTTGTTTGCCCC-CA--CGCAACAGTGA------------------------------------------TA-----------------------------------------
droEre2 scaffold_4929:5729744-5729862 + GAATCCC---AGTACCT---CC-----TT-GGGGC-ACTCAAGCTATAAGGTAGAAAAATTGTTGTCTTCCACACTAT--------------T----CGGACTGCAGTTTAACTATCTTTCAATTTGTTTGCCCC-CA--CGCAACAGTGA------------------------------------------CA-----------------------------------------
droAna3 scaffold_12916:11085088-11085210 + GGGCCCA---ACCACCT---GG-----CCGAGGGC-ACTCAAGCTATAAGGTAGAGAAAATAATGTCTTCGTCTCCAA--------------A----TAGACATCAATTTCCCTAGCTTGCATTTTGCCTGCCCC-CA--AGCAACAATGA------------------------------------------TA-----A---------------------------------CA
dp4 chr4_group4:3182204-3182349 - GAGTGCCACAAATGCCACATGATGCAAAT-GGAGC-AGTCGTGTTTTAAGGTACAGACTTTG---------AGTCTAT--------------TC---TAGGCATCAATTTTCGTATCTTTTAATTCGTCTGGCGC-CAACAGCAACAGCTA--------------------CAAAACGAGTAACGAGGAGAGATA-----------------------------------------
droPer1 super_10:2201135-2201280 - GAGTGCCACAAATGCCACATGATGCAAAT-GGAGC-AGTCGTGTTTTAAGGTACAGACTTTG---------AGTCTAT--------------TC---TAGGCATCAATTTTCGTATCTTTTAATTCGTCTGCCGC-CAACAGCAACAGCTA--------------------CAAAACGAGTAACGAGGAGAGATA-----------------------------------------
droWil1 scaffold_180708:8625857-8626006 - GGATAC-ACGTTTTCTATTTAA------TAAGGAC-CCTCAAGTTATAAGGTAGAGAAAATGTTGTCTTTATATT----TGTAACAAT-TGTT----AAGACATCACTTTCACTAGCTTTCAATTTGTCTGCTCCACA--TGCAACAACA-------------------TATAAT-------ACAATCAAACAAA-----------------------------------------
droVir3 scaffold_12963:3615418-3615613 + ACACAC-ACA--CATAA---GA-----A--AGGGCGCCTCAAATTATAAGGTAGAGAAATTGTTGTCTACT---TTACATATG--------GT----GAGACATCAAT-TCACTAGCTTTCAATTTGTACGCCCA-AA--TGCAACGGAACCATTTTGGAGGAACATCATAT-TT-------AGAATAAGCCACATGATAGGCAGCACATTTAGCATTTGAATGCCGGACTGCTCA
droMoj3 scaffold_6500:14018360-14018470 + G---------------------------T-AGAGC-GCTCAAGTTATAAGGTAGAGATATTGTTGTCTTTTTGCA----TATAGCACTCTGTTATGAAAGACATCAAT-TCACTAGCTTTCAATTTGTACGCTTA-AA--TGCAGCA-----------------------------------------------------------------------------------------
droGri2 scaffold_15252:3147228-3147335 + TCATAACACA-----CT---CA--------AGAGC-TCTCAGATTATAAGGTAGAGATTTTGTTGTCTTCTATTATA---------------A----AAGACATCAAT-TCACTAGCTTTCAATTTGTATGCTCA-AA--TGCAACGG----------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:5641283-5641404 + GAATTCA---ACTACTT---CG-----AT-GGGGC-ACTCAGGCTATAAGGTAGAGAAATTGATGCTGTCTACACTAT--------------T----CAGACTTCAGTTTCATTACCTTTCAATTTGTTTGCCCC-CA--TGCAACAGTGA------------------------------------------TA-----G---------------------------------TA
droSim1 chr2L:5434368-5434488 + GAATCT-ACAACTACCT---CG-----AT-GGGGC-GCTCAGGCTATAAGGTAGAGAAATTGATGTTGTCTACACTAT--------------T----CAGACTTCAGTTTCATTGCCTTTCAATTTGTTTGCCCC-CC--TGCAACAGTGA------------------------------------------TA-----------------------------------------
droSec1 super_5:3719023-3719143 + GAATCT-ACAACTACCT---CG-----AT-GGGGC-ATTCAGGCTATAAGGTAGAGAAATTGATGTTGTCTACACTAT--------------T----CAGACTTCAGTTTCATTGCCTTTCAATTTGTTTGCCCC-CA--TGCAACAGTGG------------------------------------------TA-----------------------------------------
droYak2 chr2L:13551914-13552032 - GAATCCA---ACCAACT---TC-----AT-GGGGC-ACACAAGCTATAAGGTAGAGAAATTGTTGTCTTCCACACTAT--------------T----CAGACATCAGTTTAACTATCTTTCAATTTGTTTGCCCC-CA--CGCAACAGTGA------------------------------------------TA-----------------------------------------
droEre2 scaffold_4929:5729744-5729862 + GAATCCC---AGTACCT---CC-----TT-GGGGC-ACTCAAGCTATAAGGTAGAAAAATTGTTGTCTTCCACACTAT--------------T----CGGACTGCAGTTTAACTATCTTTCAATTTGTTTGCCCC-CA--CGCAACAGTGA------------------------------------------CA-----------------------------------------
droAna3 scaffold_12916:11085088-11085210 + GGGCCCA---ACCACCT---GG-----CCGAGGGC-ACTCAAGCTATAAGGTAGAGAAAATAATGTCTTCGTCTCCAA--------------A----TAGACATCAATTTCCCTAGCTTGCATTTTGCCTGCCCC-CA--AGCAACAATGA------------------------------------------TA-----A---------------------------------CA
