Secondary structure and small RNA-seq evidence for dme-mir-2497

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:16678235-16678332 +	GATAAGCACGTCATCGTAAGCATTGCAAAATG--TAGTTGTTAAA-------TTCGC--------------TCTTCAATCATTA-ACAACATTT-----ACAATGTTTGCAGGCTGTCAACGTTGAT
droSim1	chr2L:16366233-16366322 +	GATAAGCACGTCATCGTAAGCATTGCAAAATA--TAGTTGTTAAA-------TTCGC--------------TCTTCAATTATTT---------A-----CTATTGATTGCAGGCTGTCAACGTTGAT
droSec1	super_7:325110-325199 +	GATAAGCATGTTATCGTAAGCATTGCAAAATA--TAGTTCTTAAA-------TTCGC--------------TCTTCAATTATTT---------A-----CTATTGATTGCAGGCTGTCAACGTTGAT
droYak2	chr2R:4424626-4424717 -	GATAAGCACGTCATCGTAAGCTTTGCTATATATGTAGATGTGAAT-------TTCGA--------------GCTTCAATTCTTT---------T-----CTATTCTCTTCAGGCTGTCAATGTTAAT
droEre2	scaffold_4845:19748460-19748547 +	GATAAGCACGTTATTGTAAGCTGCGCC--ATA--TAGTTCGTAAA-------TTCGA--------------GCTTCAATTATGT---------T-----CTATTCTCTCCAGGCTGTCAATGTTAAT
droAna3	scaffold_12916:15881689-15881781 -	GAAAAGCAAGTGATTGTAAGA--TGTAAAC---------------TCTTAGACCCTCCTAACTGCTACAA---GCTAATACTTT---------T-----GCTTTGAATCCAGGCTGTTAACGTGAAC
dp4	chr4_group3:8422191-8422279 +	CAAAAGCAGCTGATAGTGAGTACTGGAAGC---------------ATTTATAT---------CTCTGGAAAGCACTAATTCTTT---------T-----TTTAATCTTCTAGGCTGTCGAATTAAAT
droPer1	super_1:9873274-9873362 +	CAAAAGCAGCTGATAGTGAGTACTGGAAGC---------------ATTTATAT---------CTCTGGAAAGCACTAATTCTTT---------T-----TTGAATCTTCTAGGCTGTCGAATTAAAT
droWil1	scaffold_181132:892502-892596 -	GACAAAGAAGTGATTGTAGGTGTCAATGA---------------T-------TTCA----------AACTAACATCAATTTTTTATTAACGTCTTTATTTTTTCCTATTCAGGCTATCAATGTCAAT
droVir3	Unknown	-------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	-------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	-------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:16678235-16678332 +	GATAAGCACGTCATCGTAAGCATTGCAAAATGTAGTTGTTAAATTCGCTCTTCAATCATTAACAACATTTACAATGTTTGCAGGCTGTCAACGTTGAT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GATAAGCACGTCATCGTAAGCATTGCAAAA---TATAGTTGTTA--------AATTCGCTCTTCAATTATTTACT--------ATTGATTGCAGGCTGTCAACGTTGAT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

CAAAAGCAGCTGATAGTGAGTACTGGAAGCATTTATATCTCTGGAAAGCACTAATTCTTTTTTTAATC--------------------TTCTAGGCTGTCGAATTAAAT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-15.6, p-value=0.009901	dG=-15.5, p-value=0.009901	dG=-15.0, p-value=0.009901	dG=-15.0, p-value=0.009901	dG=-14.8, p-value=0.009901

droSim1

dG=-6.5, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-6.2, p-value=0.009901	dG=-6.1, p-value=0.009901

droSec1

dG=-6.5, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-6.2, p-value=0.009901	dG=-6.1, p-value=0.009901

droYak2

dG=-5.9, p-value=0.009901	dG=-5.2, p-value=0.009901	dG=-5.2, p-value=0.009901	dG=-5.0, p-value=0.009901

droEre2

dG=-6.5, p-value=0.009901	dG=-6.1, p-value=0.009901	dG=-6.0, p-value=0.009901	dG=-6.0, p-value=0.009901	dG=-6.0, p-value=0.009901

droAna3

dG=-3.9, p-value=0.009901	dG=-3.7, p-value=0.009901	dG=-3.7, p-value=0.009901	dG=-3.7, p-value=0.009901	dG=-3.7, p-value=0.009901	dG=-2.7, p-value=0.009901

dp4

dG=-6.7, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-6.1, p-value=0.009901

droPer1

dG=-9.3, p-value=0.009901	dG=-8.8, p-value=0.009901

droWil1

dG=-3.5, p-value=0.009901	dG=-2.5, p-value=0.009901	dG=-2.5, p-value=0.009901

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 04:56 PM