Secondary structure and small RNA-seq evidence for dme-mir-4978

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:9893349-9893526 - CGGAAAAG-------------CCAA-GGCGGAC---------------------------------------TTTCCAC------------------------------------TTTT----------CGTTTGG------------C-----TGGCCTGGAAAAGCTCTCTT---------TCTCTAT-TG------------CCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC----CATCGAAAAGCCTGGCAAG----------------------------------------CACACAGCTCGCACAAATTTTC
droSim1 chr2R:8329883-8330063 - CGGAAAAT-------------CCAA-GGCGCAC---------------------------------------TTTCCAC------------------------------------CTTTCCA-------CGTCTGG------------C-----TGGCCTGGAAAAGCTCTCTT---------TCTCTAT-TG------------CCTCTATGGCTCGGCCGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC----CATCGAAAAGCCTGGCAAG----------------------------------------CGCACAGCTCGCACAAATTTTC
droSec1 super_1:7418494-7418674 - CGGAAAAG-------------CCAA-GGCGCAC---------------------------------------TTTCCAC------------------------------------CTTTCCA-------CGTCTGG------------C-----TGGCCTGGAAAAGCTATCTT---------TCTCTAT-TA------------CCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTCCG---AGCCAAAAAC----CATCGAAATGCCTGGCAAG----------------------------------------CACACAGCTCGCACAAATTTTC
droYak2 chr2R:7060227-7060403 + CGGAAAAG-------------CCAA-GGTGGAC---------------------------------------TTTCCAC------------------------------------TTTT----------CGTTTGT------------C-----TGGCCTGGAAAAGCTCTCTT---------TCTCTATT--------------CCTCTATGGCTCGCCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC----CATCGAATAGCCCGGCAAG----------------------------------------CACACAGCTCGCACAAATTTTC
droEre2 scaffold_4845:15928216-15928392 + CTGAAAAG-------------CCAA-GGCGGAC---------------------------------------TTTCCAC------------------------------------TTTT----------CGTCTGG------------C-----TGGCCTGGAAAAGCTCTCTT---------TCTCTATG--------------CCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAC----CATCGAATAGCCGTGCAAG----------------------------------------CACACAGCTCGCACAAATTTTC
droAna3 scaffold_13266:6006643-6006792 + -------------------------------AC---------------------------------------TTTCCAC------------------------------------TC---------------------------------------GCTGGAAAAAGCTTTCAT------------CCATTCCGGTTGCAACTTGCCACT------C---GACTCTGGGCTCCTAATCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAACCGAGCCACCGAAA-CTGGTCAAG----------------------------------------T----AGTACGCACAAATTCAA
dp4 chr3:11241780-11242024 + CGAATGAG-------------AGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTC--------------------------------------------CCCAGTGTTTGTGTGT------------GTGGGGCGAACTGGAAAACCTCTGTT---------TT-CCATCCC------------CCTTTTTGG------CGCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAG----CCACCAAAAGCC---CAAGGAGTTGTCGCA-CTCCGGACTACGCATAAAATCCCCCAAAAGCAGAACTCGC----------
droPer1 super_4:6644552-6644788 + CGAATGAG-------------AGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTC--------------------------------------------CCCAGTGTTTGTGTGTGTGTGTGTGTGTGTGTGACGGACTGGAAAACCTCTGTT---------TT-CCATCCC------------CCTTTTTGG------CGCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCG---AGCCAAAAAG----CCACCAAAAGCC---CAAGGAGTTGTCGCA-CTC-------------------------CGG--ACTACGCATAAAAT---
droWil1 scaffold_180745:1743803-1743968 + CGGAAAAG-------------CCAA-AGCATAT---------------------------------------AC----------------------------------------------------------TAGA------------T-----TGTACTGGAAAAGCTCTGCAACCAAAAAATT-GCGTCGG------------TCATCTCTG------AGGTCTGTGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTTGGAGAGCC----------CACCACGTTGA-----AAG---------GA-GTA-------------------------CGTACAATGAAAAAAATTGGCC
