Secondary structure and small RNA-seq evidence for dme-mir-31b

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:8887323-8887479 -	TCGCTCCACGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAACATTTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACTCTATCAGCGTTG
droSim1	chrX:7083953-7084109 -	TCGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG
droSec1	super_34:250169-250325 -	TTGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG
droYak2	chrX:12425680-12425836 +	TTTCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTTTGATCGTCCGAAAAA---------------------------ATGTGAA---TATT---TTT--TAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACTCTATCAGCGTTG
droEre2	scaffold_4690:6225295-6225451 +	TCGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAA---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACACTATCAACGTTG
droAna3	scaffold_13047:712420-712562 -	AT---CCTCG------------AAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGAGGATCGAGCGAGTCATCGACCGAGACG---------------------------A----------------ATT--CCAAA------GCGGCTATGCCTCATCTAGTCAATTACATTACTTTGACACTTTCCACGAGG
dp4	chrXL_group1e:8162325-8162445 -	GTGT-CCT----------------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CAAAA-------------------------------------------------------A---GAAGATGA-----TTT--GAAAT------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG
droPer1	super_13:404315-404435 +	GTGT-CCT----------------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CAAAA-------------------------------------------------------A---GAAGATGA-----TTT--GAAAT------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG
droWil1	scaffold_181150:794468-794638 +	TCACGAAT-----GTG---ATGAAAACAACTAGTGGATTTGGCAAGATGTCGGAATAGCTGAAAGTCACACAAAATCA----------------------TAAAATGTTTGCCGTTTTGTTATTGT-TGTGAA-----T-TTTATTGATTTCAAAAATTACGGCTATGCCTCATCTAGTCAATTGCATTAGTTTGATTAAGTCAAC--TG
droVir3	scaffold_12726:2775742-2775905 -	TTGCAGCACATATATATAAATATAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAAAG--TC----------------------ATA-AAT----CCAGAATTTCTATT-T-TGTGTA-----TTTTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGACAAAAGCAACG---
droMoj3	scaffold_6473:5711141-5711289 +	GTGGTCCTCG----------------CAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAAA-TATC----------------------ATAGAAT----CCAGAATTTATATT-T-TGTGTA-----T-TTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGACAGCAGCAAC---C
droGri2	scaffold_15203:6378282-6378443 -	TCGACCACCAT--TTGCACCCGCAAACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGACAG-CACAA--GATC----------------------ACA-AAT----CAAGAAACTTTATT-T-TGTGTA-----TTTTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGAC---ATCAACAACG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:8887323-8887479 -	TCGCTCCACGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAACATTTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACTCTATCAGCGTTG
droSim1	chrX:7083953-7084109 -	TCGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG
droSec1	super_34:250169-250325 -	TTGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAT---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG
droYak2	chrX:12425680-12425836 +	TTTCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTTTGATCGTCCGAAAAA---------------------------ATGTGAA---TATT---TTT--TAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACTCTATCAGCGTTG
droEre2	scaffold_4690:6225295-6225451 +	TCGCTCCTCGT-----------TAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGCGGATCGAGCCTCTTATCGTCCGAAAAA---------------------------ATGTGAA---TATT---TTT--GAAAA------GCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACACTATCAACGTTG
droAna3	scaffold_13047:712420-712562 -	AT---CCTCG------------AAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAGAGGATCGAGCGAGTCATCGACCGAGACG---------------------------A----------------ATT--CCAAA------GCGGCTATGCCTCATCTAGTCAATTACATTACTTTGACACTTTCCACGAGG
dp4	chrXL_group1e:8162325-8162445 -	GTGT-CCT----------------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CAAAA-------------------------------------------------------A---GAAGATGA-----TTT--GAAAT------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG
droPer1	super_13:404315-404435 +	GTGT-CCT----------------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CAAAA-------------------------------------------------------A---GAAGATGA-----TTT--GAAAT------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG
droWil1	scaffold_181150:794468-794638 +	TCACGAAT-----GTG---ATGAAAACAACTAGTGGATTTGGCAAGATGTCGGAATAGCTGAAAGTCACACAAAATCA----------------------TAAAATGTTTGCCGTTTTGTTATTGT-TGTGAA-----T-TTTATTGATTTCAAAAATTACGGCTATGCCTCATCTAGTCAATTGCATTAGTTTGATTAAGTCAAC--TG
droVir3	scaffold_12726:2775742-2775905 -	TTGCAGCACATATATATAAATATAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAAAG--TC----------------------ATA-AAT----CCAGAATTTCTATT-T-TGTGTA-----TTTTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGACAAAAGCAACG---
droMoj3	scaffold_6473:5711141-5711289 +	GTGGTCCTCG----------------CAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAG-CACAAA-TATC----------------------ATAGAAT----CCAGAATTTATATT-T-TGTGTA-----T-TTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGACAGCAGCAAC---C
droGri2	scaffold_15203:6378282-6378443 -	TCGACCACCAT--TTGCACCCGCAAACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGACAG-CACAA--GATC----------------------ACA-AAT----CAAGAAACTTTATT-T-TGTGTA-----TTTTTATTGAGTACA------GCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGAC---ATCAACAACG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TCGCTCCTCGTTAGACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAGCACAGCGGATCGAGCCTCTTATCGTCCGAAAAAATGTGATTATTTTTGAAAAGCGGCTATGCCTCATCTAGTCAATTGCATTACTTTGACGCTATCAACGTTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
............................TGGCAAGATGTCGGAATAGCTGA..........................................................................................................	23	1	499.00	499	499
............................TGGCAAGATGTCGGAATAGCTG...........................................................................................................	22	1	69.00	69	69
............................TGGCAAGATGTCGGAATAGCT............................................................................................................	21	1	49.00	49	49
..........................TTTGGCAAGATGTCGGAATAGCT............................................................................................................	23	1	28.00	28	28
............................TGGCAAGATGTCGGAATAGC.............................................................................................................	20	1	9.00	9	9
............................TGGCAAGATGTCGGAATAG..............................................................................................................	19	1	2.00	2	2
...........................TTGGCAAGATGTCGGAATAGCT............................................................................................................	22	1	2.00	2	2
....................................................................................AAAATGTGATTATTTTTGAAAAGC.................................................	24	1	1.00	1	1
.................................AGATGTCGGAATAGCTGA..........................................................................................................	18	1	1.00	1	1
..................................................................................AAAAAATGTGATTATTTTTGAAAAGC.................................................	26	1	1.00	1	1
..........................TTTGGCAAGATGTCGGAATAGC.............................................................................................................	22	1	1.00	1	1
......................................................................................AATGTGATTATTTTTGAAAAGC.................................................	22	1	1.00	1	1
..........................TTTGGCAAGATGTCGGAATAG..............................................................................................................	21	1	1.00	1	1
................................AAGATGTCGGAATAGCTGA..........................................................................................................	19	1	1.00	1	1

