Secondary structure and small RNA-seq evidence for dme-mir-274

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3L:11650003-11650132 +	AG-T----TTTGGTGAC--------GAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGGCCG-CCAGGAT--TACTCGTTTTTGCGATCACAAATTATGAAATTGCAGCAAAA-CT---------CAACGA--------AATTG
droSim1	zdo16e12.g1:275-405 +	AG-T----TTTAGTGAC--------AAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGGCCA-CCAGGAT--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-TG---------CAACAA--------AAATG
droSec1	super_0:3837012-3837141 +	AG-T----TTTAGTGAC--------AAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGATCA-CCAGGAT--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CG---------CAACAA--------ATATA
droYak2	chr3L:11678621-11678750 +	TG-A----TTTTATGCC--------GAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGGTCG-CCAGGAT--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CG---------CAACAA--------AGTCG
droEre2	scaffold_4784:11632283-11632412 +	TG-A----TTTTATGGC--------CAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGGCCG-CCAGGAT--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CG---------CAACGA--------AGTCG
droAna3	scaffold_13337:5918600-5918728 +	GC-C----TTTTTTTAA--------AAAACA-------GAAATGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTATTTT--------------------AC------------------AGGACATACAGGAT--TACTCGTTTTTGCGATCACAAATCCTGAAATTGCAGCAAAA-AA---------CAGCAA--------A----
dp4	chrXR_group6:10040179-10040309 -	CC-TGGCACCTGGAACC--------TGGTCC---------CGTGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGG---------------------C------------------TGGCCG--CAGGAC--TACTCGTTTTTGCGATCACA-ATACTGAAATTGCAGCAACG-AG---------CAGCGA--------AACTG
droPer1	super_61:320241-320372 -	ACCTGGCACCTGGGACC--------TGGTCC---------CGTGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGG---------------------C------------------TGGCCG--CAGGAC--TACTCGTTTTTGCGATCACA-ATACTGAAATTGCAGCAACG-AG---------CAGCGA--------AACTG
droWil1	scaffold_180949:2705123-2705289 -	TT-T-------TGTGAT--------TATTTT---TAATATCCTGTTGCAGTTTCATTTTGTGACCGACACTAACGGGTAGTAACGGGTTAACAAAGTCGTTTTTC------------------TGGCCT------TT--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAGCAAAAGATCAACGTATACAACAAACACATAAAATGA
droVir3	scaffold_13049:23860698-23860839 +	AA-T----CCCAATGTC--------GCATCCTGT-------TTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTGGG----------------------GCA-CCTCGAATAC-G--------CTGTTT--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-AG---------CAACAA-----GAAAATTT
droMoj3	scaffold_6680:18485462-18485604 +	GA-A----TCTGTTGTCAAGT----GTATCC---------TGTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTGAG----------------------GCA-TCTCGTATTC-G--------CTGTTTTATACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-CG---------CAACGA--------AAATG
droGri2	scaffold_15110:13805592-13805748 -	AA-AGTGAAATAGTGCAACGTATACGAGTCCTGT-----GCGTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTA--------------------AAGGGCATCCTCGCATTCTG--------CTGGCT--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-AT---------CAACAA--------AACCA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3L:11650003-11650132 +	AG-T----TTTGGTGAC--------GAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGGCCG-CCAGGAT--TACTCGTTTTTGCGATCACAAATTATGAAATTGCAGCAAAA-CT---------CAACGA--------AATTG
droSim1	zdo16e12.g1:275-405 +	AG-T----TTTAGTGAC--------AAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGGCCA-CCAGGAT--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-TG---------CAACAA--------AAATG
droSec1	super_0:3837012-3837141 +	AG-T----TTTAGTGAC--------AAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGATCA-CCAGGAT--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CG---------CAACAA--------ATATA
droYak2	chr3L:11678621-11678750 +	TG-A----TTTTATGCC--------GAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGGTCG-CCAGGAT--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CG---------CAACAA--------AGTCG
droEre2	scaffold_4784:11632283-11632412 +	TG-A----TTTTATGGC--------CAATCC---------TGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG--------------------TT------------------TGGCCG-CCAGGAT--TACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAA-CG---------CAACGA--------AGTCG
droAna3	scaffold_13337:5918600-5918728 +	GC-C----TTTTTTTAA--------AAAACA-------GAAATGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTATTTT--------------------AC------------------AGGACATACAGGAT--TACTCGTTTTTGCGATCACAAATCCTGAAATTGCAGCAAAA-AA---------CAGCAA--------A----
dp4	chrXR_group6:10040179-10040309 -	CC-TGGCACCTGGAACC--------TGGTCC---------CGTGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGG---------------------C------------------TGGCCG--CAGGAC--TACTCGTTTTTGCGATCACA-ATACTGAAATTGCAGCAACG-AG---------CAGCGA--------AACTG
droPer1	super_61:320241-320372 -	ACCTGGCACCTGGGACC--------TGGTCC---------CGTGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGG---------------------C------------------TGGCCG--CAGGAC--TACTCGTTTTTGCGATCACA-ATACTGAAATTGCAGCAACG-AG---------CAGCGA--------AACTG
droWil1	scaffold_180949:2705123-2705289 -	TT-T-------TGTGAT--------TATTTT---TAATATCCTGTTGCAGTTTCATTTTGTGACCGACACTAACGGGTAGTAACGGGTTAACAAAGTCGTTTTTC------------------TGGCCT------TT--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAGCAAAAGATCAACGTATACAACAAACACATAAAATGA
droVir3	scaffold_13049:23860698-23860839 +	AA-T----CCCAATGTC--------GCATCCTGT-------TTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTGGG----------------------GCA-CCTCGAATAC-G--------CTGTTT--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-AG---------CAACAA-----GAAAATTT
droMoj3	scaffold_6680:18485462-18485604 +	GA-A----TCTGTTGTCAAGT----GTATCC---------TGTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTGAG----------------------GCA-TCTCGTATTC-G--------CTGTTTTATACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-CG---------CAACGA--------AAATG
droGri2	scaffold_15110:13805592-13805748 -	AA-AGTGAAATAGTGCAACGTATACGAGTCCTGT-----GCGTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTA--------------------AAGGGCATCCTCGCATTCTG--------CTGGCT--TACTCGTTTTTGCGATCACAAATTCTGAAATTGCAACGAAA-AT---------CAACAA--------AACCA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AGT----TTTAGTGACAAATCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGGCCACCAGGATTACTCGTTTTTGCGATCACAAATCATGAAATTGCAGCAAAATGCAACAAAAATG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
......................................TTTGTGACCGACACTAACGGGT..........................................................................	22	1	7.00	7	7
......................................TTTGTGACCGACACTAACGGGTA.........................................................................	23	1	6.00	6	6
..................................................................................CTCGTTTTTGCGATCACAAATC..............................	22	1	1.00	1	1

