Secondary structure and small RNA-seq evidence for dme-mir-287

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:17574595-17574717 + AAGCC--------CACTC-A--CA-----------------GAGGACGCCGGGGATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droSim1 chr2L:17277816-17277938 + AAGCT--------CACTC-A--CA-----------------GAGGACGCCGTGGATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droSec1 super_7:1215433-1215555 + AAGCT--------CACTC-A--CA-----------------GAGGACGCCGTGGATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droYak2 chr2R:3525115-3525236 - ACATA--------TATA-CACACA-----------------GAGCAAGCCGTGGATGTATGGG--TGT-GGGTCTGAAATTTTGCACACATTTACAGTAATTGTAAATGTGTTGAAAATCGTTTGCATG-ACTGTGAGCAA--AACAC---T-TCGGA
droEre2 scaffold_4845:6676077-6676186 - GTGTG--------GACG-------------------------------C--TGGATGTATGGGTGTGTGGGCTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGCGAGCAA--AACAC---G-TCGGA
droAna3 scaffold_12916:3302442-3302546 - ATA----------------------------------------GGG--C--TGTGTGTATTGG--TAGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA
dp4 chr4_group3:10858860-10858990 - ACACA--------CACA-CA--TA-----AATATATTCACGGAGACAGTCT--TATGTGTGAG--TGTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droPer1 super_8:2069946-2070076 - ACACA--------CACA-CA--TA-----AATATATTCACGGAGACCTGCT--TATGTGTGAG--TGTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droWil1 scaffold_180764:928810-928950 - ACTCC--------CACAT-A--CATTGGAAAGAGCTTCTCCGTAATATGTA--TATGTATTGC--TGTAAAGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACAAACTGTGAGCAA--AATCCTGTAGCTGGG
droVir3 scaffold_12963:16502531-16502646 + AGATT--------GACTC-C--CA-----------------CGCTTTCGCACACACACAAACGTGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA-------------CCGA
droMoj3 scaffold_6500:21428983-21429089 + ACTCC--------CACGC-A--CA-------------------------------CACACACGCGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--CCAAC---A---GCA
droGri2 scaffold_15252:13917089-13917209 + CAGTTTTCACTCCCACAC-A-------------------------------CTCACACACACATGCATAATGCTTGAAATTTTGCACACATTTACAATATTTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAAGCAACAC---A-CATGT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:17574595-17574717 + AAGCCCACTCACAGAGGACGCCGGGGATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACGACTGTGAGCAAAACACGTCGGA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAGCTCAC------------TCACAGAGGACGCCGTGGATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACGACTGTGAGCAAAACACGTCGGASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
ACACACACACATAAATATATTCACGGAGACAGTCTT----ATGTGTGAGTGTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACAACTGTGAGCAAAACACGTCGGASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-32.9,  p-value=0.009901 dG=-32.7,  p-value=0.009901 dG=-32.3,  p-value=0.009901 dG=-32.1,  p-value=0.009901 dG=-32.0,  p-value=0.009901 dG=-28.2,  p-value=0.009901

droSim1

dG=-34.1,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-31.2,  p-value=0.009901

droSec1

dG=-34.1,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-33.9,  p-value=0.009901 dG=-31.2,  p-value=0.009901

droYak2

dG=-30.8,  p-value=0.009901 dG=-30.7,  p-value=0.009901 dG=-30.3,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-30.1,  p-value=0.009901 dG=-26.2,  p-value=0.009901

droEre2

dG=-31.4,  p-value=0.009901 dG=-31.2,  p-value=0.009901 dG=-30.8,  p-value=0.009901 dG=-30.6,  p-value=0.009901 dG=-30.2,  p-value=0.009901

droAna3

dG=-26.0,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.4,  p-value=0.009901 dG=-25.3,  p-value=0.009901

dp4

dG=-34.4,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.2,  p-value=0.009901 dG=-34.1,  p-value=0.009901 dG=-34.1,  p-value=0.009901

droPer1

dG=-34.3,  p-value=0.009901 dG=-34.1,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-29.1,  p-value=0.009901

droWil1

dG=-35.4,  p-value=0.009901 dG=-35.3,  p-value=0.009901 dG=-35.2,  p-value=0.009901 dG=-35.2,  p-value=0.009901 dG=-35.1,  p-value=0.009901 dG=-30.6,  p-value=0.009901

droVir3

dG=-26.2,  p-value=0.009901 dG=-26.2,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-26.1,  p-value=0.009901 dG=-26.0,  p-value=0.009901 dG=-25.9,  p-value=0.009901

droMoj3

dG=-21.9,  p-value=0.009901 dG=-21.7,  p-value=0.009901 dG=-21.6,  p-value=0.009901 dG=-21.5,  p-value=0.009901 dG=-21.5,  p-value=0.009901

droGri2

dG=-26.1,  p-value=0.009901 dG=-25.9,  p-value=0.009901 dG=-25.8,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.5,  p-value=0.009901

Generated: 03/07/2013 at 05:20 PM