Secondary structure and small RNA-seq evidence for dme-mir-4945

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:7267898-7268043 - TTGGTGATGGTGATGGTGATGGTGCTGGTGGTGGTGCC------TTCATTG-------------------------TTTT---------TCTCTTCTT--TTTGTTGTTTGACTTTTACACTTTTG---------------AAC--------------------------------------AA------CAAGCCGAAAGGAA----------------------------------------------AAAG--CAT---GAA-GGAATGCAAAGTATTCGATAAAAAAT-TATGAAA
droSim1 chr3R:14102257-14102390 + TTGGTGATGG------------TGCTGGTGGTGGTGCC------TTCATTG-------------------------TTTC---------CCTCTTCTT--TTTGTTGTTTGACTTTTACACTTTTG---------------AAC--------------------------------------AA------CAAGCCGAAAGGAA----------------------------------------------AAAG--CAT---GAA-GGAATGCAAAGTATTCGATAAAAAAT-TATGAAA
droSec1 super_0:14695532-14695664 + TTGGTGATGG------------TGCTGGTGGTGGTGCC------TTCATTG-------------------------TTTC---------CCTCTTCTT--TTTGTTGTTTGACTTTTACACTTGTG---------------AAA--------------------------------------AA------CAAGCCGAAAGGAA----------------------------------------------AAAG--CAT---GAA-GGAATGCA-AGTATTCGATAAAAAAT-TATGAAA
droYak2 chr3R:11301709-11301828 - TTGGTGG---------------------------TGCC------TTCATTG-------------------------TTTT---------CCTCTTCTT--TTTGTTGTTTGACTTTTACACTTTTG---------------AAC--------------------------------------AA------CAGGCCGAAAGGAA-------------------------A--------------------AAAG--CAT---GAA-GGAATGCAAAGCATTCGATAAAAAAT-TATGAAA
droEre2 scaffold_4770:14352366-14352483 + TTGGTGG---------------------------TGCC------TTCATTG-------------------------TTTT---------CCTCATCTT--TTTGTTGTTTGACTTTTACACTTTTG---------------AAC--------------------------------------AA------CAAGCCGAAAGGA-----------------------------------------------AAAG--CAT---GAA-GGAATGCAAAGCATTTGATAAAAAAT-TATGAAA
droAna3 scaffold_13340:13702429-13702549 - TCGGCAG---------------------------TGCC------CCCATTG-------------------------TTTT---------CTTCTCATTT-TTTCTTGTTTGACTTTTACACTTTTTT--------------AAC--------------------------------------AA------CAA--CAAAAGCAA----------------------------------------------AGAGACAAT---GGACGGAATGCAAAGTATTCGATATAAAAC-CG-AAAA
dp4 chr3:2000510-2000593 + CTGGTGGTGGTGGTGGTGGTGGTCTTGGTGCTGCTGCT------------------------GCAATTCAATTTCGTTTC---------GCTTTTGTTTCTTTTTTGTTTGCCTTTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 super_6:893248-893436 - TTGGCGGCGACGGCG-------------------TCTC------TTCTCTGTCTCTCTCCCTCCCGTTCTCGTTCGCTCCCACAGGACGG------CC--TCTGTTGTTTGACTTTTGCACTTCTTT---------TTTTAAACAGGGAGTGGGAGTGGGAGTGTGAGCGAGACAAACAGACAGCA---GC-----------------------------------------------------------AAAA--CAT---AAA--GAATGCAAAGTATTCGATAAAACACACACAAAA
droWil1 scaffold_181089:4216454-4216565 + TTGGCAGCAGC--------------------------A------GCCATTG-------------------------TCTT---------AAG---------CAGTTGTTTGACTTTTACACTTCTCC--------------CGC--------------------------------------AGCAACAACAAAGCATAAAAAG----------------------------------------------A-------------A-AACATGCAAAGTATTGGAAAAACACT-GAAAAAT