dp4

CCTGGCACCTGGAACCTGGTCCCGTGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGG-CTGGCCGC-AGGACTACTCGTTTTTGCGATCACA-ATACTGAAATTGCAGCAACGAGCAGCGAAACTG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
......................................TTTGTGACCGACACTAACGGGT..........................................................................	22	1	41530.00	41530	8	41522
......................................TTTGTGACCGACACTAACGGGTA.........................................................................	23	1	5857.00	5857	1	5856
......................................TTTGTGACCGACACTAACGGG...........................................................................	21	1	937.00	937	0	937
......................................TTTGTGACCGACACTAACGGGTAA........................................................................	24	1	685.00	685	0	685
......................................TTTGTGACCGACACTAACG.............................................................................	19	1	542.00	542	0	542
......................................TTTGTGACCGACACTAACGG............................................................................	20	1	354.00	354	0	354
.......................................TTGTGACCGACACTAACGGGT..........................................................................	21	1	299.00	299	0	299
.......................................TTGTGACCGACACTAACGGGTA.........................................................................	22	1	44.00	44	0	44
..................................................................................CTCGTTTTTGCGATCACA-ATACT............................	23	1	42.00	42	0	42
........................................TGTGACCGACACTAACGGGT..........................................................................	20	1	10.00	10	0	10
..................................................................................CTCGTTTTTGCGATCACA-ATA..............................	21	1	7.00	7	0	7
.....................................TTTTGTGACCGACACTAACGGGT..........................................................................	23	1	5.00	5	0	5
...................................................................................TCGTTTTTGCGATCACA-ATACT............................	22	1	4.00	4	0	4
.......................................TTGTGACCGACACTAACGGGTAA........................................................................	23	1	4.00	4	0	4
..................................................................................CTCGTTTTTGCGATCACA-ATAC.............................	22	1	3.00	3	0	3
........................................TGTGACCGACACTAACGGGTA.........................................................................	21	1	3.00	3	0	3

Secondary Structure

dm3

dG=-26.3, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.5, p-value=0.009901

droSim1

dG=-26.3, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.5, p-value=0.009901

droSec1

dG=-24.2, p-value=0.009901	dG=-24.0, p-value=0.009901	dG=-23.8, p-value=0.009901	dG=-23.7, p-value=0.009901	dG=-23.6, p-value=0.009901

droYak2

dG=-26.3, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.5, p-value=0.009901

droEre2

dG=-26.3, p-value=0.009901	dG=-26.1, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.6, p-value=0.009901	dG=-25.5, p-value=0.009901

droAna3

dG=-19.3, p-value=0.009901	dG=-19.3, p-value=0.009901	dG=-19.1, p-value=0.009901	dG=-18.9, p-value=0.009901	dG=-18.8, p-value=0.009901

dp4

dG=-23.1, p-value=0.009901	dG=-22.9, p-value=0.009901

droPer1

dG=-23.1, p-value=0.009901	dG=-22.9, p-value=0.009901

droWil1

dG=-25.6, p-value=0.009901	dG=-25.4, p-value=0.009901

droVir3

dG=-25.9, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.3, p-value=0.009901	dG=-25.1, p-value=0.009901	dG=-25.0, p-value=0.009901

droMoj3

dG=-27.0, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.4, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-26.1, p-value=0.009901

droGri2

dG=-26.9, p-value=0.009901	dG=-26.9, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.8, p-value=0.009901	dG=-26.7, p-value=0.009901

Generated: 03/07/2013 at 05:01 PM