Secondary structure and small RNA-seq evidence for dme-mir-998

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:17447586-17447758 -	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCAAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droSim1	chr3R:4023089-4023261 +	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCCAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droSec1	super_6:4044375-4044547 +	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCCAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droYak2	chr3R:6285151-6285323 -	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCCAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATATCTCG
droEre2	scaffold_4770:4217706-4217878 +	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCCAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droAna3	scaffold_13340:5676182-5676384 +	CT-------------------------------------------------------CGTCAGCAAT-------------------CTCGT-CTCCTCTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACCTGCTGCTGCTGCTGCTCTC---------CAGTTTGGCCAATTTTGTTAATTTTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCACCAAAAACATCTCTCG
dp4	chr2:23856839-23857018 -	CT-------------------------------------------------------CGTCTGAAATA---------------TATATCGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-AT-------------TTC---------CAG---GGCCAAT--TGTTAATTTTGCGATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droPer1	super_3:6633404-6633583 -	CT-------------------------------------------------------CGTCTGAAATA---------------TATATCGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-AT-------------TTC---------CAG---GGCCAAT--TGTTAATTTTGCGATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droWil1	scaffold_181089:8480191-8480341 +	---------------------------------------------------------------------------------------------------------------------------AAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TGCTTTAAACCTGG---GGCCAAT--TGTTCATTTTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAT-CA---CA-------
droVir3	scaffold_13047:6339512-6339744 +	CTTTATGTCGATGTTTTTTCGTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAT-------AAAT-----------------GGAAA----CCATTTGCTCGCAACGCGCAAGCG-CAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCAGTG----CACTG--ACC-GT--------------TG---------CAG--AGGGCAAT--TGTTCAAATTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCACTAA-----------G
droMoj3	scaffold_6540:1739242-1739414 -	CA-------------------------------------------------------AAT-ATCAAT---------------------GGATA----CCATT------------------AAAAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCAGTG----CACTGTAACC-GT--------------TG---------CAG--AGGGCAAT--TGTTCAAATTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAGTTTCAAACATGCATTCACCAA---AAAATGAAA
droGri2	scaffold_14906:11660076-11660280 +	CTTTATGTTGCTC------------------------------------------------------AAATGGGACCATTCTGTATATC-AAT----CCAAT------CAACGCGCAAGCG-CAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCAGTG----CACTG--ACC-GT--------------TG---------CAG--AGGGCAAT--TGTTCATTTTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCACCAAAT-CAAATCA-A

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:17447586-17447758 -	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCAAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droSim1	chr3R:4023089-4023261 +	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCCAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droSec1	super_6:4044375-4044547 +	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCCAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droYak2	chr3R:6285151-6285323 -	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCCAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATATCTCG
droEre2	scaffold_4770:4217706-4217878 +	CT-------------------------------------------------------CGTCAGCAAT---------------------CGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TC---------CAG---GGCCAAT--TGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droAna3	scaffold_13340:5676182-5676384 +	CT-------------------------------------------------------CGTCAGCAAT-------------------CTCGT-CTCCTCTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACCTGCTGCTGCTGCTGCTCTC---------CAGTTTGGCCAATTTTGTTAATTTTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCACCAAAAACATCTCTCG
dp4	chr2:23856839-23857018 -	CT-------------------------------------------------------CGTCTGAAATA---------------TATATCGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-AT-------------TTC---------CAG---GGCCAAT--TGTTAATTTTGCGATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droPer1	super_3:6633404-6633583 -	CT-------------------------------------------------------CGTCTGAAATA---------------TATATCGT-C----CTCGT------------------GTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-AT-------------TTC---------CAG---GGCCAAT--TGTTAATTTTGCGATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAC-AA---CATCTCTCG
droWil1	scaffold_181089:8480191-8480341 +	---------------------------------------------------------------------------------------------------------------------------AAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTG--ACC-GC--------------TGCTTTAAACCTGG---GGCCAAT--TGTTCATTTTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCAT-CA---CA-------
droVir3	scaffold_13047:6339512-6339744 +	CTTTATGTCGATGTTTTTTCGTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAT-------AAAT-----------------GGAAA----CCATTTGCTCGCAACGCGCAAGCG-CAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCAGTG----CACTG--ACC-GT--------------TG---------CAG--AGGGCAAT--TGTTCAAATTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCACTAA-----------G
droMoj3	scaffold_6540:1739242-1739414 -	CA-------------------------------------------------------AAT-ATCAAT---------------------GGATA----CCATT------------------AAAAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCAGTG----CACTGTAACC-GT--------------TG---------CAG--AGGGCAAT--TGTTCAAATTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAGTTTCAAACATGCATTCACCAA---AAAATGAAA
droGri2	scaffold_14906:11660076-11660280 +	CTTTATGTTGCTC------------------------------------------------------AAATGGGACCATTCTGTATATC-AAT----CCAAT------CAACGCGCAAGCG-CAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCAGTG----CACTG--ACC-GT--------------TG---------CAG--AGGGCAAT--TGTTCATTTTGAAATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCACCAAAT-CAAATCA-A

