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 + AAGCC--------CACTC-A--CA-----------------GAGGACGCCGGGGATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA

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

-24.6 -24.4 -24.4 -24.3 -24.2 -24.1

droSim1

-25.7 -25.7 -25.5 -25.5 -25.4 -25.4

droSec1

-25.7 -25.7 -25.5 -25.5 -25.4 -25.4

droYak2

-23.5 -23.4 -23.1 -23.1 -23.0 -23.0

droEre2

-22.0 -22.0 -21.9 -21.9 -21.9 -21.9

droAna3

-19.6 -19.4 -19.4 -19.2 -19.1 -19.0

dp4

-24.1 -23.9 -23.1

droPer1

-21.2 -21.2 -21.0 -21.0 -20.9 -20.9

droWil1

-19.2 -19.0 -18.7 -18.7 -18.5 -18.5

droVir3

-25.6 -25.4 -24.6

droMoj3

-21.0 -20.8 -20.0

droGri2

-22.4 -22.2 -21.7 -21.5 -21.5 -21.5

Generated: 01/05/2013 at 05:14 PM