Secondary structure and small RNA-seq evidence for dme-mir-2491

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:22235261-22235434 - ACTAAATGAC---A--CCACCGCGAACCACT---T--TGTGCC-----------------------------------------------------GCTGTTGCCTTTG----CA--------GTTGCTGTTTTCCATGTT---GCTAC-------------------------------------------------------------------------------TG-----------CGGCCAATTGTTGCGCATCAGCAACATCAACAAC------------------ATCAA--CA---ACAGCAGCAGCAACTGC---AGTAGCAG------C-ACTCGT-------------GATTCACTTTCGA-CT-CAATTCGTCGCTA-
droSim1 chrX:16981360-16981475 - ACTAAATGAC---A--CCACCGCGAACCACT---T--TGTGCC-----------------------------------------------------GC---------------------------------------------TGCTAC-------------------------------------------------------------------------------TG-----------CGGCCACTTGTGGCGCATCAGCAACATCAGCAAC------------------ATCGT-GCA---ACATC---------------------G------------------------------TTCAC-TTCGA-CT-CAGTTCGTCGTTA-
droSec1 super_39:188007-188112 - ACTAAATAAC---T--CCACCGCGAACCACT---T--TGTGCC-----------------------------------------------------GC---------------------------------------------TGCTAC-------------------------------------------------------------------------------TG-----------CGGCCACTTGTGGCGCATCAGCAACATCAGCAAC------------------ATCG-----------------------------------------------------------------TTCAC-TTCGA-CT-CAATTCGTCGTTA-
droYak2 chrX:21599490-21599638 - ACTAAATGGC---A--CCACCGCGAACCACT---T--TGTGTC-----------------------------------------------------GCTGTTGCCTCTG----CT--------GTTGCTGCTTTGCATGTT---GCTAC-------------------------------------------------------------------------------TG-----------TGACCACTTGTTGCGCATCAGCAACAGCAACGAC------------------A--------------------------GC---AACAGCAG------C-ACTTGT-------------GCTTCAC-TTCGA-CT-CGATT---CGTTA-
droEre2 scaffold_4690:18518767-18518923 - ACTAAATGAC---A--CCACCGCGAACCACT---T--TGTGTC-----------------------------------------------------GCTGTTGCC--TT----CT--------GTTGCTGCTTTGT-TGTT---GCTAC-------------------------------------------------------------------------------TG-----------CGACCACTTGTTGCGCATCAGCAACATCGACGAC------------------AGCAAAGCA---------------ACAGC---AGCAGCAG------C-ACTTGT-------------GCTTCAC-TTCTA-CT-CGATT---CGTTA-
droAna3 scaffold_13417:1531274-1531445 - ATCATT-----------------------CT---G--GATGAT-----------------------------------------------------GCTGTTGCAGCTT----CT--------CTTGCTTTTCTG----------C---------------CACATGGAGACGACA-----------------CCAAAAACAATAAC---------------------AACAACAATGGTACAAC---------AACAGTAGCAACAACAGCAAC------------------A-----------GCAACAGCAACAGTAGC---AGTAGCAGCAACGGT------G-------------GCAACACTTTCAAATT-CATTT--TCGAAAT
dp4 chrXL_group1e:3403111-3403272 - ACAGAGTGGC---ATGCAACTGCCAGCCACG---C--CCTCGA-----------------------------------------------------GC------------------------------AGCTCCG----------C---------------CTCAGGGAACT--CGCCGGATCTGTTATCCTTCCAAATGGAGCAAC---------------------TG-----------CAGCAGCAGC---AACAGCAGCAGCAGCAGCAACATCACTT---------------G--CAACAGCAGCAGCAGCAACACC---AGCAGCAG------C-A-------------------------------------------------
droPer1 super_20:731421-731582 - ATCGC------------------CAA----T---C--TG-------------------------------------------------------------TTGCGGCAGCAGTCCCAGTCCCAGTCGC---------------AGT---CGCAGT---------------------------------------------------------------------------------------CACAGCCCCTGCAGCAGCAGCAGCAGCAGCAACATCCTCAGCAACAGCAGCA-----------GCAGCAGCAACATCCTC---AGCAGCAGCAGCGGC-GCGACA-------------G------CTCCGA-CAGCAATTGCTCGCTG-
droWil1 scaffold_181096:4169006-4169179 - ACAACA--GCAACA--ACAAAGAGAGCAACAAAGTTGTATG-----------------------------------------------------------TTGCCTTTGCCTTCT-----------------TCGTGTGCTGCTGCTGCTGCTGT-------------------------------------------------------------------------CG-----------ATCGGGCTTTTTGGGCAGCAGAAACATCAGCAAC------------------ATTGC--CA---GCGACAGCAACAACAGC---AGCAGCAG------CAGCTTGC-------------AATTTTCTTTTTG-CT-C------TTGCTAT
droVir3 scaffold_13324:2891413-2891591 + ACAAAGCAAC---A--ACAACCACAATCACA---G--C-------------------------------------AGCAGCGCCAGCAGCAACA-----------------------------ATTGCAGTT-------------------------------------------GCCG-----------------------GCAAC---------------------TG-----------CAGCAACGGAAGCAGCAGCAGCAACAACAACAAC------------------AACAA--CAACAACAACAGCAACAACTGC---AGCAGCAG------C-ATTCGCATTGGATTAAACAG------CTTCGA-CTGCTATGCATTGGTA-
droMoj3 scaffold_6680:19782481-19782647 + GTAACT---------------------CAAT---T--TGTTTGGCGTTTGCATCTTAAATTCTCGTAAGCATGCCATGTGTGCCATCCTGCACAAAGC---------------------------TGCTGCTTTGC-TT-------------------------------------------------------------------------------------------------------------CGATTCAGCACCAGCAACAACAACAAC------------------AACAA--CA---ACAACAGCAGCAGCAGCAGCAACAGCAG------C--------------------AGTGGACATCCAA-CT-GAAT----------
