Secondary structure and small RNA-seq evidence for dme-mir-973

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19445546-19445676 + AATATACTTC----ACTTTA-CCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTTAAG-TA--TTT--------AAATAAAATGAAATCTGTTCATTCTCCGACACAAGAAGTTCACGCAAAGGA------------------------GCTGCAGCTGCGAA
droSim1 chrX:15011303-15011407 + CG-------------------------TATACTTTTCCGGGTTGGTGGTTGAACTTCGATTTTAAG-CA--TTT--------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAA------------------------GCAGCG------AA
droSec1 super_8:1727974-1728085 + AC------------------TTCAACGTATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTTAGG-TA--TTT--------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAA------------------------GCAGCG------AG
droYak2 Unknown GTTATAA--G----AT----TTTAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGAG-TA--TAC--------AAATAGAA-CAAATCTGTTCATTCCTCGACACAACAAGTTGACGTAAAGGA------------------------GCAGCA------AA
droEre2 scaffold_4690:9682299-9682417 + ACTATAC--C----AT----TTTAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGAG-TA--TTC--------AAATAAAA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGACGTGCAGGA------------------------GCGGCA------AA
droAna3 scaffold_13417:2478622-2478750 - -----------------------GACACCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTTTAA-TT--TTC--------GAGTACGA-GAAATCTGTTCATTCCTCGACACTAGTAGTTGGCGCGACA-C------TCAGCGCACCAAACATGAACCGCGGCTCAAAT
dp4 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181096:7946449-7946592 + AAAATATATCGGGAATATTG-TCGACATGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGTTCTATATACATATATAAAAAT-ATG-TAAATCTGTTCATTCCTCGACACTAGAAGTTCATGTCAATAACTTCATTT----------------CCTGCA--------
droVir3 scaffold_13042:918337-918453 - AGAACAGTTA----AAATCATCGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTTT-TA--TAT--------A-----CA-CAAATCTGTTCATTCCTCGACACTAGAAGTTTGCGTCAATAA------------------------GCTGC---------
droMoj3 scaffold_6328:2909116-2909204 - ----------------------CGGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTAA-AA--TAT--------GAA---AA-GAAATCTGTTCATTCCTCGACACTAAGAGTTTAGG---------------------------------------------
droGri2 scaffold_15081:2051526-2051596 - -----------------------GACATTTACTTTTTGTGTTGGGTGATTC---------------------------------------------TGATTCACTTTTCGACACATCAAGTTCACCTCAATAA------------------------ACTGCA--------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19445546-19445676 + AATATACTTC----ACTTTA-CCGTCGTCGACTTTTCGTGGTTGGTGGTTGAACTTCGATTTTAAG-TA--TTT--------AAATAAAATGAAATCTGTTCATTCTCCGACACAAGAAGTTCACGCAAAGGA------------------------GCTGCAGCTGCGAA
droSim1 chrX:15011303-15011407 + CGTAT-------------------------ACTTTTCCGGGTTGGTGGTTGAACTTCGATTTTAAG-CA--TTT--------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAA------------------------GCAGCG------AA
droSec1 super_8:1727974-1728085 + AC------------------TTCAACGTATACTTTTCGGGGTTGGTGGTTGAACTTCGATTTTAGG-TA--TTT--------AAATAAGA-TAAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAA------------------------GCAGCG------AG
droYak2 Unknown GTTATAA--G----AT----TTTAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGAG-TA--TAC--------AAATAGAA-CAAATCTGTTCATTCCTCGACACAACAAGTTGACGTAAAGGA------------------------GCAGCA------AA
droEre2 scaffold_4690:9682299-9682417 + ACTATAC--C----AT----TTTAACGTCGACTTTTCGTGGTTGGTGGCTGAACTTAGATTTTGAG-TA--TTC--------AAATAAAA-TAAATCTGTTCATTCCTCGACACAAGAAGTTGACGTGCAGGA------------------------GCGGCA------AA
droAna3 scaffold_13417:2478622-2478750 - G-----------------------ACACCGACTCCTCGTGTTTGGCGATTGAACCTGGATTTTTAA-TT--TTC--------GAGTACGA-GAAATCTGTTCATTCCTCGACACTAGTAGTTGGCGCGACA-C------TCAGCGCACCAAACATGAACCGCGGCTCAAAT
droWil1 scaffold_181096:7946449-7946592 + AAAATATATCGGGAATATTG-TCGACATGGCCTTTTCGTGTTTGGTGATTGAACTTGGATTTTGTTCTATATACATATATAAAAAT-ATG-TAAATCTGTTCATTCCTCGACACTAGAAGTTCATGTCAATAACTTCATTT----------------CCTGC--------A
droVir3 scaffold_13042:918337-918453 - AGAACAGTTA----AAATCATCGGACATTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTTT-TA--TAT--------A-----CA-CAAATCTGTTCATTCCTCGACACTAGAAGTTTGCGTCAATAA------------------------GCTGC---------
droMoj3 scaffold_6328:2909116-2909204 - ----------------------CGGCTTTCACTTTTCGTGTTCGATGTTTGAACTTGGATTTTTAA-AA--TAT--------GAA---AA-GAAATCTGTTCATTCCTCGACACTAAGAGTTTAGG---------------------------------------------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGTATAC--------------------TTTTCCGGGTTGGTGGTTGAACTTCGATTTTAAGCATTTAAATAAGAT-AAATCTGTTCATTCTTCGACCCAAAAAGTTCACGTGAAGAAGC------AGCGAASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
-----------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-18.8,  p-value=0.009901 dG=-18.7,  p-value=0.009901 dG=-18.4,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-18.1,  p-value=0.009901

droSim1

dG=-17.7,  p-value=0.009901 dG=-17.1,  p-value=0.009901 dG=-16.9,  p-value=0.009901 dG=-16.7,  p-value=0.009901 dG=-16.7,  p-value=0.009901

droSec1

dG=-19.1,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-18.3,  p-value=0.009901

droYak2

dG=-13.5,  p-value=0.009901 dG=-13.3,  p-value=0.009901 dG=-12.9,  p-value=0.009901 dG=-12.9,  p-value=0.009901 dG=-12.9,  p-value=0.009901

droEre2

dG=-15.3,  p-value=0.009901 dG=-15.2,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-15.0,  p-value=0.009901 dG=-14.4,  p-value=0.009901

droAna3

dG=-18.3,  p-value=0.009901 dG=-18.0,  p-value=0.009901 dG=-18.0,  p-value=0.009901 dG=-17.6,  p-value=0.009901 dG=-17.6,  p-value=0.009901

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

dG=-18.7,  p-value=0.009901 dG=-18.5,  p-value=0.009901 dG=-18.4,  p-value=0.009901 dG=-18.3,  p-value=0.009901 dG=-18.3,  p-value=0.009901

droVir3

dG=-12.7,  p-value=0.009901 dG=-12.7,  p-value=0.009901 dG=-12.5,  p-value=0.009901 dG=-12.5,  p-value=0.009901 dG=-12.4,  p-value=0.009901

droMoj3

dG=-14.8,  p-value=0.009901 dG=-14.8,  p-value=0.009901 dG=-14.8,  p-value=0.009901 dG=-14.8,  p-value=0.009901 dG=-14.2,  p-value=0.009901

droGri2

dG=-11.6,  p-value=0.009901 dG=-11.0,  p-value=0.009901 dG=-10.6,  p-value=0.009901

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