Secondary structure and small RNA-seq evidence for dme-mir-6-3

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:15548206-15548315 -	AAA-----TTGAAAATTGTACAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTTGAAACTCT----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGGCAATCGATCTACGT
droSim1	chr2R:14253641-14253750 -	AAA-----TTGAAAATTGTACAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTCGAAACTCT----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGGCAATCGATCTACGT
droSec1	super_1:13062939-13063048 -	AAA-----TTGAAAATTGTACAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTCGAAACTCT----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGGCAATCGATCTACGT
droYak2	chr2R:13624474-13624583 +	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTCGAAACTCT----CTCAATTTATATCACAGTGGCTGTTCTTTTTTATTTGGCAATCGATCTACAT
droEre2	scaffold_4845:9748460-9748569 -	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTGGCTGATGATGTAGTTCGAAACTCT----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCTGCGT
droAna3	scaffold_13266:9732107-9732212 +	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTCGCTGCTGATGTAGTT----ATTCG----CATCATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCTACGT
dp4	chr3:12676789-12676898 -	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTTGCTGCTGATGTAGTTCAAGTTTTG----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCACCGA
droPer1	super_2:8906774-8906883 +	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTTGCTGCTGATGTAGTTCAAGTTTCG----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCAACGA
droWil1	scaffold_180701:1650985-1651090 -	CAT-----TT----TTTGTTTAAAAAGAAGGGAACGGTTGCTGTTGATGTAGTATACCATTTTGTTTAACAA--TATATCACAGTGGCTGTTCTTTTTTGTTTAACAATCAATCAAC--
droVir3	scaffold_12875:4112942-4113050 +	CGC-----TCGTCAATTGTTTAAAAGGAAGAGAACGTTCGCTGTTGATGTAGT-CGACCTTTG----TACTCTTTATATCACAGTGGCTGTTCTTTTTTGTTTAGCAATTTCTCAACTT
droMoj3	scaffold_6496:20935943-20936057 -	AATCGTGGCCGTAAATTGCTTAAAGAGAAGAGAACGTTCGCTGTTGATGTAGTCGAATTCATT----TAATCTTTATATCACAGTGGCTGTTCTTTTTTGTTTAACAATTTTTCAACGT
droGri2	scaffold_15112:2107905-2108014 -	A-C-----TCATAAATTGTTTAAAAGGAAGAGAACGCTCGCTGCTGATGTAGTTCATGATTCA----AATATTTTATATCACAGTGGCTGTTCTTTTTTGTTTATCAATGATTCAACTT