droVir3 scaffold_12855:9719552-9719632 - TTGGTTCGCG------------------------CGCGCGCACGGCCATTG-------------------------TCTT---------AAG---------CAGTTGTTTGACTTTTGCACTTTTTT--------------AAC--------------------------------------AACA---ACAAAGAA-----------------------------------------------------A------------------------------------------AGTCA--
droMoj3 scaffold_6540:24748319-24748394 - TTCGCGCAGG----------------------------------GCCATTG-------------------------TCTT---------A------CG--ACAGTTGTTTGACTTTTGCACTTTTTT--------------AAG------------------------------A-------AA------C------------------------------------------------------------------------------------------AAACAAAAAAC-AATGAGC
droGri2 scaffold_14830:2094020-2094205 - TTTGGCG-----------------------------CC----C-AGTATTG-------------------------TTTT---------AAG---------CAGTTGTTTGACTCTTGCACTTTTTTCTTCTTTTTTTTT-AAT------------------------------AAGCAAACAACA---ACAAAGCCAAGTCAGCAACCTGTACACAGTCTGAAGGGGGAAGGGCTGGAGTTTGCTTGAAAAAG--TATCTGCAA-AGAATGCAAAGTATTGTATACAAAGTGTGTAGAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:7267898-7268043 - TTGGTGATGGTGATGGTGATGGTGCTGGTGGTGGTGCCTTCATTGTTTTTCTCTTCTT-TTTGTTGTTTGACTTTTACACTTT-TGAACAACAAGCCGAAAGGAAA-A-AGC-ATG-AAGGAATGCAAAGTATTCGATAAAAAATTATGAAA
droSim1 chr3R:14102257-14102390 + TTGGTGA------------TGGTGCTGGTGGTGGTGCCTTCATTGTTTCCCTCTTCTT-TTTGTTGTTTGACTTTTACACTTT-TGAACAACAAGCCGAAAGGAAA-A-AGC-ATG-AAGGAATGCAAAGTATTCGATAAAAAATTATGAAA
droSec1 super_0:14695532-14695664 + TTGGTGA------------TGGTGCTGGTGGTGGTGCCTTCATTGTTTCCCTCTTCTT-TTTGTTGTTTGACTTTTACACTTG-TGAAAAACAAGCCGAAAGGAAA-A-AGC-ATG-AAGGAATGCA-AGTATTCGATAAAAAATTATGAAA
droYak2 chr3R:11301709-11301828 - TTGG---------------------------TGGTGCCTTCATTGTTTTCCTCTTCTT-TTTGTTGTTTGACTTTTACACTTT-TGAACAACAGGCCGAAAGGAAAAA-AGC-ATG-AAGGAATGCAAAGCATTCGATAAAAAATTATGAAA
droEre2 scaffold_4770:14352366-14352483 + TTGG---------------------------TGGTGCCTTCATTGTTTTCCTCATCTT-TTTGTTGTTTGACTTTTACACTTT-TGAACAACAAGCCGAAAGGAA--A-AGC-ATG-AAGGAATGCAAAGCATTTGATAAAAAATTATGAAA
droAna3 scaffold_13340:13702429-13702549 - TCGG---------------------------CAGTGCCCCCATTGTTTTCTTCTCATTTTTTCTTGTTTGACTTTTACACTTTTTTAACAACAA--CAAAAGCAAAGAGA-CAATGGACGGAATGCAAAGTATTCGATATAAAACCG-AAAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTGGTGATGGTG------------CTGGTGGTGGTGCC----------TTCATTGTTTCCCTCTTCTT--TTTGTTGTTTGACTTTTACACTTTTGAACAACAAGCCGAAAGGAAAAAGCATGAAGGAATGCAAAGTATTCGATAAAAAATTATGAAASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CTGGTGGTGGTGGTGGTGGTGGTCTTGGTGCTGCTGCTGCAATTCAATT---TCGTTTCGCTTTTGTTTCTTTTTTGTTTGCCTTTT-----------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-31.5 -31.4 -31.2 -31.2 -31.1 -30.9

droSim1

-25.5 -25.5 -25.4 -25.4 -25.2 -25.2

droSec1

-25.0 -25.0 -24.5 -24.5 -24.5 -24.5

droYak2

-28.0 -27.6 -27.5 -27.5 -27.2 -27.2

droEre2

-29.5 -28.6 -28.6 -28.6

droAna3

-15.7 -15.7 -15.7 -15.7 -15.5 -15.5

dp4

-8.5 -8.3 -8.0

droPer1

-46.0 -45.9 -45.6 -45.6 -45.6 -45.4

droWil1

-9.2 -8.8 -8.7 -8.5 -8.2

droVir3

-5.6 -5.2 -4.9 -4.7 -4.6

droMoj3

-6.1 -5.9 -5.9 -5.7 -5.6 -5.5

droGri2

-32.6 -32.2 -32.1 -32.1 -32.1 -32.0

Generated: 01/05/2013 at 05:22 PM