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

dG=-15.6,  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

droSim1

dG=-14.3,  p-value=0.009901 dG=-13.8,  p-value=0.009901 dG=-13.4,  p-value=0.009901 dG=-13.3,  p-value=0.009901

droSec1

dG=-14.3,  p-value=0.009901 dG=-14.2,  p-value=0.009901 dG=-13.5,  p-value=0.009901 dG=-13.3,  p-value=0.009901 dG=-13.3,  p-value=0.009901

droYak2

dG=-16.5,  p-value=0.009901 dG=-15.7,  p-value=0.009901

droEre2

dG=-15.3,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-15.1,  p-value=0.009901

droAna3

dG=-7.0,  p-value=0.009901 dG=-7.0,  p-value=0.009901 dG=-7.0,  p-value=0.009901 dG=-6.7,  p-value=0.009901 dG=-6.7,  p-value=0.009901

dp4

dG=-1.6,  p-value=0.009901 dG=-1.4,  p-value=0.009901 dG=-1.1,  p-value=0.009901

droPer1

dG=-41.1,  p-value=0.009901 dG=-41.1,  p-value=0.009901 dG=-40.8,  p-value=0.009901 dG=-40.8,  p-value=0.009901 dG=-40.5,  p-value=0.009901 dG=-38.1,  p-value=0.009901

droWil1

dG=-3.7,  p-value=0.009901 dG=-3.7,  p-value=0.009901 dG=-3.6,  p-value=0.009901 dG=-3.6,  p-value=0.009901 dG=-3.4,  p-value=0.009901

droVir3

dG=-4.4,  p-value=0.009901 dG=-3.5,  p-value=0.009901

droMoj3

dG=-4.6,  p-value=0.009901 dG=-4.4,  p-value=0.009901 dG=-4.4,  p-value=0.009901 dG=-4.4,  p-value=0.009901 dG=-4.0,  p-value=0.009901

droGri2

dG=-27.1,  p-value=0.009901 dG=-26.9,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.6,  p-value=0.009901 dG=-26.4,  p-value=0.009901

Generated: 03/07/2013 at 05:42 PM