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:15548206-15548315 -	AAA-----TTGAAAATTGTACAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTTGAAACTCT----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGGCAATCGATCTACGT
droSim1	chr2R:14253641-14253750 -	AAA-----TTGAAAATTGTACAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTCGAAACTCT----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGGCAATCGATCTACGT
droSec1	super_1:13062939-13063048 -	AAA-----TTGAAAATTGTACAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTCGAAACTCT----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGGCAATCGATCTACGT
droYak2	chr2R:13624474-13624583 +	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTCGAAACTCT----CTCAATTTATATCACAGTGGCTGTTCTTTTTTATTTGGCAATCGATCTACAT
droEre2	scaffold_4845:9748460-9748569 -	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTGGCTGATGATGTAGTTCGAAACTCT----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCTGCGT
droAna3	scaffold_13266:9732107-9732212 +	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTCGCTGCTGATGTAGTT----ATTCG----CATCATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCTACGT
dp4	chr3:12676789-12676898 -	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTTGCTGCTGATGTAGTTCAAGTTTTG----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCACCGA
droPer1	super_2:8906774-8906883 +	AAA-----TTGAAAATTGTTCAAAAAGAAGGGAACGGTTGCTGCTGATGTAGTTCAAGTTTCG----CACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCAACGA
droWil1	scaffold_180701:1650985-1651090 -	CAT-----TT----TTTGTTTAAAAAGAAGGGAACGGTTGCTGTTGATGTAGTATACCATTTTGTTTAACAA--TATATCACAGTGGCTGTTCTTTTTTGTTTAACAATCAATCAAC--
droVir3	scaffold_12875:4112942-4113050 +	CGC-----TCGTCAATTGTTTAAAAGGAAGAGAACGTTCGCTGTTGATGTAGT-CGACCTTTG----TACTCTTTATATCACAGTGGCTGTTCTTTTTTGTTTAGCAATTTCTCAACTT
droMoj3	scaffold_6496:20935943-20936057 -	AATCGTGGCCGTAAATTGCTTAAAGAGAAGAGAACGTTCGCTGTTGATGTAGTCGAATTCATT----TAATCTTTATATCACAGTGGCTGTTCTTTTTTGTTTAACAATTTTTCAACGT
droGri2	scaffold_15112:2107905-2108014 -	A-C-----TCATAAATTGTTTAAAAGGAAGAGAACGCTCGCTGCTGATGTAGTTCATGATTCA----AATATTTTATATCACAGTGGCTGTTCTTTTTTGTTTATCAATGATTCAACTT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AAATTGAAAATTGTACAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTCGAAACTCTCACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGGCAATCGATCTACGT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................AGGGAACGGTTGCTGATGATGTA................................................................	23	1	76.00	76	76
.......................AGGGAACGGTTGCTGATGATG..................................................................	21	1	13.00	13	13
.......................AGGGAACGGTTGCTGATGATGT.................................................................	22	1	12.00	12	12
......................AAGGGAACGGTTGCTGATGATGTA................................................................	24	1	2.00	2	2
.......................AGGGAACGGTTGCTGATGAT...................................................................	20	1	1.00	1	1
....................AGAAGGGAACGGTTGCTGATG.....................................................................	21	1	1.00	1	1
....................AGAAGGGAACGGTTGCTGATGA....................................................................	22	1	1.00	1	1
...................................................................TATCACAGTGGCTGTTCTTTTT.....................	22	3	1.00	3	3
...........................AACGGTTGCTGATGATGTA................................................................	19	1	1.00	1	1
.......................AGGGAACGGTTGCTGATGATGTAGT..............................................................	25	1	1.00	1	1

dp4

AAATTGAAAATTGTTCAAAAAGAAGGGAACGGTTGCTGCTGATGTAGTTCAAGTTTTGCACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTGCCAATCGATCACCGA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.......................AGGGAACGGTTGCTGCTGATGTA................................................................	23	1	135.00	135	135	0
.......................AGGGAACGGTTGCTGCTGATG..................................................................	21	1	6.00	6	6	0
.......................AGGGAACGGTTGCTGCTGATGT.................................................................	22	1	6.00	6	6	0
...................................................................TATCACAGTGGCTGTTCTTTTT.....................	22	3	1.00	3	3	0
....................AGAAGGGAACGGTTGCTGCTGAT...................................................................	23	1	1.00	1	1	0
...................................................................TATCACAGTGGCTGTTCTTTT......................	21	3	0.67	2	2	0

Secondary Structure

dm3

-31.2	-30.6	-30.3	-30.3

droSim1

-28.6	-28.3	-28.0	-27.7	-27.7

droSec1

-28.6	-28.3	-28.0	-27.7	-27.7

droYak2

-29.5	-28.6

droEre2

-29.1	-28.8	-28.5	-28.2	-28.2

droAna3

-31.6	-31.0	-30.7

dp4

-28.7	-28.6	-28.1	-28.1	-28.0	-27.9

droPer1

-28.7	-28.6	-28.1	-28.0	-27.8	-27.7

droWil1

-26.7	-26.7	-26.3	-26.3	-26.2	-26.2

droVir3

-24.3	-24.3	-24.3	-24.3	-24.2	-24.2

droMoj3

-27.0	-27.0	-26.9	-26.9	-26.3	-26.3

droGri2

-24.7	-24.6	-24.4	-24.3	-24.3	-24.2

Generated: 01/05/2013 at 05:29 PM