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 - ACTAAATGAC---A--CCACCGCGAACCACT---T--TGTGCC-----------------------------------------------------GCTGTTGCCTTTG----CA--------GTTGCTGTTTTCCATGTT---GCTAC-------------------------------------------------------------------------------TG-----------CGGCCAATTGTTGCGCATCAGCAACATCAACAAC------------------ATCAA--CA---ACAGCAGCAGCAACTGC---AGTAGCAG------C-ACTCGT-------------GATTCACTTTCGA-CT-CAATTCGTCGCTA-

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

-50.5 -50.5 -49.8 -49.8 -49.7 -49.7

droSim1

-20.6 -20.5 -20.5 -20.5 -20.4 -20.4

droSec1

-19.1 -19.1 -19.0 -19.0 -19.0 -19.0

droYak2

-46.2 -45.5 -45.4 -45.3 -45.2 -45.2

droEre2

-48.9 -48.9 -48.7 -48.7 -48.6 -48.6

droAna3

-33.6 -33.1 -32.8 -32.8 -32.7 -32.7

dp4

-35.9 -35.5 -35.4 -35.4 -35.4 -35.2

droPer1

-35.3 -34.9 -34.7 -34.6 -34.5

droWil1

-53.9 -53.7 -53.6 -53.5 -53.5 -53.4

droVir3

-30.44 -29.84 -29.6 -29.6 -29.54

droMoj3

-39.69 -39.59 -38.69

droGri2

-64.4 -64.0 -64.0 -64.0 -64.0 -63.8

Generated: 01/05/2013 at 05:10 PM