Secondary structure and small RNA-seq evidence for dme-mir-2501

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:8104192-8104292 +	GGTGGTAAAAGTGGAGTAAGTTTGGAGTG----CCTGGGCTAAGAACTTCCATT---------------------------------------------------------CTGAAACTTAACTCTTGCAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAG
droSim1	chr3L:7572156-7572239 +	GGTGGTAAAAGTGGAGTAAGTTTGGAGTC----CCTGGGCTAAGAACTTCCATT--------------------------------------------------------------------------CAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAG
droSec1	super_0:391632-391715 +	GGTGGTAAAAGTGGAGTAAGTTTGGAGTC----CCTGGGCTAAGAACTTCCATT--------------------------------------------------------------------------GAAGCAAACTTTC------------------------------------------------------------------TTTTAGAACCAAGCGTGGTAG
droYak2	chr3L:8691884-8691979 +	CGTTGTAAAAGTGGAGTAAGTTTGCGA----------------------------------------------------------------CTTACGTTC-CTTTTATATACCG-ACATACCGTCTTACAACCAAACTTTC------------------------------------------------------------------TTTCAGAACTAAGCGCGGCAG
droEre2	scaffold_4784:3260723-3260819 -	GGTGGTAAAAGTGGAGTAAGCTTGCAA----------------------------------------------------------------CTTGAGTTATATCTTTTATCCCG-CTATACTTACTTACAATCAAACTTTC------------------------------------------------------------------TCGCAGAACCAAGCGCGGCAG
droAna3	scaffold_13337:13543116-13543232 -	AGTGGTTAAAGTGGAGTAAGTGGCGT----------------------TTAAGGG------AGTGATG----------G---ATAGATGGACCTGAGTCT-TTTTTAGT---TGTTCTCTTTCTCTAACATTCATAATCCG------------------------------------------------------------------TTTCAGAAACAAACGTGGCCG
dp4	chrXR_group3a:1131777-1131868 +	GGTGGTCAAAGTAGAGTAAGTGATCC----------------------CCACCGA------ACTATTGTGACTTTACGC------T-------------C-TAATTGGG----------------------TACATTTTTT------------------------------------------------------------------GTGCAGAACCAAGCGTGGCCG
droPer1	super_23:1158678-1158769 +	GGTGGTCAAAGTAGAGTAAGTGATCC----------------------CCACCGA------ACTATTGTGGCTTTACGC------T-------------C-TAATTGGG----------------------TACATTTTTT------------------------------------------------------------------GTGCAGAACCAAGCGTGGCCG
droWil1	scaffold_180727:72451-72556 +	AGTGGTCAAAGTACAGTAAGTACATGG-----------AATGACCAATCCAATTAACTATA--TA-TGTACATATATGT------T-------------A-AATCCAAC----------------------CATCTCTTTT------------------------------------------------------------------ATCCAGAAATAGACGTGGCCG
droVir3	scaffold_13049:9356761-9356852 -	GGTTGTCAAAGTTGAGTAAGTTTCTA----------------------TCAAC----AATAACTA-AGCTTGGTTATGG------TA------------A-TAATTTG------------------------ACACTTTTC------------------------------------------------------------------TGTTAGAAATAAGCGCGGTCG
droMoj3	scaffold_6680:11400964-11401055 +	CGTTGTCAAGGTTGAGTAAGTTTGTAGGC----TCTTAACT-----------------------GGCGAAACCAGATGA------T-------------C-TAATTAC-----------------------ACAATTTTCC------------------------------------------------------------------CATTAGAAACAAACGTGGTCG
droGri2	scaffold_15110:6804388-6804550 +	CGTTGTCAAAGTCGAGTGAGTAATTTGGCAAAAACTGGCTT-------TTAATG-------------------AGATTACTCC--T-------------C-TTATCAG-----------------------ACAGTTCTCCAAACTCCTCATTTATCTTAGAGCAAATATCAGATTTAAAAATAAAATTATTTTTTCTTCTTTTGATCTTCAGAAATAAGCGCGGTCG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:8104192-8104292 +	GGTGGTAAAAGTGGAGTAAGTTTGGAGTG----CCTGGGCTAAGAACTTCCATT---------------------------------------------------------CTGAAACTTAACTCTTGCAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCTGGGCTAAGAACTTCCATT-----------------------------------CAATCAAACTTTCTTTCAGAACCAAGCGTGGCAG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

GGTGGTCAAAGTAGAGTAAGTG------------------ATC---C------CCACCGAACTATTGTGACTTTACGCTCTAATTGGGTACATTTTTTGTGCAGAACCAAGCGTGGCCG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-14.6	-13.9

droSim1

-8.7	-8.0

droSec1

-8.8	-8.7	-8.3	-8.1	-8.1	-8.0

droYak2

-6.3	-5.4	-5.4

droEre2

-4.4	-4.0

droAna3

-15.3	-15.2	-14.9	-14.8	-14.4

dp4

-8.6	-8.5

droPer1

-10.4	-10.0	-9.9	-9.7	-9.6	-9.6

droWil1

-7.8	-6.9

droVir3

-7.3	-7.1	-6.9	-6.8	-6.8	-6.7

droMoj3

-8.0	-7.3

droGri2

-22.5	-21.6	-21.6	-21.5

Generated: 01/05/2013 at 05:11 PM