Secondary structure and small RNA-seq evidence for dme-mir-961

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:5641176-5641294 + GTAGTGAGCTC--GT-------T------ATCAAG-----GGCCGAGTTACCTTTGATCACCAGTAACTGAGATT-GT--TTCTGATA---CGGTTTCGTTTTCTGGCAATCAA-AAGAACTTGGACTCGA-CTTGAA----------------------------------------------------------TTCAACTAC
droSim1 chr2L:5434262-5434381 + GTAATGTGCTC--GT-------T------ATCATG-----GGCCGAGTTACCTTTGATCATCAGTAAGTGAGATT-GT--TTCTGATA---CGATTTCGTTTTCTGGCAATCAA-AGGAACTCGA-CTCGA-CTTGAA-TC-------------------------------------------------------TACAACTAC
droSec1 super_5:3718917-3719036 + GTAATGTACTC--TT-------T------ATCAAG-----GCCCGAGTTACCTTTGATCACCAGTAAGTGAGATT-GT--TTCTGATA---CGATTTCGTTTTCTGGCAATCAA-AGGAACTCGA-CTCGA-CTTGAA-TC-------------------------------------------------------TACAACTAC
droYak2 chr2L:13552021-13552135 - GAAAA----TCTAAT---------------TCATG-----GGTCGAGTTACCATTGATCACCGGTTACTGAGGTT-GT--TCCTTCTT---TGGCTTCGTTTTCTGGCGATCAA-AAGAACTCGA-CTCGA-CTCGAA----------------------------------------------------------TCCAACCAA
droEre2 scaffold_4929:5729649-5729755 + TG-----------AT---------------TCATG-----GGTCGAGTTACCATTGATCACCGGTTACTGAGGTT-GT--GCCACATT---CGGCTTCGTTTCCTGGCGATCAA-AAGAACTCGA-CTCGG-CTCGAA----------------------------------------------------------TCCCAGTAC
droAna3 scaffold_12916:11084979-11085099 + ACAAAGGACTA--CAGGAAAGCG------ACT-TA----AGTCCGAGCACTATTTGATCACTGGTTACTGAGGTT-GT--TTTGTCAT---AAGCTTCGTTTTCTGGCGATCAA-ATACGCTCGA-CTT-----TGGG----------------------------------------------------------CCCAACCAC
dp4 chr4_group4:3182338-3182458 - GAGGAGAGCTG--TT---------------TCGCCGGACAGTCAGAGTTTGATTTGATCTCTAGTTACTGGGCTTTGA--TTCGAAATAAGTAGCTTATTATTCTAGTGATTGAAATGAACTCGA-CTCG------AG----------------------------------------------------------TGCCACAAA
droPer1 super_10:2201269-2201389 - GAGGAGAGCTG--TT---------------TCGCCGGACAGTCAGAGTTTGAGTTGATCTCTAGTTACTGGGCTTTGA--TTCGAAATAAGTAGCTTATTATTCTAGTGATTGAAATGAACTCGA-CTCG------AG----------------------------------------------------------TGCCACAAA
droWil1 scaffold_180708:8625990-8626125 - GTGTGAAACT-----------------------TG----AGTTTGAGTTTACATTGATCACTGGTTAGTGAGGTT-CAAAGTCAGACC---CAACTTCGTTATCTGGCGATCAA-ATAAACCTGG-CTTACA----AAAGCTATAATTGCTGAAATGGATACACGT-----------------------T------T---TCTAT
droVir3 scaffold_12963:3615378-3615429 + G---------------------------------------------------------------------------------------------TTTCATTTTTCAGTGAATTA-AACAACTCAA-TTTACACACACA----------------------------------------------------------CACACACAT
droMoj3 scaffold_6500:14018312-14018360 + ATTTAAATGTA--TT---------------CCGGTCTATGGCG--------------------TTTACGG--------------------------TCGTTTTGTCGTA---------------------------------------------------------------------------------------------CTC
droGri2 scaffold_15252:3147112-3147237 + GTTGTTAGCAG--CCACATCTCTGAATTGAAT-TG----GATTCGTT-----------------TTACT--------------------------TTCTTTTATTACTGAAATG-AGTTGTTCAG-TTC-T-TTTAAA-TT-------------------------TCAGTCTACAAACTAAGAGCAGGTTACTTTCATAACACA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:5641176-5641294 + GTAGTGAGCTC--GTTATCAAG------------GGCCGAGTTACCTTTGATCACCAGTAACTGAGATT--GTTTCTGATA---CGGTTTCGTTTTCTGGCAATCA-AAAGAACTTGGACTCGACTTGAAT-T--CAA-----------------------CTAC
droSim1 chr2L:5434262-5434381 + GTAATGTGCTC--GTTATCATG------------GGCCGAGTTACCTTTGATCATCAGTAAGTGAGATT--GTTTCTGATA---CGATTTCGTTTTCTGGCAATCA-AAGGAACTCG-ACTCGACTTGAAT-CTACAA-----------------------CTAC
droSec1 super_5:3718917-3719036 + GTAATGTACTC--TTTATCAAG------------GCCCGAGTTACCTTTGATCACCAGTAAGTGAGATT--GTTTCTGATA---CGATTTCGTTTTCTGGCAATCA-AAGGAACTCG-ACTCGACTTGAAT-CTACAA-----------------------CTAC
droYak2 chr2L:13552021-13552135 - GAAAA----TCTAATT--CATG------------GGTCGAGTTACCATTGATCACCGGTTACTGAGGTT--GTTCCTTCTT---TGGCTTCGTTTTCTGGCGATCA-AAAGAACTCG-ACTCGACTCGAAT-C--CAA-----------------------CCAA
droEre2 scaffold_4929:5729649-5729755 + TG-----------ATT--CATG------------GGTCGAGTTACCATTGATCACCGGTTACTGAGGTT--GTGCCACATT---CGGCTTCGTTTCCTGGCGATCA-AAAGAACTCG-ACTCGGCTCGAAT-C--CCA-----------------------GTAC
droAna3 scaffold_12916:11084979-11085099 + ACAAAGGACTA--CA-----GGAAAGCGACTTAAGTCCGAGCACTATTTGATCACTGGTTACTGAGGTT--GTTTTGTCAT---AAGCTTCGTTTTCTGGCGATCA-AATACGCTCG-ACT----TTGGGC-C--CAA-----------------------CCAC
dp4 chr4_group4:3182338-3182458 - GAGGAGAGCTG--TTTCGCCGGA---------CAGTCAGAGTTTGATTTGATCTCTAGTTACTGGGCTTT-GATTCGAAATAAGTAGCTTATTATTCTAGTGATTGAAATGAACTCG-ACT-----CGAGT-G--CCA-----------------------CAAA
droPer1 super_10:2201269-2201389 - GAGGAGAGCTG--TTTCGCCGGA---------CAGTCAGAGTTTGAGTTGATCTCTAGTTACTGGGCTTT-GATTCGAAATAAGTAGCTTATTATTCTAGTGATTGAAATGAACTCG-ACT-----CGAGT-G--CCA-----------------------CAAA
droWil1 scaffold_180708:8625990-8626125 - GTGTGAAACTT----------G-----------AGTTTGAGTTTACATTGATCACTGGTTAGTGAGGTTCAAAGTCAGACC---CAACTTCGTTATCTGGCGATCA-AATAAACCTG-GCTTA---CAAAAGCTATAATTGCTGAAATGGATACACGTTTTCTAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GTAATGTGCTCGTTATCATG---GGCCGAGTTACCTTTGATCATCAGTAAGTGAGATTGTTTCTGATA----CGATTTCGTTTTCTGGCAATC-AAAGGAACTC-GACTCGACTTGAATCTACAACTACSizeHit CountTotal NormTotalGSM343915
Embryo
...................................TTTGATCATCAGTAAGTGAGAT........................................................................2213.0033
dp4
GAGGAGAGCTGTTTCGCCGGACAGTCAGAGTTTGATTTGATCTCTAGTTACTGGGCTTTGATTCGAAATAAGTAGCTTATTATTCTAGTGATTGAAATGA------ACTCGACTCGAGT--GCCACAAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
...................................TTTGATCTCTAGTTACTGGGC.........................................................................2111.00101
...................................TTTGATCTCTAGTTACTGGGCT........................................................................2211.00101
...................................TTTGATCTCTAGTTACTGGG..........................................................................2011.00101