droVir3 scaffold_12875:2042187-2042370 + CAGGAAAAGCATGCGGAAAAGTGCG-TGTATGGAAAAGCAGCAAT---------------------------CGC--AAACGCCTGGAAAAGCGACCGACTG----------------------------------------------------------------CCGCCGTT---------TG-CCA------CAGCA---C-GCTTTTTCG------ATATCTGTGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTAG---AGCTAG----------TTCAAGGCA----CACGCAGTTCGC--AGC---------------------------TC-------------CACTGTG
droMoj3 scaffold_6496:23220919-23221095 - TGGAAAAG-------------CGCG-TGTGGAGACAAGCAGCGAC---------------------------CGTACGCCCGCCTGGAAAGCCGACTGCCCGCCAGCATTTGTAGCTC---------------------------------------------------------------------------TGTAGCA-----GCTTGTTGG------ATAGCTGAGCGCCTAATCCAAATTGCGAGAAAGATCCGCTTTTAG---AGCTAG----------TTCAAGGCACACGCAGC----------------------------------------TCCACAGCGGGCACAA------
droGri2 scaffold_15112:4157535-4157620 + CGGAAAAG-------------C-----GCAAAA---------------------------------------TTTGCGA------------------------------------CACT----------CGCTCAA------------C-----TGGC----------------------------------------------------------------AGCTGGGCGCCTAATCCAAACTGCGAGAAAGATCCGCTTTTAG---AGCTA------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:9893349-9893526 - CGGAAAAGCCAAGGCGGACTTTCCACTTTT---CGTTTGGCTGGCCTGGAAAAGCTCTCTTTCTCTATTGCCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAAAAGCCTGGCAAGCACACAGCTCGCACAAATTTTC
droSim1 chr2R:8329883-8330063 - CGGAAAATCCAAGGCGCACTTTCCACCTTTCCACGTCTGGCTGGCCTGGAAAAGCTCTCTTTCTCTATTGCCTCTATGGCTCGGCCGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAAAAGCCTGGCAAGCGCACAGCTCGCACAAATTTTC
droSec1 super_1:7418494-7418674 - CGGAAAAGCCAAGGCGCACTTTCCACCTTTCCACGTCTGGCTGGCCTGGAAAAGCTATCTTTCTCTATTACCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTCCGAGCCAAAAACCATCGAAATGCCTGGCAAGCACACAGCTCGCACAAATTTTC
droYak2 chr2R:7060227-7060403 + CGGAAAAGCCAAGGTGGACTTTCCACTTTT---CGTTTGTCTGGCCTGGAAAAGCTCTCTTTCTCTATT-CCTCTATGGCTCGCCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAATAGCCCGGCAAGCACACAGCTCGCACAAATTTTC
droEre2 scaffold_4845:15928216-15928392 + CTGAAAAGCCAAGGCGGACTTTCCACTTTT---CGTCTGGCTGGCCTGGAAAAGCTCTCTTTCTCTAT-GCCTCTATGGCTCGGCAGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAATAGCCGTGCAAGCACACAGCTCGCACAAATTTTC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGGAAAATCCAA-GGCGC---------------------------------------ACTTT--CCACCTTTCCACGTCT-----GGCTGGCCTGGAAAAGCTCTCTTTCTCTATTGCCTCTATGGCTCGGCCGCGCTGGGCGCCTAATCCGAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAACCATCGAAAAGCCTGG------------------------------------CAAGCGCACAGCTCGCACAAATTTTCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CGAATGAGAGAAAGGTGGAGATACAAAGAGAGAAACAATGTTGCCTGCCTTTTCCCCAGTTTCCCCAGTGTT---TGTGTGTGTGGGGCGAACTGGAAAACCTCTGTTTTCCATCCCCCTTTTTGGC------GCGCTGAGCGCCTATTCCAAATTGCGAGAAAGATCCGCTTTTCGAGCCAAAAAGCCACCAAAAGCCCAAGGAGTTGTCGCACTCCGGACTACGCATAAAATCCCCCAAAAGCAGAACTCGC----------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-48.6 -47.8 -47.7

droSim1

-46.0 -45.3 -45.1

droSec1

-39.9 -39.9 -39.9 -39.9 -39.9 -39.9

droYak2

-42.1 -42.0 -41.4 -41.2 -41.2 -41.1

droEre2

-43.4 -43.2 -42.7 -42.6 -42.5 -42.5

droAna3

-26.7 -26.6 -26.5 -26.4 -25.9 -25.9

dp4

-57.2 -56.9 -56.4 -56.3 -56.2

droPer1

-48.3 -48.3 -48.3 -48.2 -48.2 -48.2

droWil1

-31.3 -31.1 -30.8 -30.5 -30.3

droVir3

-32.7 -32.7 -32.6 -32.6 -32.5 -32.5

droMoj3

-38.0 -37.7 -37.5 -37.4 -37.3 -37.3

droGri2

-15.0 -14.5 -14.3 -14.1 -14.1

Generated: 01/05/2013 at 05:27 PM