Secondary structure and small RNA-seq evidence for dme-mir-4958

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:15974940-15975104 - GTCCG------------------------------------A------ACCGTACGATCTCT--------------------------------GGCAGCTGCAGTTCCGTTT------CCGGAGCGGGATCTGGAACGGGCTCTGGTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTACCGCTCCAGGTCCCGTTCCCGGAAACGGTGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droSim1 wgm54c09.g1:392-557 + GTCCG------------------------------------A------ACCGCACGATCTCT--------------------------------GGCAGCTGCAGTTCCGTTT------CCGCAGCGGGATCTGGGACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCAGGTCCCGTACCCGGAAGCGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droSec1 super_47:33133-33297 - GTCCG------------------------------------A------ACCGTACGATCTCT--------------------------------GGCAGCTGCAGTTCCGTTT------CCGCAGCGGGATCTGGCACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCATGTCCCGTACCCGGAAACGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droYak2 chrX:10123735-10123899 - GTCCA------------------------------------A------ATCCCACGATCTCT--------------------------------GGCAGCTGCAGTTCCGTTT------CCGCAGCGGGTTCTGGAACGGGCTCTGGTTCTGGATCCGGATCCAATATGGCATCCGGTCCTGGTACCGCTCCAGTTCCCGTACCCGGAAACGGTGCCACCGCCAATGCAGCTGCAGCGGCCTTCA
droEre2 scaffold_4690:11103030-11103194 + GTCCA------------------------------------A------ATCCCACGATCTCT--------------------------------GGCAGCTGCAGTTCTGTTT------CCGGAACGGGTTCTGGAACGGGCTCTGGTTCGGGATCCGGATCCAATCTGGCACCCGGTCCTGGTACTGCTCCAGTTCCCGTACCCGGTAACGGTGGCACCGCCAATGCAGCTGCAGCGGCATTCA
droAna3 scaffold_13165:312527-312640 - GCATA------------------------------------A------GCCACATGGACTCT--------------------------------G---------------------------------------------------------GATCAGGCTCCGTATCTGCGTCAATTTTGGGCACCGGTCCAGGCCCTTTACATGGAAATAGTGCGACCTCGAATGTCTCTTCTGCACCCTTTA
dp4 chrXL_group1e:9575758-9575916 - GCCCC------------------------------------A------ATCCCAATGCCAGC-----------------------------AACGGCAGCTGTGGCTCCGCCTCTGCCTCCGGTTCGTCCAGTGGCTCG-GCACCGGCTCCGGCTCAGGGTCAGACTCAGGCCACGACTCAGGCACCG-----------ACTCACGGCAACACTTCGG---CCGGTGGCACAGCCTCGGCGTACT
droPer1 super_22:633193-633346 + GCCCC------------------------------------A------ATCCCAATGCCAGC-----------------------------AACGGCAGCTGTGGCTCCGCCT------CCGGTTCGTCCAGTGGCTCGGCACCGGTTCCGGGCTCAGGGTCAGACTCAGGCCACGACTCAGGCACC-----------AGCTCACGGCAACACTTCGG---CCGGTGGCACAACCTCGGCGTACT
droWil1 scaffold_181096:10624772-10624892 + CTGCATCATCGGCATCGCCAACTTATCAGAAGGGCAGTCCGAATCCAAATCCCAAT---------------------CTGAATGCAAATGCAACGGC--------------------------------------------------------------------------T------------------------------GGTGGCTCTGGAGCCAGTTCATCTGCTGCCACCGCTGCCTTTA
