Secondary structure and small RNA-seq evidence for dme-mir-4973

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:20562282-20562463 + GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT--------TGGACTGCTCC--------------------------------------------------------------------------------TCCTCCAACTACTACTGCGGCC-----------------------------------GCTGCTGCTGCTGCTG---CGG-----------------------CTGCTGCATCCGC---CTGCAACCT--------------------------GCAACACTCACACCACGGCAA----------------------------------------------------CAGAAGTAGACGCGTCGC
droSim1 chr2L:20133895-20134076 + GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT--------TGGACTGCTCC--------------------------------------------------------------------------------TCCTCCAGCTACTACTGCGGCC-----------------------------------GCTGCTGCTGCTGCTG---CGG-----------------------CTGCTGCATGCGC---CTGCAACCT--------------------------GCAACACTCACACCACGGCAA----------------------------------------------------CAGAAGTAGACGCGTCGC
droSec1 super_18:446156-446334 + GGTCCTTGGGCCA-TCGCTGGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT--------TGGACTGCTCC--------------------------------------------------------------------------------TCCTCCAGCTACTACTGCGGCC-----------------------------------GCTGCCGCTGCTGCTG---CG--------------------------GCTGCATCCGC---CTGCAACCT--------------------------GCAACACTCACACCACGGCAA----------------------------------------------------CAGAAGTAGACGCGTCGC
droYak2 chr2R:6918558-6918738 + GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT--------TGGACTGCTCC--------------------------------------------------------------------------------TGCTCCAACTACTACTGCGGCC-----------------------------------GCTGCT---GCTGCTG---CGG-----------------------CTGCTGCATCTGC-ATCTGCAACCT--------------------------GCAACACTCACACCACGGCAA----------------------------------------------------CAGAAATAGACGCGTCGC
droEre2 scaffold_4845:3882318-3882503 - GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTTTGGACGTTTGGACTGCGCC--------------------------------------------------------------------------------TCCTCCAACTACTACTGCGGCC-----------------------------------GCCGCTGCTGCTGCTG---CGG-----------------------CTGCTGCATCT-------GCAACCT--------------------------GCAACACTCACACCACGGCAA----------------------------------------------------CAGAAGTAGACGCGTCGC
droAna3 scaffold_13117:435722-435893 + GGCC-TTGGTC---TCCATCTT-GGGGTAGCCGTAGGGAGC----GATGGCCTTGT-TGGTGAG-TTCCA----------GGGGCTTCTCT--------------------------------------------------------------------------------GGGGCCATTTGCTGCAGCTGCT-----------------------------------GCTGCTGCTGCTGCTGGTGTTG-----------------------CTGCTGCTTCT-C---C-TCGGCGT-------------------------CGCGTCGCTCGCGCAGCTGCT------------------------------------------------------CGTAGTAGGGACGATGC
dp4 chr4_group3:7758140-7758314 - GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTTGTAGGTGGActggtctgctctg-ctccgct------------ctgc---------------------------tctgc---cc-------------------------------------------------------------------------------------------------------agcactgctGTTGCTC---C---------------------------ACTGCATCTCTCTC-------CTacacacacacacacgcacgcacacacacg-caagca---cacaACAG----------------------------------------------------CAAAAAT-CTCGCGACGC
droPer1 super_1:9204247-9204421 - GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTCGTAGGTGGACTGGTGCGGTCTG-ATCCGCT------------TTGC---------------------------TCTGC---CC-------------------------------------------------------------------------------------------------------AGCACTGCTGTTGATC---C---------------------------ACTGCATCTCTCTC-------CTacacacacacacacgcacgcacacacacg-caagca---cacaACAG----------------------------------------------------CAAAAAT-CTCGCGACGC
droWil1 scaffold_180708:1965385-1965667 + GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGtggcctggtctggtctggcttggac--------tggactggtctgAAGTTTTTGGCAAGTTTTTTTGCTCTGC---C--------------------ACTGCCACAACCAG----TG-------TTCTTCAACTAAtgctgcttct-----------------------------------actgctaaagctgctg---ctg-----------------------ctgctgcATCT-TCAC-------CTGCACACATAGCCACGT-CG-----ACTCGTCGGGGT---CACCAAGGA-AAAAATCAACGAAAAATAAT------AA---TAACTGCTAAAAATGAAAGAAAAAAGAGTCTCGTCGC
