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 + TCGCCATGCTTCGACAATT----------------------------TT---------------------------TGAATGGTCCTTTT----------CATGCCCAAGG---------------------CGAATAAATAT------------GTATTTATGTATATTTTTTTATATGGTACGTATTTATTTGTCTGCAAATGGCTGCCAAG-----------------------------------GAGT---------------------GCTACATAATCAATTTGTTTG-TT

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

-32.4 -32.4 -32.4 -32.4 -32.4 -32.4

droSim1

-21.6 -21.5 -21.4 -21.1 -21.1 -21.1

droSec1

-18.6 -18.5 -18.4 -18.1 -18.1 -18.0

droYak2

-23.2 -23.2 -23.1 -23.1 -22.3 -22.3

droEre2

-20.2 -19.8 -19.5 -19.3 -19.3 -19.2

droAna3

No secondary structure predictions returned

dp4

-34.8 -34.3 -34.2 -34.0 -34.0 -33.9

droPer1

-45.2 -45.0 -44.9 -44.7 -44.6 -44.6

droWil1

-6.2 -6.1 -5.8 -5.3 -5.3 -5.2

droVir3

-1.1 -0.9 -0.7 -0.7 -0.7 -0.6

droMoj3

-24.1 -23.8 -23.5 -23.4 -23.2 -23.1

droGri2

-25.3 -25.3 -24.9 -24.9 -24.5 -24.5

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