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

Legend:

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 +	GATAAGCACGTCATCGTAAGCATTGCAAAATG--TAGTTGTTAAA-------TTCGC--------------TCTTCAATCATTA-ACAACATTT-----ACAATGTTTGCAGGCTGTCAACGTTGAT

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

-15.6	-15.5	-15.0	-15.0	-14.8	-14.7

droSim1

-6.5	-6.3	-6.3	-6.2	-6.1	-6.0

droSec1

-6.5	-6.3	-6.3	-6.2	-6.1	-6.0

droYak2

-5.9	-5.2	-5.2	-5.0

droEre2

-6.5	-6.1	-6.0	-6.0	-6.0	-5.7

droAna3

-3.9	-3.7	-3.7	-3.7	-3.7	-3.6

dp4

-6.7	-6.3	-6.1

droPer1

-9.3	-8.8

droWil1

-3.5	-2.5	-2.5

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:10 PM