Secondary structure and small RNA-seq evidence for dme-mir-4912

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:4829965-4830054 - CATTCGCAGCTTTAAGTGAGTAGTC---G--------------------TATGTTTATTA---------------------AGATT-TACT----TTCTATA--AATTAATGTCCA-----------------------CTACTTTTAGTCTCTATGACGATGA
droSim1 chr2L:4699797-4699886 - CATTCGCAGCTTTAAGTGAGTAATC---G--------------------TATGTTTATTA---------------------AGATT-CACT----TTCTATA--AACTAATTTGCA-----------------------CTACTTGTAGTCTCTATGACGACGA
droSec1 super_5:2925673-2925762 - CATTCGCAGCTTTAAGTGAGTAATC---G--------------------TATGTTTATTA---------------------AGATT-CACT----TTCTATA--AACTAATTTGCA-----------------------CTACTTGTAGTCTCTATGACGACGA
droYak2 chr2L:4839794-4839887 - CATTCGCAGCTTTAAGTGAGTAAAA---C--------------------TATGTCTATTA----------GGTG-------AAATT-AACT----TTCTATA--AATTACTTTTCT-----------------------TTATTTTTAGTCTATATGACGACGA
droEre2 scaffold_4929:4910720-4910828 - CATTCGCAGTTTTAAGTGAGTAAAA---T--------------------TAGGTTTAATTTGGTTTATTAGGAGAATTTTAAAAT--TAC-----TTTTTTA--AATTGCTTTTCA-----------------------TTATTTGCAGTCTCTATGACGACGA
droAna3 scaffold_12916:9399289-9399374 - CATTCGAAGCTTCAAGTATGTTAAGA---------AATCCACGATT-----------------------------------TTT--T-TATATTTTCATACA--AAAT-----TC------------------------ATTTTTTCAGCTTGTACGACGACGA
dp4 chr4_group3:3587822-3587933 - CATACGCACATTTAAGTGAGTAGGAA---------AAATCGTTGTTTAAGCTGTTTACTG---------------------CGATTGTA--------------------CTTTACTGTATTTACTGTATTTGGTA--CATGCCTTGCAGCCTCTATGATTCCGA
droPer1 super_1:5067398-5067508 - CATACGCACATTTAAGTGAGTAGGA----------AAATCGCTGTTTAAGCTGTTTACTG---------------------CGATTGTA--------------------CTTTACTGTATTTACTGTATTTGGTA--CATGCCTTGCAGCCTCTATGATTCCGA
droWil1 scaffold_180772:1562219-1562313 - CATTAAAACGTTTAAGTGAGTAGTAAATCTTGGTTAAC----------------CCAATA---------------------CGATTT-CATTGGCGTTTATA--AATT-----CC------------------------TCCACCTTAGCCTTTACGACGACGA
droVir3 scaffold_12963:8507047-8507138 + CATACGCACATTCAAGTATGTCA---------------------------------ACTA---------------------TGAT----------------A--AAATGCTTTGCAGTACTCTTTAAATATTGTATTCTCATTCGATAGCCTCTATGACGACGA
droMoj3 scaffold_6500:1118880-1118971 + CATACGTACATTCAAGTAAGCCCAA---T-TCGCC-------GACG-----------------------------------TTA--T-GGTATTCATATACAAATGCTAATCATTT-----------------------ATCCCTTTAGCCTCTATGACGACGA
droGri2 scaffold_15252:11699277-11699378 + CATACGCACCTTCAAGTATGTGCAA---T-GGGTAAACCATATGTGAGAGATTTAAACCT---------------------TAATTTTA--------------------CTTTCCTATATCT-----------------GCCCAAACAGTCTGTACGATGACGA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:4829965-4830054 - CATTCGCAGCTTTAAGTGAGTAGTCGTATGTTTATTAAGATTTACTTTCTATAAATTAATGTCCACTACTTTTAGTCTCTATGACGATGA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CATTCGCAGCTTTAAGTGAGTAA------TCGT--------ATGTTTATTAAGAT------TCACTTTCTATAAACTAAT--TTGCACTACTTGTAGTCTCTATGACGACGASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CATACGCACATTTAAGTGAGTAGGAAAAATCGTTGTTTAAGCTGTTTACTGCGATTGTACTTTACTGTATTTACTGTATTTGGTACATGCCTTGCAGCCTCTATGATTCCGASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-8.5,  p-value=0.009901 dG=-7.7,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.5,  p-value=0.009901

droSim1

dG=-5.1,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-4.7,  p-value=0.009901 dG=-4.6,  p-value=0.009901

droSec1

dG=-5.1,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-5.0,  p-value=0.009901 dG=-4.7,  p-value=0.009901 dG=-4.6,  p-value=0.009901

droYak2

dG=-2.2,  p-value=0.009901 dG=-1.8,  p-value=0.009901 dG=-1.5,  p-value=0.009901 dG=-1.5,  p-value=0.009901 dG=-1.3,  p-value=0.009901

droEre2

dG=-8.7,  p-value=0.009901 dG=-8.3,  p-value=0.009901 dG=-8.2,  p-value=0.009901 dG=-7.9,  p-value=0.009901 dG=-7.8,  p-value=0.009901

droAna3

dG=-5.5,  p-value=0.009901 dG=-4.8,  p-value=0.009901

dp4

dG=-14.0,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-11.5,  p-value=0.009901

droPer1

dG=-15.4,  p-value=0.009901 dG=-15.2,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-15.1,  p-value=0.009901 dG=-14.8,  p-value=0.009901 dG=-11.5,  p-value=0.009901

droWil1

dG=-6.2,  p-value=0.009901 dG=-6.1,  p-value=0.009901 dG=-6.0,  p-value=0.009901 dG=-5.5,  p-value=0.009901 dG=-5.4,  p-value=0.009901

droVir3

dG=-6.5,  p-value=0.009901 dG=-5.8,  p-value=0.009901 dG=-5.6,  p-value=0.009901 dG=-4.4,  p-value=0.009901

droMoj3

dG=-4.8,  p-value=0.009901 dG=-3.8,  p-value=0.009901 dG=-3.8,  p-value=0.009901

droGri2

dG=-11.2,  p-value=0.009901 dG=-10.8,  p-value=0.009901 dG=-10.5,  p-value=0.009901 dG=-10.4,  p-value=0.009901 dG=-10.4,  p-value=0.009901

Generated: 03/07/2013 at 05:31 PM