droVir3 scaffold_12963:13534067-13534330 - GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGTCTGGTCTGCTCTG-TGCT------------GGTCTGC---------------------------GCTGCTGCCC----AGATTTTTGCTGCC-ACTGGCACACACTGATTGGGATGCCTc------tgccgctgctgccgttgctgtcgagccgacgttgctgctgattttgctgttgctgttgctgttgctg---ttg-----------------------ctgctACATCT-TCC---------------------------------------------------------GCAATG----ACGACGACCAACCC---AAA---CTTCTGTTTCAATTG----CCGTACGCGACGCGACGC
droMoj3 scaffold_6500:24644505-24644771 + GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCgttgcgtgttgtaggtggtctggtctgctctg-gtct------------ggcctgc---------------------------gctgctgttcagcctactttttgatgcc-actgccacacactgatggtgatgcctt------cgctgctgctgctgctgctgct-----tctgttgctgct---gccgtcgttgctgtcgtcgctgcta---ttg-----------------------ctgcCACATCT-TCT---------------------------------------------------------ACAACGACCGACGACGACCAACCC---AAACTGCTTCTGTTTCAATTG----CCGTACGCGACGCGACGC
droGri2 scaffold_15126:6330398-6330651 + GGTCCTTTCGCAA-TCGTTCGT-TCAGTCGTCGTTGCGTGTTGTAGGtggtctggtctgctctg-gtct------------ggtctAC---------------------------GCAGCTGCTCC-CCAAACTTTTGCTGTCTGCTGA-----ACTGAATGTAATGGCTc------tgctgatgctgatgcc-----------------------------------gccgatgccgctgatg---ccgctgctgcCCATCGCTGCCCAATGCAGCCACATCT-TCG---------------------------------------------------------ACAATG----ACGACGACTAACCCACCAAA---CTTCTGTTTCAATTG----CTATACGCGACGCGACGC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:20562282-20562463 + GGTCCTTGGGCCATCGCTCGTTCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAGCTCCGTTT--------GGACTGCTCCTCCTCCAACTACTACTGCGGCCGCTGCTGCTGCTGCTGCGGCTGCTGCATCCGC--CTGCAACCTGCAACACTCACACCACGGCAACAGAAGTAGACGCGTCGC
droSim1 chr2L:20133895-20134076 + GGTCCTTGGGCCATCGCTCGTTCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAGCTCCGTTT--------GGACTGCTCCTCCTCCAGCTACTACTGCGGCCGCTGCTGCTGCTGCTGCGGCTGCTGCATGCGC--CTGCAACCTGCAACACTCACACCACGGCAACAGAAGTAGACGCGTCGC
droSec1 super_18:446156-446334 + GGTCCTTGGGCCATCGCTGGTTCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAGCTCCGTTT--------GGACTGCTCCTCCTCCAGCTACTACTGCGGCCGCTGCCGCTGCTGCTGCGGC---TGCATCCGC--CTGCAACCTGCAACACTCACACCACGGCAACAGAAGTAGACGCGTCGC
droYak2 chr2R:6918558-6918738 + GGTCCTTGGGCCATCGCTCGTTCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAGCTCCGTTT--------GGACTGCTCCTGCTCCAACTACTACTGCGGCCGCTGCTG---CTGCTGCGGCTGCTGCATCTGCATCTGCAACCTGCAACACTCACACCACGGCAACAGAAATAGACGCGTCGC
droEre2 scaffold_4845:3882318-3882503 - GGTCCTTGGGCCATCGCTCGTTCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAGCTCCGTTTGGACGTTTGGACTGCGCCTCCTCCAACTACTACTGCGGCCGCCGCTGCTGCTGCTGCGGCTGCTGCAT------CTGCAACCTGCAACACTCACACCACGGCAACAGAAGTAGACGCGTCGC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAGCTCCGTT-TGGACTGCTCCTCCTCCAGCTACTACTGCGGCCGCTGCTGCTGCTGCTGCGGCTGCTGCATGCGCCTGCAACCTGCAACACTCACAC-------------------------CACGGCAACAGAAGTAGACGCGTCGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTTGTAGGTGGActggtctgctctgctccgctctgctctgccc-------------------ag-cactgctGTTGCT---CC----ACTGCATCTCTCTCC----T---acacacacacacacgcacgcacacacacgcaagcacacaACAGCAAAAAT-CTCGCGACGCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.........................AGTCGTCGTTGCGTGTTG.......................................................................................................................................................................1811.00101
.........................................TGTAGGTGGACTGGTCTGCTCTGC.................................................................................................................................................2411.00101

Secondary Structure

dm3

-61.4 -60.9 -60.8 -60.6 -60.4

droSim1

-61.8 -61.8 -61.6 -61.6 -61.6 -61.6

droSec1

-62.9 -62.1 -61.9

droYak2

-58.2 -58.0 -57.4 -57.4 -57.3 -57.2

droEre2

-62.9 -62.7 -62.6 -62.4 -62.2 -62.1

droAna3

-62.0 -61.7 -61.7 -61.4 -61.4 -61.4

dp4

-35.1 -35.1 -34.9 -34.8 -34.6 -34.4

droPer1

-45.2 -45.2 -44.6 -44.6

droWil1

-69.7 -69.6 -69.5 -69.2 -69.2 -69.1

droVir3

-63.2 -63.2 -63.2 -63.2 -63.1 -63.1

droMoj3

-68.4 -68.4 -68.4 -68.4 -68.4 -68.4

droGri2

-62.7 -62.7 -62.4 -62.4 -62.2 -62.2

Generated: 01/05/2013 at 05:26 PM