Secondary Structure

dm3

dG=-17.9,  p-value=0.009901 dG=-17.6,  p-value=0.009901 dG=-17.4,  p-value=0.009901 dG=-17.0,  p-value=0.009901 dG=-17.0,  p-value=0.009901

droSim1

dG=-23.0,  p-value=0.009901 dG=-22.6,  p-value=0.009901

droSec1

dG=-26.0,  p-value=0.009901 dG=-25.6,  p-value=0.009901

droYak2

dG=-18.0,  p-value=0.009901 dG=-17.4,  p-value=0.009901 dG=-17.1,  p-value=0.009901 dG=-17.1,  p-value=0.009901

droEre2

dG=-20.2,  p-value=0.009901 dG=-19.7,  p-value=0.009901

droAna3

dG=-18.7,  p-value=0.009901 dG=-17.8,  p-value=0.009901 dG=-17.8,  p-value=0.009901 dG=-17.7,  p-value=0.009901

dp4

dG=-13.0,  p-value=0.009901 dG=-12.7,  p-value=0.009901 dG=-12.5,  p-value=0.009901 dG=-12.4,  p-value=0.009901 dG=-12.2,  p-value=0.009901

droPer1

dG=-15.2,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-14.7,  p-value=0.009901 dG=-14.4,  p-value=0.009901 dG=-14.3,  p-value=0.009901

droWil1

dG=-16.4,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.5,  p-value=0.009901 dG=-15.5,  p-value=0.009901

droVir3

dG=-1.9,  p-value=0.009901 dG=-1.6,  p-value=0.009901 dG=-1.2,  p-value=0.009901 dG=-0.9,  p-value=0.009901

droMoj3

dG=-1.7,  p-value=0.009901 dG=-1.3,  p-value=0.009901 dG=-0.8,  p-value=0.009901

droGri2

dG=-1.7,  p-value=0.009901 dG=-0.9,  p-value=0.029703 dG=-0.7,  p-value=0.009901 dG=-0.7,  p-value=0.009901

Generated: 03/07/2013 at 07:09 PM