Secondary structure and small RNA-seq evidence for dme-mir-4913

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:8347269-8347356 -	TGTTCAACTACTTGAGTGAGTTCGATT---GGAA-------------------------------AAT---------TTAAATTTAA----TGT---TTAATTAACCAATTCGAATTGCTTAGATTGCTATATTGGCT
droSim1	chr3L:7807265-7807357 -	TATTCAACTATTTGAGTGAGTTCGATT---GAAA---------------------AT--TTGGAAAAT---------TTAA-------ATATGT---TTAATTAACCAATTCAATTTGCATAGATTGCTACATTGGCT
droSec1	super_0:643746-643838 -	TATTCAACTATTTGAGTGAGTTCAATT---GGAT---------------------AT--TTAGAAAAT---------TTAA-------ATATGT---TTAATTAACGAATTCAATTTGCATAGATTGCTACATTGGCT
droYak2	chr3L:3551197-3551288 +	TATTCAACTACTTGAGTGAGTTCGATT---GGAC---------------------AT--TCGGAATAT---------TTCA-------ATATGT---ATAATCT-CCAATTCCAATGGTTTAGATTGCTACATTGGCT
droEre2	scaffold_4784:5683607-5683696 +	TATTCAACTATTTGAGTGAGTTCGATT---GAA----------------------GT--TCGGAATAT---------ATTA-------ATA-GT---TTAATTGT-CAATTCCAATGGCTTAGATTGCTACATTGGCT
droAna3	scaffold_13337:7445991-7446073 +	TGTTCAACTATTTGAGTGAGTATCTTC---CTA------------------AGAAGGAAGT-------GTC--AT--T---TATTTA----TGAT---------------A-TTACTGCATAGATTGCTACATCGGCT
dp4	chrXR_group6:12821045-12821128 -	TTTTCAACTATTTGAGTGAGTACCACG---AGAGAT-----------------------CC-------CTC--CTTCTGATTGTTAA----TGTT---------------TTTTGTGCCGCAGATTGCTATATCGGCT
droPer1	super_33:845496-845579 -	TTTTCAACTATTTGAGTGAGTACCACG---AGAGAA-----------------------CC-------CTC--CTTCTGATTGTTAA----TGTT---------------TTTTGTGCCGCAGATTGCTATATCGGCT
droWil1	scaffold_181009:3090042-3090138 +	TCTTCAATTATTTGAGTGAGCGAGGCTACGA-AT--------ATTCTCTAGAGGAAT--TTGGAATG----------------CTAAGATTCGT---TT-----------TTCTTTTCCGTAGATTGCTACATTGGCT
droVir3	scaffold_13049:4752940-4753026 -	TCTTCAACTACTTGAGTGAGTGAGGCTT--AGAGG------------------------CTG-------TCGACTACTTTC-GCTTA----TGCCTG-------------AATCTCTCTGCAGATTGCTATATCGGCT
droMoj3	scaffold_6680:3143577-3143662 -	TCTTCAATTATTTGAGTGGGTAGAGTG---AAGTAT-----------------------TT-------CTT--ATACTCCAGCCTAA----TGTTGG-------------TCTCTCCTTATAGATTGCTATATTGGCT
droGri2	scaffold_15110:10166029-10166124 +	TCTTCAACTATTTGAGTGAGTACTTTG---AGT-TTGTCTTAATCCCCTGGATAGGTGAG--------------TGCTGAGTGGTGA----TC--------------------TCTTTCACAGATTGCTATATCGGTT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:8347269-8347356 -	TGTTCAACTACTTGAGTGAGTTCGATTGGAAAATTTAAATTTAATGTTTAATTAACCAATTCGAATTGCTTAGATTGCTATATTGGCT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TATTCAACTATTTGAGTGAGTTCGATTGAAAATTTGGAA--AATTTAAAT---ATGTTTAATTAACCAATTCAATTTGCATAGATTGCTACATTGGCT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

TTTTCAACTATTTGAGTGAGTACCACGAGAGATCCCT--CCTTCTGATTGTTAATGTTTTTTG------------TGCCGCAGATTGCTATATCGGCT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-11.7, p-value=0.009901	dG=-11.7, p-value=0.009901	dG=-11.5, p-value=0.009901	dG=-11.5, p-value=0.009901	dG=-11.5, p-value=0.009901

droSim1

dG=-6.8, p-value=0.009901	dG=-6.8, p-value=0.009901	dG=-6.5, p-value=0.009901	dG=-6.5, p-value=0.009901	dG=-6.5, p-value=0.009901

droSec1

dG=-10.3, p-value=0.009901	dG=-10.2, p-value=0.009901	dG=-10.1, p-value=0.009901	dG=-10.1, p-value=0.009901	dG=-9.9, p-value=0.009901

droYak2

dG=-8.3, p-value=0.009901	dG=-8.1, p-value=0.009901	dG=-7.8, p-value=0.009901	dG=-7.5, p-value=0.009901	dG=-7.4, p-value=0.009901

droEre2

dG=-6.1, p-value=0.009901	dG=-5.8, p-value=0.009901	dG=-5.8, p-value=0.009901	dG=-5.8, p-value=0.009901	dG=-5.6, p-value=0.009901

droAna3

dG=-12.1, p-value=0.009901	dG=-9.4, 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	dG=-5.8, p-value=0.009901	dG=-5.7, p-value=0.009901

droPer1

dG=-6.6, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-5.6, p-value=0.009901

droWil1

dG=-9.5, p-value=0.009901	dG=-8.7, p-value=0.009901	dG=-8.7, p-value=0.009901	dG=-8.6, p-value=0.009901	dG=-8.6, p-value=0.009901

droVir3

dG=-11.2, p-value=0.009901	dG=-11.2, p-value=0.009901	dG=-11.0, p-value=0.009901	dG=-11.0, p-value=0.009901	dG=-10.7, p-value=0.009901

droMoj3

dG=-12.5, p-value=0.009901	dG=-12.5, p-value=0.009901	dG=-11.8, p-value=0.009901	dG=-10.6, p-value=0.009901

droGri2

dG=-12.9, p-value=0.009901	dG=-12.9, p-value=0.009901	dG=-12.6, p-value=0.009901	dG=-12.0, p-value=0.009901	dG=-12.0, p-value=0.009901	dG=-10.0, p-value=0.009901

Generated: 03/07/2013 at 05:31 PM