Secondary structure and small RNA-seq evidence for dme-mir-4972

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:3636951-3637088 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCG--------------GC---------------------------------------------------------------------------------------TTTACAGATATATATATATATATCGTGTATATATCTGTGCGATCGGG-A-TTGAGACTGAGGTTGGT-----CCGAG-TACTTTTGTGGCCA--TTTACACC
droSim1 chr2L:3596396-3596533 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCAACTCG--------------GC---------------------------------------------------------------------------------------TTTATATATATGTATATATATCGTGTATATATATCTGAGAGATCGGG-A-TTGAGACTGAGGTTGGT-----CCGAG-TACTTTTGTGGCCA--TTTACACC
droSec1 super_5:1737908-1738045 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCG--------------GC---------------------------------------------------------------------------------------TTTATATATATGTATATATATCGTGTATATATATCTGAGAGATCGGG-A-TTGAGACTGAGGTTGGT-----CCGAG-TACTTTTGTGGCCA--TTTACACC
droYak2 chr2L:3630931-3631061 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCAACTCG--------------AC---------------------------------------------------------------------------------------TATATATGTATATATATA-------TATATATATCTGTGAGATCGGG-A-TTGAGACTGAGGTTGGT-----CTCAG-TACTTTTGTGGCCA--TTTACACC
droEre2 scaffold_4929:3675838-3675960 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCT-CCACCTCA--------------GC---------------------------------------------------------------------------------------TATATATATATGT---------------GTGTATCTGTGGGATCGGG-A-TTGAGACTGAGGTTGGT-----CTTAG-TACTTTTGTGGCCA--TTTGCACC
droAna3 scaffold_12916:5691742-5691836 - CACTTGCAAGGCATAAATCAAAAGCGCCGTAGGCCT-CCGCCACT------------------------------------------------------------------------------------------------------------------------------------------------ATGAGT-C-TGGAGTCTGGTGATGGT-----GGAGT-GCCTTTTGTGGCCA--TTGGCACC
dp4 chr4_group3:5095808-5095886 + CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTT-TGGAGTTTTTTGTGGCACAG-------------------------------------------------------------------------------------TGTGTGT--GTG----------------------------------------------------------------------------------TGTGTG
droPer1 super_1:6587322-6587402 + CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCT-GAGACTT-TGGAGTTTTTTGTGGCACAG-------------------------------------------------------------------------------------TGTGTGTATGTG----------------------------------------------------------------------------------TGTGTG
droWil1 scaffold_180708:9512363-9512488 + CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTTCCACCTCT---------ATAT-------AGTATAATGTGTTCCACATACTCGAC---------------------------------------------------------------------------------------------------TTGGG-AGTTGAATTCGAAGTTG-T-----CCATG-T-CTTTTGTGGCCAATTTTACACC
droVir3 scaffold_12963:15108661-15108745 + CACTCGCGTGGCATAAATCAAATGCGTTGCAGGCCG-CCGGCGCT-------CCACGTT-----------------------GCACTCGACTC--------------------------------------------------------------CT-------------------------------------------------------------------C-TA--CTTGCGGCTA--GCAGCTCC
droMoj3 scaffold_6500:18077427-18077576 + CACTTGTGTGGCATAAATCAAATGCGCAGCAGGCCG-CCAGCTGA--------------------CGCTGACCGTGTT----GCACTCGAGTCGAG------------------------TTGAGTGGA---GTCAACTCGCCGCAGCTTTTCATTCGCATATACCCA-----------------------------------------GCCAAGCCAAG-----TGGTCTTTGGGGCCA--TTTACACG
droGri2 scaffold_15126:4287105-4287265 - CACTTGCATGGCATAAATCAAATGCGCCGCGGGCCT-TTGCTACG-----------------------------TGCCACATGCACTCGACTCTCGCCTCTCAACACGACTGACCGAACATTGGCTGGACAAGCCAAGCTGCAG------------------------------------------CAGATCGGGGCATTCCACTCCAAG---------------TGGTCTTTGAGGCCA--TTTGCACG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:3636951-3637088 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCTCGGCTTTACAGATATATATATATATATCGTGT--ATATATCTGTGCGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTTTGTGGCCATTTACACC
droSim1 chr2L:3596396-3596533 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAACTCGGCTTTATA--TATATGTATATATATCGTGTATATATATCTGAGAGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTTTGTGGCCATTTACACC
droSec1 super_5:1737908-1738045 - CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCACCTCGGCTTTATA--TATATGTATATATATCGTGTATATATATCTGAGAGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTTTGTGGCCATTTACACC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CACTTGCATGGCATAAATCAAAAGCGCCGTAGGCCTCCAACTCGGCTTTATA------------------TATATGTATATATATCGTGTATATATATCTGAGAGATCGGGATTGAGACTGAGGTTGGTCCGAGTACTTTTGTGGCCATTTACACCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
CACTTGCGTGGCATAAATCACAAGCGCCGCAGGCCTGAGACT-----TTGGAGTTTTTTGTGGCACAGTGTGTGTGTGTGTGTG------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-34.7 -34.7 -33.8

droSim1

-27.6 -27.6 -27.3 -27.3 -27.2 -27.2

droSec1

-29.9 -29.9 -29.8 -29.8 -29.4 -29.4

droYak2

-26.6 -26.4 -26.3 -26.3 -26.1 -26.1

droEre2

-22.8 -22.6 -22.6 -22.5 -22.5 -22.4

droAna3

-25.1 -24.2

dp4

-15.8 -15.8 -15.0 -15.0 -15.0

droPer1

-16.5 -15.8 -15.8 -15.7

droWil1

-16.6 -16.1 -15.9 -15.8 -15.7 -15.7

droVir3

-7.3 -7.3 -7.2 -7.0 -7.0 -6.6

droMoj3

-33.2 -33.1 -32.4 -32.3

droGri2

-35.3 -34.6 -34.5 -34.5 -34.4 -34.4

Generated: 01/05/2013 at 05:26 PM