dp4

GTGTCCT------GACAAATAATGAATTTGGCAAGATGTCGGAATAGCTGAGAGCA----------------------------AAAAGAAGATGAT--TTGAAATGCGGCTATGCCTCATCTAGTCAATTGCATTCATTTGATTCTATCAACGATG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
............................TGGCAAGATGTCGGAATAGCTGA..........................................................................................................	23	1	677.00	677	454	223
............................TGGCAAGATGTCGGAATAGCTG...........................................................................................................	22	1	319.00	319	71	248
............................TGGCAAGATGTCGGAATAGCT............................................................................................................	21	1	114.00	114	13	101
............................TGGCAAGATGTCGGAATAGC.............................................................................................................	20	1	18.00	18	2	16
................................AAGATGTCGGAATAGCTGA..........................................................................................................	19	1	2.00	2	2	0
...........................TTGGCAAGATGTCGGAATAGCT............................................................................................................	22	1	1.00	1	0	1
...........................TTGGCAAGATGTCGGAATAGCTG...........................................................................................................	23	1	1.00	1	1	0
...............................CAAGATGTCGGAATAGCT............................................................................................................	18	1	1.00	1	0	1
...........................TTGGCAAGATGTCGGAATAGC.............................................................................................................	21	1	1.00	1	0	1
..........................TTTGGCAAGATGTCGGAATAGCT............................................................................................................	23	1	1.00	1	1	0
............................TGGCAAGATGTCGGAATAG..............................................................................................................	19	1	1.00	1	0	1
.....................................................GCA----------------------------AAAAGAAGATGAT--TTGAAATGC.................................................	25	1	1.00	1	1	0

Secondary Structure

dm3

-34.3	-34.2	-33.9	-33.8	-33.6	-33.5

droSim1

-35.2	-34.8	-34.5	-34.3

droSec1

-35.2	-34.8	-34.5	-34.3

droYak2

-35.2	-34.8	-34.6	-34.5	-34.3	-34.2

droEre2

-34.3	-33.9	-33.7	-33.6	-33.6	-33.4

droAna3

-32.1	-31.7	-31.2

dp4

-26.9	-26.5	-26.0

droPer1

-26.9	-26.5	-26.0

droWil1

-39.1	-39.1	-38.9	-38.9	-38.8	-38.8

droVir3

-32.3	-32.3	-32.0	-31.9	-31.9	-31.6

droMoj3

-32.4	-32.0	-31.6

droGri2

-31.9	-31.6	-31.6	-31.5	-31.5	-31.5

Generated: 01/05/2013 at 05:18 PM