dp4 chr4_group4:3182204-3182349 - GAGTGCCACAAATGCCACATGATGCAAAT-GGAGC-AGTCGTGTTTTAAGGTACAGACTTTG---------AGTCTAT--------------TC---TAGGCATCAATTTTCGTATCTTTTAATTCGTCTGGCGC-CAACAGCAACAGCTA--------------------CAAAACGAGTAACGAGGAGAGATA-----------------------------------------
droPer1 super_10:2201135-2201280 - GAGTGCCACAAATGCCACATGATGCAAAT-GGAGC-AGTCGTGTTTTAAGGTACAGACTTTG---------AGTCTAT--------------TC---TAGGCATCAATTTTCGTATCTTTTAATTCGTCTGCCGC-CAACAGCAACAGCTA--------------------CAAAACGAGTAACGAGGAGAGATA-----------------------------------------
droWil1 scaffold_180708:8625857-8626006 - GGATAC-ACGTTTTCTATTTAA------TAAGGAC-CCTCAAGTTATAAGGTAGAGAAAATGTTGTCTTTATATT----TGTAACAAT-TGTT----AAGACATCACTTTCACTAGCTTTCAATTTGTCTGCTCCACA--TGCAACAACA-------------------TATAAT-------ACAATCAAACAAA-----------------------------------------
droVir3 scaffold_12963:3615418-3615613 + ACACAC-ACA--CATAA---GA-----A--AGGGCGCCTCAAATTATAAGGTAGAGAAATTGTTGTCTACT---TTACATATG--------GT----GAGACATCAAT-TCACTAGCTTTCAATTTGTACGCCCA-AA--TGCAACGGAACCATTTTGGAGGAACATCATAT-TT-------AGAATAAGCCACATGATAGGCAGCACATTTAGCATTTGAATGCCGGACTGCTCA
droMoj3 scaffold_6500:14018360-14018470 + G---------------------------T-AGAGC-GCTCAAGTTATAAGGTAGAGATATTGTTGTCTTTTTGCA----TATAGCACTCTGTTATGAAAGACATCAAT-TCACTAGCTTTCAATTTGTACGCTTA-AA--TGCAGCA-----------------------------------------------------------------------------------------
droGri2 scaffold_15252:3147228-3147335 + TCATAACACA-----CT---CA--------AGAGC-TCTCAGATTATAAGGTAGAGATTTTGTTGTCTTCTATTATA---------------A----AAGACATCAAT-TCACTAGCTTTCAATTTGTATGCTCA-AA--TGCAACGG----------------------------------------------------------------------------------------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GAATC-TACAACTACCTC--------GATGGGGCGCTCAGGCTATAAGGTAGAGAAATTGATGTTGTCTACACTATTCAGACTTCAGTTTCATTGCCTTTCAATTTGTTTGCCCCC--CTGCAACAGT----------------------GATA---SizeHit CountTotal NormTotalGSM343915
Embryo
...........................................ATAAGGTAGAGAAATTGATGTTGTC.........................................................................................2516.0066
...........................................ATAAGGTAGAGAAATTGATGTT............................................................................................2213.0033
...........................................ATAAGGTAGAGAAATTGATGTTGTCT........................................................................................2611.0011
dp4
GAGTGCCACAAATGCCACATGATGCAAATGGAGCAGTCGTGTTTTAAGGTACAGACTTTGAG----TCTAT----TCTAGGCATCAATTTTCGTATCTTTTAATTCGTCTGGCGCCAACAGCAACAGCTACAAAACGAGTAACGAGGAGAGATA---SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..........................................TTTAAGGTACAGACTTTGAG----TC.........................................................................................2218.00808
..........................................TTTAAGGTACAGACTTTGAG----...........................................................................................2012.00202
..........................................TTTAAGGTACAGACTTTGAG----TCT........................................................................................2312.00202
..........................................TTTAAGGTACAGACTTTGAG----T..........................................................................................2111.00101
..........................................TTTAAGGTACAGACTTTGA................................................................................................1911.00101

Secondary Structure

dm3

-32.3 -32.2 -31.8 -31.6 -31.5

droSim1

-31.6 -31.0 -30.9

droSec1

-33.7 -33.1 -33.0

droYak2

-32.6 -31.8

droEre2

-30.6 -29.8

droAna3

-25.5 -24.6

dp4

-26.4 -25.6

droPer1

-27.8 -27.0

droWil1

-25.0 -24.3

droVir3

-30.9 -30.9 -30.6 -30.6 -29.9

droMoj3

-31.1 -30.8 -30.7 -30.5 -30.4 -30.2

droGri2

-24.3 -24.0

Generated: 01/05/2013 at 05:32 PM