droGri2 scaffold_15245:7434254-7434426 - ACCAGATGAT---A--CCCACAAGCGTCACG--------------------------------------------------------------------------------------AACTCACCGCC---------------AGC---CGCTGGCTTGGCC-------------------------------CAAAATGGAGCAGCTGCTGTTGTTGTTGTTGTTGGTG-----------GTGGCAGTTCTGCTGCAGCAGCAGCAGCAGCAGC------------------ATCAA--CA---GCAGCAGTGGCAGCA-C---AGCAGCAG-----------------------------AGCAATTACAA-TT-CAATT---------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:22235261-22235434 - ACTAAATGACACCACCGCGAACCACTTTGTGCCGCTGTTGCCTTTGCAGTTGCTGTTTTCCATGTTGCTACTGCGGCCAATTGTTGCGCATCAGCAACATCAACAACATCAACAACAGCAGCAGCAACTGCAGTAGCAGCACTCGTGATTCACTTTCGACTCAATTCGTCGCTA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ACTAAATGACA--CCACCGCGAACCACTT---TGTGCCGC--------------------------------------------------TGCTACTGCGGCCACTTGTGGCGCATCAGCAACATCAGCAACATCG--TGCAACATCGT-------------------------------TCACT-TCGACTCAGTTCGTCGTTASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
ACAGAGTGGCATGCAACTGCCAGCCACGCCCTCGAGCAGCTCCG-CCTCAGGGAACTCGCCGGATCTGTTATCCTTCCAAATGGAGCAACTGCAGCAGCAGCAA---------CAGCAGCAGCAGCAGCAACATCACTTGCAACAGCAGCAGCAGCAACACCAGCAGCAG---------------------------------CASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
...........................................................................................GCAGCAGCAGCAA---------CAGCAGCA....................................................................................2112.00220
............................................................................................................................................CAACAGCAGCAGCAGCAACA.............................................2012.00220
..............................................................................................................................................ACAGCAGCAGCAGCAACA.............................................1812.00220
.................................................................................................................CAGCAGCAGCAGCAGCAACA........................................................................2012.00211
..............................................................................................GCAGCAGCAA---------CAGCAGCAGCA.................................................................................2111.00101
....................................................................................................GCAA---------CAGCAGCAGCAGCAGCA...........................................................................2111.00110
....................................................................................................GCAA---------CAGCAGCAGCAGCAGC............................................................................2011.00110
..................................................................................................CAGCAA---------CAGCAGCAGCAGCA..............................................................................2011.00110
...............................................................................................CAGCAGCAA---------CAGCAGCAGCAGCA..............................................................................2311.00110
............................................................................................CAGCAGCAGCAA---------CAGCAGCAGCA.................................................................................2311.00110
.................................................................................................GCAGCAA---------CAGCAGCAGCAGCA..............................................................................2111.00110
.................................................................................................................CAGCAGCAGCAGCAGCAAC.........................................................................1911.00101
...................................................................................................AGCAA---------CAGCAGCAGCAGCA..............................................................................1911.00110
.................................................................................................GCAGCAA---------CAGCAGCAGCAGCAGC............................................................................2311.00110
............................................................................................CAGCAGCAGCAA---------CAGCAGC.....................................................................................1911.00110
..................................................................................................CAGCAA---------CAGCAGCAGCAGCAGC............................................................................2211.00110
...............................................................................................................................................CAGCAGCAGCAGCAACACC...........................................1911.00110
...............................................................................................CAGCAGCAA---------CAGCAGCAGCA.................................................................................2011.00110
..................................................................................................................AGCAGCAGCAGCAGCAACA........................................................................1911.00101
............................................................................................................................................CAACAGCAGCAGCAGCAAC..............................................1911.00110
......................................................................................................AA---------CAGCAGCAGCAGCAGCA...........................................................................1920.50110

