Secondary structure and small RNA-seq evidence for dme-mir-133

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:20616602-20616729 +	CAT--------TCGAGAA---------------------------TTTCCACC--------TGCAAC-ACTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-T-TCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGACAACGAAAG-CCTA----------------GTGAAC
droSim1	chr2L:20179920-20180047 +	CAT--------TCGAGAA---------------------------TTTGCACC--------TGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-T-TTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGCTGACATCGAAAG-CCGA----------------GCGAAC
droSec1	super_18:496867-496993 +	CAT--------TCGAGA----------------------------TTTGCACC--------TGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-T-TTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGCTGACATCGAAAG-CCTA----------------GCGAAC
droYak2	chr2R:6964793-6964921 +	TAT--------TCCAGAA---------------------------TTTCCTCC--------TGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-TTCCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGACAACGAAGT-ACGA----------------GTAAAC
droEre2	scaffold_4845:3836606-3836724 -	AT---------------------------------------------TTCCTC--------TGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-T-CCTAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGCCAACTAAAT-TCGA----------------GTGAAC
droAna3	scaffold_12916:7117508-7117634 +	T----------TCGTGAA---------------------------TGATTATC--------TGCAAC-GCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATCT-TTTCAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATGACAACAAAGT-ACAA----------------GTGAAA
dp4	chr4_group3:7699977-7700121 -	GAC--------GCGTGTG---------------------------TGCTTATG--------TACAACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-TATCAAGTATTTGGTCCCCTTCAACCAGCTGTAT-CAGTGGTTGATTCCAACAAAAA-ACAAAAGGCGCCAACAAATAATAAAG
droPer1	super_1:9145698-9145865 -	TAT--------TTGTATGTGTAT--TT--GTATGTGACGCGTGTGTGCTTATG--------TACAACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-TATCAAGTATTTGGTCCCCTTCAACCAGCTGTAT-CAGTGGTTGATTCCAACAAAAA-ACAAAAGGCGCCAACAAATAATAAAG
droWil1	scaffold_180708:2027542-2027651 +	-------------------------------------------------------------TACAAC-ACTGAATGTAGCTGGTTGACATCGGGTCAGATCTATTTATTTGAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATCCCAACAAAAA-GCAA-----------------TGGAA
droVir3	scaffold_12963:13475783-13475914 -	CAA--------ACGAAGATATAT--ATTGCCAA--------TCGAATCACATT--------CACAAC-GCTGTGTGTAGTTGGTTGACATCGGGTCAGATCTATTT-CTGAAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGAAGCCAACAA------------------------------
droMoj3	scaffold_6500:24707638-24707772 +	CATGAAATAAATTGTGT------------------------TGTGTACTCAAACAAACATCCACAAC-GCTGTGTGTAGTTGGTTGACATCGGGTCAGATCTGTTT-T-TCGAGAATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATGACAACAAGT----------------------------
droGri2	scaffold_15126:6389834-6389991 +	CAA--------ACAAAACTATATACATGATTAA--------TTTGAATTTATT--------TACAAC-GCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-ATTCGAGTATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATGTCAACAAGTGAACTTAAG-----AAC-AATAGTGAAA

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:20616602-20616729 +	CAT--------TCGAGAA---------------------------TTTCCACC--------TGCAAC-ACTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-T-TCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGACAACGAAAG-CCTA----------------GTGAAC
droSim1	chr2L:20179920-20180047 +	CAT--------TCGAGAA---------------------------TTTGCACC--------TGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-T-TTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGCTGACATCGAAAG-CCGA----------------GCGAAC
droSec1	super_18:496867-496993 +	CAT--------TCGAGA----------------------------TTTGCACC--------TGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-T-TTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGCTGACATCGAAAG-CCTA----------------GCGAAC
droYak2	chr2R:6964793-6964921 +	TAT--------TCCAGAA---------------------------TTTCCTCC--------TGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-TTCCAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGACAACGAAGT-ACGA----------------GTAAAC
droEre2	scaffold_4845:3836606-3836724 -	AT---------------------------------------------TTCCTC--------TGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTT-T-CCTAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGATGCCAACTAAAT-TCGA----------------GTGAAC
droAna3	scaffold_12916:7117508-7117634 +	T----------TCGTGAA---------------------------TGATTATC--------TGCAAC-GCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATCT-TTTCAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATGACAACAAAGT-ACAA----------------GTGAAA
dp4	chr4_group3:7699977-7700121 -	GAC--------GCGTGTG---------------------------TGCTTATG--------TACAACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-TATCAAGTATTTGGTCCCCTTCAACCAGCTGTAT-CAGTGGTTGATTCCAACAAAAA-ACAAAAGGCGCCAACAAATAATAAAG
droPer1	super_1:9145698-9145865 -	TAT--------TTGTATGTGTAT--TT--GTATGTGACGCGTGTGTGCTTATG--------TACAACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-TATCAAGTATTTGGTCCCCTTCAACCAGCTGTAT-CAGTGGTTGATTCCAACAAAAA-ACAAAAGGCGCCAACAAATAATAAAG
droWil1	scaffold_180708:2027542-2027651 +	-------------------------------------------------------------TACAAC-ACTGAATGTAGCTGGTTGACATCGGGTCAGATCTATTTATTTGAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATCCCAACAAAAA-GCAA-----------------TGGAA
droVir3	scaffold_12963:13475783-13475914 -	CAA--------ACGAAGATATAT--ATTGCCAA--------TCGAATCACATT--------CACAAC-GCTGTGTGTAGTTGGTTGACATCGGGTCAGATCTATTT-CTGAAAGCATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGAAGCCAACAA------------------------------
droMoj3	scaffold_6500:24707638-24707772 +	CATGAAATAAATTGTGT------------------------TGTGTACTCAAACAAACATCCACAAC-GCTGTGTGTAGTTGGTTGACATCGGGTCAGATCTGTTT-T-TCGAGAATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATGACAACAAGT----------------------------
droGri2	scaffold_15126:6389834-6389991 +	CAA--------ACAAAACTATATACATGATTAA--------TTTGAATTTATT--------TACAAC-GCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTT-ATTCGAGTATTTGGTCCCCTTCAACCAGCTGTAG-CAGTGGTTGATGTCAACAAGTGAACTTAAG-----AAC-AATAGTGAAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CATTCGAGAATTTGCACCTGCAAC-GCTGTGTGTAGCTGGTTGACATCGGGTCAGATCTGTTTT-TTAAGCATTTGGTCCCCTTCAACCAGCTGTAGCCAGTGGTTGCTGACATCGAAAGCC----------------GAGCGAAC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................................................................TTGGTCCCCTTCAACCAGCTGT...................................................	22	1	1993.00	1993	1993
..................................AGCTGGTTGACATCGGGTCAGAT.........................................................................................	23	1	221.00	221	221
..................................AGCTGGTTGACATCGGGTCAGA..........................................................................................	22	1	174.00	174	174
.........................................................................TTGGTCCCCTTCAACCAGCTG....................................................	21	1	94.00	94	94
..................................AGCTGGTTGACATCGGGTCAG...........................................................................................	21	1	15.00	15	15
.........................................................................TTGGTCCCCTTCAACCAGCT.....................................................	20	1	9.00	9	9
.........................................................................TTGGTCCCCTTCAACCAGCTGTA..................................................	23	1	3.00	3	3
.........................................................................TTGGTCCCCTTCAACCAG.......................................................	18	1	2.00	2	2
...................................GCTGGTTGACATCGGGTCAGAT.........................................................................................	22	1	1.00	1	1

