Secondary structure and small RNA-seq evidence for dme-mir-983-1

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:4262327-4262447 -	ATATGCATATGCTATTATATTGCAATAATTAAATAAT-ACGTTTCGAACTAATGATTTTCAGTTCATTCATTAGGTAGTTACGCATTATCTAGTTGTTGTAAACATTCAACTCGCTGGC-GTA
droSim1	chrX:3277334-3277447 -	---TGCAT---ATGATATCTTGCAGTAATTTAGTAAT-ACCTTTCGAACACATGATTTTCAG-TCATTCATGAGTTCGTCAGGTATTATCTAGTTATTGTAAACATTCAACTCGCTGGC-GGA
droSec1	super_4:2462215-2462328 +	---TGCAT---ATGATATGTTGCAGTAATTTAGTAAT-ACCTTTCGAACATATGATTTTCAG-TCATTCATGAGTTCGTTAGGTATTATCTAGTTATTGTAAACATTCAACTCGCTGGC-GGA
droYak2	Unknown	---------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:1633112-1633231 -	GGAATTGTGTGATATTATGTTACAGTGATTTAATAAT-TCGATTCGAAGTTATGTGCTTTAA-TCATTCATAAATGCGAAACGGATTATTAAGTTATTGTTAACATTCAACTCGTTGGC-GTG
droAna3	Unknown	---------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	---------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	---------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	---------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	---------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6540:31109889-31110001 -	AACAACGTATGTTACTATATTAAAATAACTAAATAATTAAAACCAAAACCTATCAATTTAAT-CAATAAACG------AAATTTGTTATCTAGCT---TTAAGTACTTGAAAAGCTCATGATA
droGri2	Unknown	---------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:4262327-4262447 -	ATATGCATATGCTATTATATTGCAATAATTAAATAATACGTTTCGAACTAATGATTTTCAGTTCATTCATTAGGTAGTTACGCATTATCTAGTTGTTGTAAACATTCAACTCGCTGGCGTA
droSim1	chrX:3277334-3277447 -	---TGCATATGA---TATCTTGCAGTAATTTAGTAATACCTTTCGAACACATGATTTTCAG-TCATTCATGAGTTCGTCAGGTATTATCTAGTTATTGTAAACATTCAACTCGCTGGCGGA
droSec1	super_4:2462215-2462328 +	---TGCATATGA---TATGTTGCAGTAATTTAGTAATACCTTTCGAACATATGATTTTCAG-TCATTCATGAGTTCGTTAGGTATTATCTAGTTATTGTAAACATTCAACTCGCTGGCGGA
droEre2	scaffold_4690:1633112-1633231 -	GGAATTGTGTGATATTATGTTACAGTGATTTAATAATTCGATTCGAAGTTATGTGCTTTAA-TCATTCATAAATGCGAAACGGATTATTAAGTTATTGTTAACATTCAACTCGTTGGCGTG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

---TGCATATGAT---ATCTTGCAGTAATTTAGTAATACCTTTCGAACACATGATTTTCAG-TCATTCATGAGTTCGTCAGGTATTATCTAGTTATTGTAAACATTCAACTCGCTGGCGGA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...............................AGTAATACCTTTCGAACACATGA...................................................................	23	3	1.67	5	5
.....................................................................TGAGTTCGTCAGGTATTATCT...............................	21	3	0.67	2	2
.....................................................................TGAGTTCGTCAGGTATTATC................................	20	3	0.33	1	1
.....................................................................TGAGTTCGTCAGGTATTATCTA..............................	22	3	0.33	1	1

dp4

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

Secondary Structure

dm3

dG=-11.9, p-value=0.009901	dG=-10.9, p-value=0.009901

droSim1

dG=-22.8, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-22.3, p-value=0.009901	dG=-22.0, p-value=0.009901

droSec1

dG=-22.8, p-value=0.009901	dG=-22.4, p-value=0.009901	dG=-22.3, p-value=0.009901	dG=-22.0, p-value=0.009901

droYak2

No secondary structure predictions returned

droEre2

dG=-18.4, p-value=0.009901

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

dG=-0.59, p-value=0.019802	dG=-0.2, p-value=0.019802	dG=0.0, p-value=0.019802	dG=0.4, p-value=0.009901	dG=0.4, p-value=0.029703

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 07:18 PM