Secondary Structure

dm3

dG=-46.0,  p-value=0.009901 dG=-45.3,  p-value=0.009901 dG=-45.2,  p-value=0.009901 dG=-45.0,  p-value=0.009901

droSim1

dG=-16.0,  p-value=0.009901 dG=-15.4,  p-value=0.009901 dG=-15.4,  p-value=0.009901 dG=-15.4,  p-value=0.009901 dG=-15.4,  p-value=0.009901 dG=-14.5,  p-value=0.009901

droSec1

dG=-14.5,  p-value=0.009901 dG=-14.5,  p-value=0.009901 dG=-14.2,  p-value=0.009901 dG=-14.0,  p-value=0.009901 dG=-13.9,  p-value=0.009901

droYak2

dG=-41.4,  p-value=0.009901 dG=-40.7,  p-value=0.009901 dG=-40.5,  p-value=0.009901 dG=-40.4,  p-value=0.009901 dG=-40.4,  p-value=0.009901

droEre2

dG=-44.1,  p-value=0.009901 dG=-44.1,  p-value=0.009901 dG=-43.9,  p-value=0.009901 dG=-43.9,  p-value=0.009901 dG=-43.8,  p-value=0.009901

droAna3

dG=-30.4,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-29.6,  p-value=0.009901 dG=-29.5,  p-value=0.009901 dG=-29.5,  p-value=0.009901 dG=-25.9,  p-value=0.009901

dp4

dG=-32.1,  p-value=0.009901 dG=-32.1,  p-value=0.009901 dG=-31.7,  p-value=0.009901 dG=-31.7,  p-value=0.009901 dG=-31.6,  p-value=0.009901

droPer1

dG=-32.6,  p-value=0.009901 dG=-32.2,  p-value=0.009901 dG=-31.9,  p-value=0.009901 dG=-31.8,  p-value=0.009901 dG=-31.7,  p-value=0.009901 dG=-26.9,  p-value=0.009901

droWil1

dG=-42.9,  p-value=0.009901 dG=-42.7,  p-value=0.009901 dG=-42.7,  p-value=0.009901 dG=-42.6,  p-value=0.009901 dG=-42.5,  p-value=0.009901

droVir3

dG=-26.04,  p-value=0.009901 dG=-22.3,  p-value=0.009901

droMoj3

dG=-33.79,  p-value=0.009901 dG=-33.59,  p-value=0.009901 dG=-33.49,  p-value=0.009901 dG=-33.49,  p-value=0.009901 dG=-33.39,  p-value=0.009901

droGri2

dG=-62.0,  p-value=0.009901 dG=-61.0,  p-value=0.009901

Generated: 03/07/2013 at 04:59 PM