Secondary structure and small RNA-seq evidence for dme-mir-4966

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:19452387-19452544 + GTTTCCAGGACATTGAGCTGTGTGACAACAAACTTGTCGGCACTGGAGTACTAAATA--TATTGCACATGTTCATGC----------ATGTTCAACATATTTAGCACTCAAGTACCGAA--------------------------AAATGAACAACGAAACGAAAAATAACACG-AA---CATCATGCTGCCCATTATAT
droSim1 chrX:15018266-15018398 + ACTTTGTCGG------------------------------CACTGGAGTGCTAAATA--TATTGCTCATGTTC--------TCATACATGTACAACGTATTTAGCACACGAGTACTGAA--------------------------AAATTAACAACGAAACGGTTG--AACTCGGAAGTGCAATATTGAGTTTTTGATTT
droSec1 super_8:1734644-1734797 + GTTTCCAGGACATCGAGCTGTGTGACGG------------CACTAGAGTACTAAATA--TATTGCACATGTTCATACATGTTCATACATGTAAAACATATTTAGCACTCAAGTACCGAA--------------------------AAATGAACATCGAAACGGGAG--AACACG-AG---CATCTTGCTACCCATTATAT
droYak2 chrX:11886103-11886223 - GTTTCCGGGACTTCGTACTGTATGACAGA---------------------CTATATATACAA-------------------TACGAAGCCTCTGAAATTTTCTGCGCTCAAGTACCAAAAACTACCAGCA-------------------AACCAACGAAACTGGAG--AACTACGGA---CGGCA---------------
droEre2 scaffold_4690:9688657-9688714 + GTTTCAGGGACTTCGCACTGTATGACAA-------------------------------------------------------------ACTATAAATTTTGTGCACTCAAGTACCAAA---------------------------------------------------------------------------------
droAna3 scaffold_13417:2468043-2468174 - GTTTCCGGGATCTCGTACTGTATGAAGTT---------------------TTCTATATACAA-------------------TTCGAAAACTCAGAAACTTCCTGCCGTGAGCTACCATTGATCAACGGCTGAGTATGCGACCGGAAAGGGGACGCGAATGCGAGGACTAA----------------------------AG
dp4 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:19452387-19452544 + GTTTCCAGGACATTGAGCTGTGTGACAACAAACTTGTCGGCACTGGAGTACTAAATATATTGCACATGTTCATGCATG----------TTCAACATATTTAGCACTCAAGTACCGAAAAATGAACAACGAAACGAAAAATAACACGA----ACATCATGCTGCCCATTATAT
droSim1 chrX:15018266-15018398 + ACTT------------------------------TGTCGGCACTGGAGTGCTAAATATATTGCTCATGTTC--------TCATACATGTACAACGTATTTAGCACACGAGTACTGAAAAATTAACAACGAAACGGTTG--AACTCGGAAGTGCAATATTGAGTTTTTGATTT
droSec1 super_8:1734644-1734797 + GTTTCCAGGACATCGAGCTGTGTGA------------CGGCACTAGAGTACTAAATATATTGCACATGTTCATACATGTTCATACATGTAAAACATATTTAGCACTCAAGTACCGAAAAATGAACATCGAAACGGGAG--AACACGA----GCATCTTGCTACCCATTATAT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
A------------------------------CTTTGTCGGCACTGGAGTGCTAAATATATTGCTCATGTTCTCATACATGTACAACGTATTTAGCACACGAGTACTGAAAAATTAACAACGAAACGGTTG--AACTCGGAAGTGCAATATTGAGTTTTTGATTTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
--------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-30.8 -30.8 -30.7 -30.6 -30.4 -30.3

droSim1

-28.8 -28.7 -28.6 -28.5 -27.8 -27.8

droSec1

-28.8 -28.7 -28.5 -28.5 -28.4 -28.4

droYak2

-13.4 -13.0 -12.8 -12.7 -12.6 -12.6

droEre2

-3.3 -2.9 -2.8 -2.8

droAna3

-22.1 -22.1 -22.0 -22.0 -22.0 -22.0

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:25 PM