Secondary structure and small RNA-seq evidence for dme-mir-4960

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:463920-464051 + TGGAGTGACCAGCACAACACAAGGCCTGCCGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGAAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGG-G------ACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT
droSim1 chrX_random:776904-777034 + CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGGAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGGGG------CCT-T-GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droSec1 super_10:310837-310968 + CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGGAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGGG-------GCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droYak2 chrX:383437-383616 + TGCAATGCCCACCACAACACAAGGCCTGATGCCCGAGAAT-CGGTTTATTTCCTCCTCT------------------T-------------------------------------------------------------------------------CCGCAGGCCCAGGAGTCCGGCAGTC----------------GAGCAGTCGAGCTGTTCACCCGGTCAGTCCTT-GGTCCTTGGTCCTTGGGCCTTGGGCTTTCGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droEre2 scaffold_4644:409107-409303 + TGCAATGACCCTCACCACACAAGGCCCGATGCCCGGGAAT-CGGTTTATTTCCTCTTCT------------------T-------------------------------------------------------------------------------CCGCAGGCCCAGGAGTCCGGCAGTCCGACAGTCCAGCAGTCCGGCAGTCGAGTTGTCGAGTAGTCCAGTCATGAGGGGCTGGGGCCTTGGGCCTTGGGCTTACGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droAna3 scaffold_12929:357992-358198 + TGGAATGACC---ACAGCAGAAGGCCTTCTGCCAA-GACTTGGGTGTAGATATGAGTGTGTGTGGGTGTGGGTGTGTTTT--GGCCAGAATATGGTGGGTGATTGTGCAGGGAGGCGTGGCAGATGGGGG-GGCG-------GAGGATGAAGAAGAAGCAGTAGCAGAGGAG--------------------------------------------------------------------G------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
dp4 chrXL_group1e:196231-196421 + TGGAATGACC---ACGGCACAAGGCCT--TG-CCAAGACT-TGTTTTATTTTTTGCTGA------------------TTTGGGGGCAGGAACT-GTAGGTGCCT--GCCGCGCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAG---GACGCAGGAGGCTT-------------CGCAGGA----------------GAG--------------------------------------AA------CTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCAT
droPer1 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_180777:2769923-2769983 + CAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGATTGACG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droVir3 scaffold_12970:10710181-10710231 + G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droMoj3 scaffold_6473:10704148-10704209 - GGGG--------------------------------GGCTTGGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droGri2 scaffold_14853:6069294-6069344 - G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:463920-464051 + TGGAGTGACCAGCACAACACAAGGCCTGCCGCCCAAGAAACGCAAGCCCAGAAGTCCGGCAGTCGAGAATCACGAGGGACTGGGACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT
droSim1 chrX_random:776904-777034 + CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAAACGCAAGCCCAGGAGTCCGGCAGTCGAGAATCACGAGGGACTGGGGCCTTG-GCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droSec1 super_10:310837-310968 + CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAAACGCAAGCCCAGGAGTCCGGCAGTCGAGAATCACGAGGGACTGGGGCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGGAGTGACCAGCACATCACAAGGCCT------------------------------------------------------GGTGCCCAAGAAACGCAAGCC----------------------CAGGAGTCC-GGCAGTCGAGAATCACGAGGGACTGGGGCCTT-GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCATSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TGGAATGACC---ACGGCACAAGGCCTTGCCAAGACTTGTTTTATTTTTTGCTGATTTGGGGGCAGGAACTGTAGGTGCCTGCCGCGCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAGGACGCAGGAGGCTTCGCAGGAGAGAA---------------CTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCATSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-33.5 -33.3 -33.3 -33.2 -33.1 -33.0

droSim1

-29.6 -29.6 -29.6 -29.4 -29.4 -29.4

droSec1

-36.7 -36.5 -36.5 -36.4 -36.4 -36.3

droYak2

-52.8 -52.0 -52.0

droEre2

-57.5 -57.3 -57.1 -57.0 -57.0 -56.9

droAna3

-40.9 -40.8 -40.7 -40.6 -40.6 -40.6

dp4

-50.9 -50.6 -50.3 -50.3 -50.1 -50.1

droPer1

No secondary structure predictions returned

droWil1

-8.2 -8.1 -8.1 -7.7 -7.7 -7.6

droVir3

-3.3 -3.2 -3.2 -2.9 -2.6 -2.5

droMoj3

-5.7 -5.2 -5.1 -5.1

droGri2

-3.3 -3.2 -3.2 -2.9 -2.6 -2.5

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