Secondary structure and small RNA-seq evidence for dme-mir-4964

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:8859818-8859960 + TCGCCATGCTTCGACAATT----------------------------TT---------------------------TGAATGGTCCTTTT----------CATGCCCAAGG---------------------CGAATAAATAT------------GTATTTATGTATATTTTTTTATATGGTACGTATTTATTTGTCTGCAAATGGCTGCCAAG-----------------------------------GAGT---------------------GCTACATAATCAATTTGTTTG-TT
droSim1 chrX:7057967-7058102 + TCGCCATGCTTCGACAATT----------------------------TT---------------------------TGAATGGTCCTTTT----------CATGCCCAAGG---------------------CGAATAAATAT------------GTATTTATGTATATATATTTATA-------TACGCATTTGTCTGCAAATGGCTGCCATG-----------------------------------GAGT---------------------GCTACATAATCAATTTGTTTG-TT
droSec1 super_34:222375-222488 + TCGCCATGCTTCGACAATT----------------------------TT---------------------------TGAATGGTCCTTTT----------CATGCCCAAGG---------------------CGAATAAATAT------------GTATTTATGTTTATATATT-----------------------------TGGCTGCCATG-----------------------------------GAGT---------------------GCTACATAATCAATTTGTTTG-TT
droYak2 chrX:12451967-12452096 - TTGCCATGCTTGGACAATT----------------------------TT---------------------------TGAATGGTCCTTTT----------CATGCCCAAGG---------------------CGAATAAATAT------------GTATTTATGTGTAGATA-------------TATGTATTTGTCTGAAAATGGCTGCCAAG-----------------------------------GAGT---------------------GCTACATAATCAATTTGCTTA-TT
droEre2 scaffold_4690:6251913-6252052 - TTGCCATGCTTGGACAATT----------------------------TT---------------------------TGAATGGTCCTTTC----------CATCCCCAAGG---------------------CGAATAAATATGTTTGTGTGTACGAGTATATATTTATA---------------TATGTATCGGTCTGCAAATGGCTGCCAAT-----------------------------------GAGT---------------------GCTTCAAAATCAAATTGTTTG-TT
droAna3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4 chrXL_group1e:8134181-8134346 + TTTCCATGCTTGGACAATT---------------------------CTT---------------------------TGAACGGTCGTCCCT----TTTTGCCAGCCCAAGGGGGGAGGGATGGGGGGGGGGGGGAATAAATAT--------------ATCAACAA----AAA-------------TAC--------------------------TCGTAAGGCGAATAATGGCAACGTCTGGGGTGAGC----GATTGAGAGTTGTATCTGGAAGCTATATAATC-------------
droPer1 super_13:433852-434017 - TTTCCATGCTTGGACAATT---------------------------CCT---------------------------TGAACGGTCGTCCCGCCCGGTTTGCCAGCCCAAGGGGC----GGCGGGGGGAGGGGGGAATAAGTAT--------------ATCAACAA----AAA-------------TAC--------------------------TCGTAAGGCGAATAATGGCAACGCCTGGGGTGAGC----GATTGAGAGTTGTATCTGGAAGCTATATAATC-------------
droWil1 scaffold_181150:832777-832852 + ATGTCTTCCATTCCCTATT----------------------------TG---------------------------CGTATTTTCTT------------------TCAGTA---------------------TAAATGAATAT------------GTATGAGTCG----AAA-------------TAC--------------------------CTATA------------------------------------------------------------------------AATG-AT
droVir3 scaffold_12726:2732407-2732514 + TGGA------TCAACAAAT----------------------------GCCGCACATTTCTTTCTTGCTTTCGTTCACAATTTCTCTT------------------GTAATA---------------------TAATCAAT-TT------TT----ATTCAATTC-------------------------------------------------------------------------------------ATAC---------------------GATTCACATTCAATTCGTTTGACT
droMoj3 scaffold_6500:9117978-9118115 - CA----AGCTGCGACTATGTAATTAAAATTGTATGTATCAGCGGGTC-T-----------------------AT----------------------------TGCTATGTG---------------------TGTATAGGTGT------------GTGTGTGTGTGTATG---------------TGTGTGTATGTGTGCATATACAAAGCCAT-----------------------------------AATA---------------------GCATAAAACTCGATAAGCCTG-GC
droGri2 scaffold_15110:597989-598133 + TCGCCATATTTCGTTGAAT---------------------------T-C-----------------------TT----CGCCATATATCG----------TATGATTT---------------------------ATATATAT------ATATATAAATATATATATATATTTCGGCTCCAAATATTTTTTATATTTTGCAAAGACTTGCTGTG-----------------------------------G--TTTTTCATAAGTGAGTTTGAAT-----------------ATTG-TA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:8859818-8859960 + TCGCCATGCTTCGACAATTTTTGAATGGTCCTTTTCATGCCCAAGGCGAATAAATATGTATTTATGTATATTTTTTTATATGGTACGTATTTATTTGTCTGCAAATGGCTGCCAAGGAGTGCTACATAATCAATTTGTTTGTT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TCGCCATGCTTCGACAATTT-TTGAATGGTCCTTTT------CATGCCCAAGG---------------------CGAATAAATATGTATTTATGTATATATATTTATAT---ACGCAT----TTGTCTGCAAATGGCTGC-------------CATGGAG-------------TGCTACATAATCAATTTGTTTGTTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TTTCCATGCTTGGACAATTCTTTGAACGGTCGTCCCTTTTTGCCAGCCCAAGGGGGGAGGGATGGGGGGGGGGGGGAATAAATAT--ATCAAC----------AAAAAT---ACTCGT----AAGGCGAATAATGGCAACGTCTGGGGTGAGCGATTGAGAGTTGTATCTGGAAGCTATATAATC------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-23.0,  p-value=0.009901 dG=-23.0,  p-value=0.009901 dG=-23.0,  p-value=0.009901 dG=-22.9,  p-value=0.009901 dG=-22.9,  p-value=0.009901

droSim1

dG=-15.1,  p-value=0.009901 dG=-14.9,  p-value=0.009901 dG=-14.1,  p-value=0.009901

droSec1

dG=-8.9,  p-value=0.009901 dG=-8.2,  p-value=0.009901

droYak2

dG=-13.7,  p-value=0.009901 dG=-13.6,  p-value=0.009901 dG=-13.3,  p-value=0.009901 dG=-13.2,  p-value=0.009901 dG=-12.8,  p-value=0.009901

droEre2

dG=-13.3,  p-value=0.009901 dG=-12.9,  p-value=0.009901 dG=-12.4,  p-value=0.009901

droAna3

No secondary structure predictions returned

dp4

dG=-4.0,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.9,  p-value=0.009901 dG=-3.7,  p-value=0.009901 dG=-3.6,  p-value=0.009901

droPer1

dG=-5.9,  p-value=0.009901 dG=-5.0,  p-value=0.009901

droWil1

dG=-0.7,  p-value=0.019802 dG=-0.6,  p-value=0.019802 dG=-0.5,  p-value=0.019802 dG=-0.4,  p-value=0.019802 dG=-0.2,  p-value=0.009901

droVir3

dG=0.0,  p-value=1.0

droMoj3

dG=-10.7,  p-value=0.009901 dG=-10.4,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-10.1,  p-value=0.009901 dG=-9.9,  p-value=0.009901 dG=-9.1,  p-value=0.009901

droGri2

dG=-14.9,  p-value=0.009901 dG=-12.4,  p-value=0.009901

Generated: 03/07/2013 at 06:12 PM