Secondary structure and small RNA-seq evidence for dme-mir-4954

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:1923021-1923142 - ATATAAGTGTTCG--------ATTTGGCGCTTGGAATCGATACCCGAGCCATGATAGATTGAAGTCAA-CCCA-ATC----G----------ATC-GC-GGT-TCGAGTGCTCGAGTCTTGTGCGCCGGCATGC-TTGAGAT---GTCCACTA
droSim1 vgb65a08_5.b1:263-385 - ATATAAGTGTTCG--------ATTTGGCGCTTGGAATCGATACCCGAGCCCTGATAGATTGAAGTCAA-CCCA-ATC----G----------ATC-GC-GGT-TCGGGTGCTCGAGTCCTGTGCGCCGGCATGC-TTGAGAT---GTCCACTA
droSec1 super_10:1708076-1708197 - ATATAAGTGTTCG--------ATTTGGCGCTTGGAATCGACACCCGTGCCCTGATAGATTGAAGTCAA-CCCA-ATC----G----------ATC-GC-GGT-TCGGGTGCTCGAGTCTTGTGCGCCGGCATGC-TTGAGAT---GTCCACTA
droYak2 chrX:6403257-6403382 + ACATAAAAGTTCA--------ATTTGGCGCTTGGAATCGTAACTCGAGCCCTCAAAGATTGAAGTCAAATGCA-ATC----G----------ATCCGG-GGTGTCGAGTGCTCGATTCTGGTGCGCCGGCATGCTTTGAGAT---GTCCACTA
droEre2 scaffold_4644:1895276-1895400 - ATATAAGTGTTCG--------ATTTGGCGCTTGGAATCGAACCTCGAGCCCTGACAGATTGAAGTCAA-CCCAAAAC----G----------ATC-CCGGGG-TCGAGTGTTCGAGTCCGGTGCGCCGGCATGCTTTGAGTT---GTCCACTA
droAna3 scaffold_12929:1917028-1917098 - ATATCCTTGACTT-------------------------CATAA-GGAACAATGA---------------------------------------TC-AT--GT--------------TAAGGTTCTCAGGCATGTCTCGAGATTATATCGAATC
dp4 chrXL_group1a:2597066-2597203 - ATATAAATACATACTGCATAGTGTAGCAGAATGGACTCGGAACTCGATCCATGCATGCCACATGCCACATGCC-ACATGTCGCAGAGGGGGCAGC-GT-GGC-TCGAGTGCCAGAGTCCGGCGAG-------GC-ATGAGAC---TACTTACC
droPer1 super_28:1034311-1034357 - A--------------------------------------------------------------------------------------------GC-GT-GGC-TCGAGTGCCAGAGTCCGGCGAG-------GC-ATGAGAC---TACTTACC
droWil1 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6473:2911987-2912050 + ATATATGTGTGTG--------TGTTTGTGTATTGTATTTAGATTTGAGCTATAAAATGTTTAATAAAA-CTCA--------------------------------------------------------------------------------
droGri2 Unknown ---------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:1923021-1923142 - ATATAAGTGTTCGATTTGGCGCTTGGAATCGATACCCGAGCCATGATAGATTGAAGTCAACCC-AATCGATC-GC-GGT-TCGAGTGCTCGAGTCTTGTGCGCCGGCATGCT-TGAGATGTCCACTA
droSim1 vgb65a08_5.b1:263-385 - ATATAAGTGTTCGATTTGGCGCTTGGAATCGATACCCGAGCCCTGATAGATTGAAGTCAACCC-AATCGATC-GC-GGT-TCGGGTGCTCGAGTCCTGTGCGCCGGCATGCT-TGAGATGTCCACTA
droSec1 super_10:1708076-1708197 - ATATAAGTGTTCGATTTGGCGCTTGGAATCGACACCCGTGCCCTGATAGATTGAAGTCAACCC-AATCGATC-GC-GGT-TCGGGTGCTCGAGTCTTGTGCGCCGGCATGCT-TGAGATGTCCACTA
droYak2 chrX:6403257-6403382 + ACATAAAAGTTCAATTTGGCGCTTGGAATCGTAACTCGAGCCCTCAAAGATTGAAGTCAAATGCAATCGATCCGG-GGTGTCGAGTGCTCGATTCTGGTGCGCCGGCATGCTTTGAGATGTCCACTA
droEre2 scaffold_4644:1895276-1895400 - ATATAAGTGTTCGATTTGGCGCTTGGAATCGAACCTCGAGCCCTGACAGATTGAAGTCAACCCAAAACGATC-CCGGGG-TCGAGTGTTCGAGTCCGGTGCGCCGGCATGCTTTGAGTTGTCCACTA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATATAAGTGT--------TCGATTTGGCGCTTGGAATCGATACCCGAGCCCTGATAGATTGAAGTCAACC--CAATCG-------------ATCGCGGTTCGGGTGCTCGAGTCCTGTGCGCCGGCATGCTTGAGATGTCCACTASizeHit CountTotal NormTotalGSM343915
Embryo
.......................................ATACCCGAGCCCTGATAGATTG....................................................................................2211.0011
dp4
ATATAAATACATACTGCATAGTGTAGCAGAATGGACTCGGAACTCGATCCATGCATGCCACATGCCACATGCCACATGTCGCAGAGGGGGCAGCGTGGCTCGAGTGCCAGAGTCCGGCGAG-------GCATGAGACTACTTACCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-37.7 -37.6 -37.2 -37.0 -36.9

droSim1

-45.8 -45.7 -45.3 -45.1 -45.0

droSec1

-42.1 -42.0 -41.6 -41.4 -41.3

droYak2

-40.4 -40.3 -40.2 -40.1 -40.1 -40.0

droEre2

-43.8 -43.7 -43.3 -43.2 -43.1 -42.8

droAna3

-4.9

dp4

-49.5 -48.6

droPer1

-10.2

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

-2.9 -2.3 -2.2

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:23 PM