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTCGTCAGCAA------TCGTCCTCGTGTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTGACCGC-TCCAGGGCCAATTGTTCATTTTGAAATTGAAATTCTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCACAACATCTCTCG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................................................................................................................TAGCACCATGAGATTCAGCTC......................................	21	1	3876.00	3876	3876
.........................................................................................................................TAGCACCATGAGATTCAGCT.......................................	20	1	251.00	251	251
.........................................................................................................................TAGCACCATGAGATTCAGCTCT.....................................	22	1	78.00	78	78
............................................ACTGAATTCTCGTGGGTCTGC...................................................................................................................	21	1	35.00	35	35
............................................ACTGAATTCTCGTGGGTCTGCA..................................................................................................................	22	1	27.00	27	27
.........................................................................................................................TAGCACCATGAGATTCAGC........................................	19	1	11.00	11	11
...........................................................................................................................GCACCATGAGATTCAGCTC......................................	19	1	4.00	4	4
..........................................................................................................................AGCACCATGAGATTCAGCTC......................................	20	1	2.00	2	2
.........................................................................................................................TAGCACCATGAGATTCAG.........................................	18	1	1.00	1	1
........................................TGGAACTGAATTCTCGTGGGTCT.....................................................................................................................	23	1	1.00	1	1
..........................................................................................................................AGCACCATGAGATTCAGCTCT.....................................	21	1	1.00	1	1
............................................ACTGAATTCTCGTGGGTCT.....................................................................................................................	19	1	1.00	1	1

dp4

CTCGTCTGAAATATATATCGTCCTCGTGTCAAATTCATTTTGGAACTGAATTCTCGTGGGTCTGCACTGACAACACTGACCATTTCCAGGGCCAATTGTTAATTTTGCGATTGAAATTTTGTAGCACCATGAGATTCAGCTCTGGCGTGAATTTCAAACATGCATCCACAACATCTCTCG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
.........................................................................................................................TAGCACCATGAGATTCAGCTC......................................	21	1	8601.00	8601	3679	4922
.........................................................................................................................TAGCACCATGAGATTCAGCT.......................................	20	1	1007.00	1007	191	816
............................................ACTGAATTCTCGTGGGTCTGC...................................................................................................................	21	1	441.00	441	29	412
.........................................................................................................................TAGCACCATGAGATTCAGCTCT.....................................	22	1	184.00	184	76	108
............................................ACTGAATTCTCGTGGGTCTG....................................................................................................................	20	1	141.00	141	4	137
............................................ACTGAATTCTCGTGGGTCT.....................................................................................................................	19	1	128.00	128	2	126
............................................ACTGAATTCTCGTGGGTCTGCA..................................................................................................................	22	1	83.00	83	58	25
.........................................................................................................................TAGCACCATGAGATTCAGC........................................	19	1	58.00	58	3	55
............................................ACTGAATTCTCGTGGGTC......................................................................................................................	18	1	24.00	24	1	23
..........................................................................................................................AGCACCATGAGATTCAGCTC......................................	20	1	13.00	13	8	5
.........................................................................................................................TAGCACCATGAGATTCAG.........................................	18	1	6.00	6	1	5
...........................................................................................................................GCACCATGAGATTCAGCTC......................................	19	1	4.00	4	1	3

Secondary Structure

dm3

-41.3	-41.3	-41.2	-41.2	-40.9	-40.9

droSim1

-42.2	-42.2	-42.1	-42.1	-42.1	-42.1

droSec1

-42.2	-42.2	-42.1	-42.1	-42.1	-42.1

droYak2

-42.2	-42.2	-42.1	-42.1	-42.1	-42.1

droEre2

-42.2	-42.2	-42.1	-42.1	-42.1	-42.1

droAna3

-49.3	-49.3	-48.5	-48.5

dp4

-44.1	-44.1	-43.2	-43.2

droPer1

-44.1	-44.1	-43.2	-43.2

droWil1

-36.8	-36.8	-36.7	-36.7	-36.7	-36.7

droVir3

-44.1	-44.1	-44.0	-44.0	-44.0	-44.0

droMoj3

-41.2	-41.2	-41.0	-41.0	-40.8	-40.8

droGri2

-43.1	-43.1	-43.0	-43.0	-43.0	-43.0

Generated: 01/05/2013 at 05:37 PM