dp4

GACGCGTGTGTGCTTATGTACAACGGCTGTATGTAGCTGGTTGACATCGGGTCAGATCTATTTTATCAAGTATTTGGTCCCCTTCAACCAGCTGTA-TCAGTGGTTGATTCCAACAAAAAACAAAAGGCGCCAACAAATAATAAAG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.........................................................................TTGGTCCCCTTCAACCAGCTGT...................................................	22	1	44359.00	44359	3811	40548
.........................................................................TTGGTCCCCTTCAACCAGCTG....................................................	21	1	2507.00	2507	218	2289
.........................................................................TTGGTCCCCTTCAACCAGCT.....................................................	20	1	609.00	609	13	596
..................................AGCTGGTTGACATCGGGTCAGAT.........................................................................................	23	1	190.00	190	150	40
..................................AGCTGGTTGACATCGGGTCAGA..........................................................................................	22	1	161.00	161	148	13
.........................................................................TTGGTCCCCTTCAACCAG.......................................................	18	1	150.00	150	9	141
..........................................................................TGGTCCCCTTCAACCAGCTGT...................................................	21	1	69.00	69	12	57
.........................................................................TTGGTCCCCTTCAACCAGCTGTA-.................................................	23	1	38.00	38	4	34
..................................AGCTGGTTGACATCGGGTCAG...........................................................................................	21	1	15.00	15	12	3
...........................................................................GGTCCCCTTCAACCAGCTGT...................................................	20	1	9.00	9	1	8
.............................................................................TCCCCTTCAACCAGCTGT...................................................	18	1	3.00	3	0	3

Secondary Structure

dm3

dG=-27.2, p-value=0.009901	dG=-26.7, p-value=0.009901	dG=-26.6, p-value=0.009901

droSim1

dG=-27.2, p-value=0.009901	dG=-26.7, p-value=0.009901	dG=-26.6, p-value=0.009901

droSec1

dG=-27.2, p-value=0.009901	dG=-26.7, p-value=0.009901	dG=-26.6, p-value=0.009901

droYak2

dG=-26.3, p-value=0.009901	dG=-26.2, p-value=0.009901	dG=-25.8, p-value=0.009901	dG=-25.7, p-value=0.009901	dG=-25.7, p-value=0.009901

droEre2

dG=-27.1, p-value=0.009901	dG=-26.6, p-value=0.009901	dG=-26.5, p-value=0.009901

droAna3

dG=-24.7, p-value=0.009901	dG=-24.7, p-value=0.009901

dp4

dG=-25.5, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.5, p-value=0.009901

droPer1

dG=-25.5, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.5, p-value=0.009901

droWil1

dG=-24.6, p-value=0.009901	dG=-24.6, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-24.2, p-value=0.009901	dG=-23.9, p-value=0.009901

droVir3

dG=-23.5, p-value=0.009901	dG=-23.0, p-value=0.009901	dG=-22.9, p-value=0.009901	dG=-22.7, p-value=0.009901

droMoj3

dG=-25.4, p-value=0.009901	dG=-25.4, p-value=0.009901	dG=-24.9, p-value=0.009901	dG=-24.9, p-value=0.009901

droGri2

dG=-24.7, p-value=0.009901	dG=-24.7, p-value=0.009901	dG=-24.3, p-value=0.009901	dG=-24.3, p-value=0.009901	dG=-24.1, p-value=0.009901

Generated: 03/07/2013 at 04:50 PM