Secondary structure and small RNA-seq evidence for dme-mir-4911

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:11661994-11662091 -	TGCGGATTCTGTCAGGTGAGGA---GGA-GCAAAGTGGCGCCACAA---------------------T-----------TTACTAGAAACTAATTGCA-----------TCTTTTTGTC------CCCCCGCGTAGGAAGCCTGTCCCGTG
droSim1	chr3R:9814135-9814231 +	TGCGGATTCTGTCAGGTGAGGA---GGA-GCGCAGTGGCGCCACTA---------------------T-----------TTACTAGAAACTAATTGGA-----------TATTCTTGTC------CACCC-CGCAGGAAGCCTGTCCCGTG
droSec1	super_0:10292637-10292733 +	TGCGGATTCTGTCAGGTGAGGA---GGA-GCGCAGTGGCGCCACTA---------------------T-----------TTACTAGATACTAATTGGA-----------TATTCTTGTC------CACCC-CGCAGGAAGCCTGTCCCGTG
droYak2	chr3R:14775389-14775483 +	TGCGGATTCTGTCAGGTGAGGA---GGA-GCACACTCTTGCCACTG---------------------T-----------TTACGGGAAAATAATTGCA-----------TTTCCTTA--------CCCCC-TTCAGGAAGCCTGTCCCGTG
droEre2	scaffold_4770:11186817-11186911 -	TGCGGATTCTGTCAGGTGAGGA---GAA-GCACAGTGGTGCCACTG---------------------T-----------GAAATGGAATCTTATAGCA-----------AATCCTT-T-------CCGCC-TTCAGGAAGCCTGTCCCGTG
droAna3	scaffold_13340:16266860-16266959 -	TGCGGTTTCTGTCAGGTGAGGA---ACC-TTTCA---------------ATTTAAATTTATAAGAAGC-----------AAGTTC---------TAAA-----------TATTCTTGTATCATCAATTTA-CACAGGAGGCTTGCCCAGTT
dp4	chr2:20340730-20340823 -	TGTGGCTTCTGTCAGGTAAGGAATGGGAGTCGAAATTTTTACATAA---------------------T-----------TTCAAGTCGATTCATTGAC-----------TT------T-------TTGCT-CGTAGGAGGCCTGCCCTGTG
droPer1	super_3:3092221-3092314 -	TGTGGCTTCTGTCAGGTAAGGAATGGGAGTCGAAATTTTTACATCA---------------------T-----------TTCAAGTCGATTCATTGAC-----------TT------T-------TTGCT-CGCAGGAGGCCTGCCCTGTG
droWil1	scaffold_181130:15806459-15806551 +	TGCGGATTCTGTCAGGTGAGTG---TGA-CTGAAATTCCAATTCAG---------------------C-----------ATATTTGAACTATATTA-------------T--------ATTTTCTGCCCC-TGCAGGAAGCTTGTCCCGTG
droVir3	scaffold_12855:5731320-5731404 +	TGCGGTTTTTGTCAGGTAATTA---T------------------TA---------------------C-----------CCATAAGTATCCCATATAAAACTCATGGTGT------GTT------TCCTT-TGCAGGAGGCCTGTCCAGTC
droMoj3	scaffold_6540:6055055-6055141 +	TGCGGTTTTTGTCAGGTAATT-----------------------TATCCATATGGATA-----------------TAATTTTGAGTGGGGT----T------CA-----TGATT--CTT------CCATT-AATAGGAGGCTTGCCCAGTC
droGri2	scaffold_14906:8272376-8272477 -	TGCGGTTTTTGTCAGGTAATCT-----------------------ATTATTCTATATGTCCAGCAAGAAATTTAACAATTTTAATTATGTT----C-------------C--------ACATTTAAATGT-TGCAGGAGGCCTGTCCCGTC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:11661994-11662091 -	TGCGGATTCTGTCAGGTGAGGAGGAGCAAAGTGGCGCCACAATTTACTAGAAACTAATTGCATCTTTTTGTCCCCCCGCGTAGGAAGCCTGTCCCGTG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGCGGATTCTGTCAGGTGAGGA---GGAG-CGCAGTGGCGCCACTATTTACTAGAAACTAATTGGATATTCTTGTCCACCC-CGCAGGAAGCCTGTCCCGTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

TGTGGCTTCTGTCAGGTAAGGAATGGGAGTCGAAATTTTTACATAATTTCAAGTCGATTCATTGACT--TTTTG-----CT-CGTAGGAGGCCTGCCCTGTG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-13.4, p-value=0.009901	dG=-13.4, p-value=0.009901	dG=-13.1, p-value=0.009901	dG=-13.1, p-value=0.009901	dG=-13.1, p-value=0.009901

droSim1

dG=-17.5, p-value=0.009901	dG=-17.1, p-value=0.009901	dG=-16.9, p-value=0.009901	dG=-16.7, p-value=0.009901	dG=-11.6, p-value=0.009901

droSec1

dG=-17.5, p-value=0.009901	dG=-17.1, p-value=0.009901	dG=-16.9, p-value=0.009901	dG=-16.7, p-value=0.009901	dG=-11.6, p-value=0.009901

droYak2

dG=-14.8, p-value=0.009901	dG=-14.0, p-value=0.009901	dG=-13.9, p-value=0.009901

droEre2

dG=-14.9, p-value=0.009901	dG=-14.4, p-value=0.009901	dG=-14.3, p-value=0.009901	dG=-14.2, p-value=0.009901	dG=-14.2, p-value=0.009901	dG=-12.5, p-value=0.009901

droAna3

dG=-5.6, p-value=0.009901	dG=-5.4, p-value=0.009901	dG=-5.3, p-value=0.009901	dG=-5.3, p-value=0.009901	dG=-5.3, p-value=0.009901	dG=-4.5, p-value=0.009901

dp4

dG=-10.9, p-value=0.009901	dG=-10.3, p-value=0.009901	dG=-10.2, p-value=0.009901	dG=-9.1, p-value=0.009901

droPer1

dG=-11.0, p-value=0.009901	dG=-11.0, p-value=0.009901	dG=-10.7, p-value=0.009901	dG=-10.3, p-value=0.009901	dG=-10.3, p-value=0.009901

droWil1

dG=-12.1, p-value=0.009901	dG=-11.7, p-value=0.009901	dG=-11.2, p-value=0.009901	dG=-9.3, p-value=0.009901

droVir3

dG=-7.0, p-value=0.009901

droMoj3

dG=-7.8, p-value=0.009901	dG=-7.5, p-value=0.009901	dG=-7.4, p-value=0.009901	dG=-7.3, p-value=0.009901	dG=-7.1, p-value=0.009901	dG=-6.7, p-value=0.009901

droGri2

dG=-2.8, p-value=0.009901	dG=-2.6, p-value=0.009901	dG=-2.4, p-value=0.009901	dG=-2.4, p-value=0.009901	dG=-2.4, p-value=0.009901

Generated: 03/07/2013 at 05:30 PM