Secondary structure and small RNA-seq evidence for dme-mir-4939

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:18872718-18872857 - ATGCACATTTATTTGGCATCATG------------------------------------------C---------------------------------------TTCTGCGATCTCTACCAATTTTCCTTGCACTCT------TTGTCCTTTCCAAAAGTGACACGGGT----GCAGGTGAAGATTCG---GAAGAGGACGACGAAAACGACT---GCAAC-CGGACGACTCTTGGT
droSim1 chr2R:17459524-17459663 - ATCCACATTTATTTGGCATCATG------------------------------------------C---------------------------------------TTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGAT----GCAGGTGAAGATTCG---GAGGAGGACGACAGCGAAGACT---GCAAC-AGGACGACTCTTGGT
droSec1 super_9:2164747-2164886 - ATCCACATTTATTTGGCATCATG------------------------------------------C---------------------------------------TTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGAT----GCAGGTGAAGATTCA---GAGGAGGACGACAGCGAAGACT---GCAAC-AGGACGACTCTTGGT
droYak2 chr2R:18832811-18832950 - AACCGCGTTTATTTGCCAAAATG------------------------------------------C---------------------------------------TGCTCCGAGCTCTACCACTTCTGCTCACACTCTGTGTGTTGGTCCTCTCCAACGACGACACGGAT----GCAGATGAAGAAGAG---GAAGAGGACGA------CGACT---GCAAC-AAGGCGACTCTTGGT
droEre2 scaffold_4845:20234099-20234238 - AACCACGTTTATTTGCCATAATG------------------------------------------C---------------------------------------TGCTCCGAACTCTGCTC------CTTACGCTCTTCGTGTTTGTCCTTGCCAAAAACGATACGATT----GCAGAAGTAGAGGAA---GAGTCGGACGAGGACGAAGGAT---GCAAC-AAGGCGACTCTTGGT
droAna3 scaffold_13266:15204126-15204261 - ATTTAAGA-GCTTTTCCCTTCAAAGCCT----------------------------------------------------------------------------------------------AAACAGTTGACACAAAATGTGGCTACCCTTCTTGCTAGTGGCACTGCC----TTGGGGGACTGTGGTGGG---GGGAGGTCCTCTGACATTGGCCAATCTTAGCCGAATCATTGGA
dp4 chr3:14089101-14089284 - AAGCA-ATTAGTTTGCCATTTGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATTCGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTT----------------------------------------------AGTAACTCCCAGAACAACAAAATGAA---CAAAGCTCGATCCGCGTTC---GCCGC-CGCCCTTCTTTTGCT
droPer1 super_4:1228949-1229132 + AAGCA-ATTAGTTTGCCATTTGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATTCAAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTT----------------------------------------------AGTAGCTCCCAGAACAACAAAATGAA---CAAAGCTCGATCCGCGTTC---GCCGC-CGCCCTTCTTTTGCT
droWil1 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6496:24343095-24343103 - AT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTGGC
droGri2 scaffold_15112:3934700-3934745 - ATATTCAATATGCT-------------------------------------------GAGCACATC---------------------------------------TTCTGAAAGCATTTCAGACTTTC--------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:18872718-18872857 - ATGCACATTTATTTGGCATCATGCTTCTGCGATCTCTACCAATTTTCCTTGCACTCT------TTGTCCTTTCCAAAAGTGACACGGGTGCAGGTGAAGATTCGGAAGAGGACGACGAAAACGACTGCAACCGGACGACTCTTGGT
droSim1 chr2R:17459524-17459663 - ATCCACATTTATTTGGCATCATGCTTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGATGCAGGTGAAGATTCGGAGGAGGACGACAGCGAAGACTGCAACAGGACGACTCTTGGT
droSec1 super_9:2164747-2164886 - ATCCACATTTATTTGGCATCATGCTTCTGCGAGCTCTACCACTTCTCCTTGCACTCT------TTGTCCTTTCCAAAAGCGACACTGATGCAGGTGAAGATTCAGAGGAGGACGACAGCGAAGACTGCAACAGGACGACTCTTGGT
droYak2 chr2R:18832811-18832950 - AACCGCGTTTATTTGCCAAAATGCTGCTCCGAGCTCTACCACTTCTGCTCACACTCTGTGTGTTGGTCCTCTCCAACGACGACACGGATGCAGATGAAGAAGAGGAAGAGGACGAC------GACTGCAACAAGGCGACTCTTGGT
droEre2 scaffold_4845:20234099-20234238 - AACCACGTTTATTTGCCATAATGCTGCTCCGAACTCTGCTCCTT------ACGCTCTTCGTGTTTGTCCTTGCCAAAAACGATACGATTGCAGAAGTAGAGGAAGAGTCGGACGAGGACGAAGGATGCAACAAGGCGACTCTTGGT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATCCACATTTATTTGGCATCATGCTTCTGCGAGCT----------CTACCACTTCTCCTTGCACTCTTTGTCC-------------------------------------------TTTCCAAAAGCGACACTGATGCAGGTGAAGAT--------TCGGAGGAGGACGACAGC-----GAA------------GACTGCAACAGGACGACTCTTGGTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AAGCA-ATTAGTTTGCCATTTGCCA-------TCTTATCGGGGTAATACCCAATC-----CAATTTATTGACCAATTCGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGA------------------AATTTTAGTAACTCCCAG---AACAACAAAATGAACAAAGCTCGATCCGCGTTCGCCGCCGCCCTTCTTTTGCTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-42.7,  p-value=0.009901 dG=-42.7,  p-value=0.009901 dG=-42.4,  p-value=0.009901 dG=-42.2,  p-value=0.009901 dG=-42.2,  p-value=0.009901 dG=-39.2,  p-value=0.009901

droSim1

dG=-35.6,  p-value=0.009901 dG=-35.6,  p-value=0.009901 dG=-35.5,  p-value=0.009901 dG=-35.5,  p-value=0.009901 dG=-35.5,  p-value=0.009901 dG=-32.3,  p-value=0.009901

droSec1

dG=-32.9,  p-value=0.009901 dG=-32.9,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-32.6,  p-value=0.009901 dG=-29.7,  p-value=0.009901

droYak2

dG=-37.7,  p-value=0.009901 dG=-37.6,  p-value=0.009901 dG=-37.2,  p-value=0.009901 dG=-37.1,  p-value=0.009901 dG=-37.1,  p-value=0.009901

droEre2

dG=-32.2,  p-value=0.009901 dG=-32.2,  p-value=0.009901 dG=-32.2,  p-value=0.009901 dG=-32.2,  p-value=0.009901 dG=-32.2,  p-value=0.009901

droAna3

dG=-36.7,  p-value=0.009901 dG=-36.5,  p-value=0.009901 dG=-36.3,  p-value=0.009901 dG=-36.3,  p-value=0.009901 dG=-36.1,  p-value=0.009901 dG=-29.6,  p-value=0.009901

dp4

dG=-23.1,  p-value=0.009901 dG=-22.8,  p-value=0.009901 dG=-22.7,  p-value=0.009901 dG=-22.5,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-16.6,  p-value=0.009901

droPer1

dG=-22.2,  p-value=0.009901 dG=-22.1,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-22.0,  p-value=0.009901 dG=-21.9,  p-value=0.009901 dG=-16.2,  p-value=0.009901

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

dG=0.0,  p-value=1.0

droGri2

dG=-5.5,  p-value=0.009901 dG=-5.4,  p-value=0.009901 dG=-5.3,  p-value=0.009901 dG=-5.2,  p-value=0.009901 dG=-5.0,  p-value=0.009901

Generated: 03/07/2013 at 07:17 PM