droVir3 scaffold_12472:523224-523310 + GCCCG------------------------------------A------ATCCCAATGGCGGT--------------------------------GGCTCCAGCGGTGCC------------------------------------------------------------------------------------AGTCTATCTGGCAGTAACAATGTGACTGCCACCGCTACAGCCGCCGCCTTTG
droMoj3 scaffold_6308:2944361-2944510 - GCCCG------------------------------------A------ATCCCAATGGCGGCGGCAGCGGCGCCGGTGG--------------------CGGTGGCGGTGCCGCTGCTGCTGGCTCCAACGGTGGC------------------------GGAAGTCT---------CTCGGGCAGCAGCAGCAGCAATGCAGCCACAGCCAATGCTACAGCCACCGCCGGTGGCGCGGGCTTTG
droGri2 scaffold_15203:4433131-4433217 - GCCCG------------------------------------A------ATCCCAATGGCTGT--------------------------------GTCTCCAGCGGTGCC------------------------------------------------------------------------------------AGTCTCTCTGGCAGCAACACTGTGACTGCCACCGCTACTGCCGCCGCCTTTG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:15974940-15975104 - GTCCGAACCGTACGATCTCTGGCAGCTGCAGTTCCGTTTCCGGAGCGGGATCTGGAACGGGCTCTGGTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTACCGCTCCAGGTCCCGTTCCCGGAAACGGTGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droSim1 wgm54c09.g1:392-557 + GTCCGAACCGCACGATCTCTGGCAGCTGCAGTTCCGTTTCCGCAGCGGGATCTGGGACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCAGGTCCCGTACCCGGAAGCGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droSec1 super_47:33133-33297 - GTCCGAACCGTACGATCTCTGGCAGCTGCAGTTCCGTTTCCGCAGCGGGATCTGGCACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCATGTCCCGTACCCGGAAACGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCA
droYak2 chrX:10123735-10123899 - GTCCAAATCCCACGATCTCTGGCAGCTGCAGTTCCGTTTCCGCAGCGGGTTCTGGAACGGGCTCTGGTTCTGGATCCGGATCCAATATGGCATCCGGTCCTGGTACCGCTCCAGTTCCCGTACCCGGAAACGGTGCCACCGCCAATGCAGCTGCAGCGGCCTTCA
droEre2 scaffold_4690:11103030-11103194 + GTCCAAATCCCACGATCTCTGGCAGCTGCAGTTCTGTTTCCGGAACGGGTTCTGGAACGGGCTCTGGTTCGGGATCCGGATCCAATCTGGCACCCGGTCCTGGTACTGCTCCAGTTCCCGTACCCGGTAACGGTGGCACCGCCAATGCAGCTGCAGCGGCATTCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GTCCGAACCGCACGATC---TCTGGCAGCTGCAGTTCCGTTTCCGCAGCGG-----------GATCTGGGACGGGCTCTGCTTCTAGATCAGGATCCAATCATGCACCCGGTCCAGGTGCCGCTCCAGGTCCCGTACCCGGAAGCGGAGCCACCGCCAATGCAGCTGCAGCGGCATTCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GCCCCAATCCCAATGCCAGCAACGGCAGCTGTGGCTCCGCCTCTGCCTCCGGTTCGTCCAGTGGCTCGGCACCGGCTCCGGCTCAGGGTCAGACTCAGGCCAC------GACTCAGGCACCGACTCA-----------CGGCAAC---ACTTCGGCCGGTGGCACAGCCTCGGCGTACTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-64.1 -64.1 -64.1 -64.0 -64.0 -64.0

droSim1

-58.2 -58.2 -58.1 -58.1 -57.8 -57.8

droSec1

-51.4 -51.4 -51.3 -51.3 -51.0 -51.0

droYak2

-60.6 -60.3 -60.3 -60.2 -60.2 -59.9

droEre2

-60.2 -60.2 -60.0 -60.0 -59.8 -59.8

droAna3

-14.6 -14.5 -14.4 -14.3 -14.3 -14.3

dp4

-42.7 -42.2 -42.1 -41.9 -41.9 -41.8

droPer1

-42.7 -42.7 -41.9 -41.9 -41.8 -41.8

droWil1

-13.0

droVir3

-26.5 -25.5

droMoj3

-63.3 -62.6 -62.4 -62.3

droGri2

-21.1 -20.4 -20.1

Generated: 01/05/2013 at 05:24 PM