Secondary structure and small RNA-seq evidence for dme-mir-34

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr3R:5926643-5926771 +	CAAACAA-GTATTC------TTAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TT--ATTGC-CGTTGACAA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CTTATAA---
droSim1	chr3R:15449371-15449500 -	CAATCAAAGTATTC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TT--ATTGC-CGTTGACAA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CTTATGG---
droSec1	super_0:15986833-15986962 -	CAATCAAAGTATTC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TT--ATTGC-CGTTGACAA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CTTATAG---
droYak2	chr3R:9974454-9974582 +	CAATCAA-GTATTC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TT--ATTGC-CGTTGACAA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CGTACTC---
droEre2	scaffold_4770:15673299-15673427 -	CAATCAA-GTATTC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TC--ATTGC-TTGTGACAA----CTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CGTACTC---
droAna3	scaffold_13340:6489967-6490093 +	TAATTCA-GTTACC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCTGG-------TGCTCGTTGGCAATTAATTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAGAGCAA----------CTTA------
dp4	chr2:5019555-5019683 -	AAATCCA-GAAAAT------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAAAT--ATTGC-CTTTGACCA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCCATAACAA----------CG-ATAA---
droPer1	super_19:724982-725124 -	AAATCCA-GAAAAT------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAAAT--ATTGC-CTTTGACCA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCCATAACAACGATAAGCAACATATAATCG
droWil1	scaffold_181089:11166523-11166648 -	TAAC------AT--------TCTATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TTAAATTGC-CAA-AACAA-TAAACCACAGCCACTATCTTCACTGCCGCCGCGACAGGCCATGACAA----------CAATCGG---
droVir3	scaffold_12855:2682541-2682664 -	AAAAAAA-ATTACCTTAAATCCGATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCAA-T------------TGACAA----ATCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTATGACAG----------CAAA--A---
droMoj3	scaffold_6540:11883356-11883481 -	CGAAAAA-ATACCCTTTAATCCGATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCAC-T------------TGAAAA----ATCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTATGACAC----------CGAGAGA---
droGri2	scaffold_14624:2267430-2267555 +	AAACCAA-ATTCCAT-----TGAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCAA-C------------TGACAA----ATCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTATGACACCAATAA-----ATATAA---

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr3R:5926643-5926771 +	CAAACAA-GTATTC------TTAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TT--ATTGC-CGTTGACAA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CTTATAA---
droSim1	chr3R:15449371-15449500 -	CAATCAAAGTATTC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TT--ATTGC-CGTTGACAA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CTTATGG---
droSec1	super_0:15986833-15986962 -	CAATCAAAGTATTC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TT--ATTGC-CGTTGACAA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CTTATAG---
droYak2	chr3R:9974454-9974582 +	CAATCAA-GTATTC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TT--ATTGC-CGTTGACAA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CGTACTC---
droEre2	scaffold_4770:15673299-15673427 -	CAATCAA-GTATTC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TC--ATTGC-TTGTGACAA----CTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAA----------CGTACTC---
droAna3	scaffold_13340:6489967-6490093 +	TAATTCA-GTTACC------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCTGG-------TGCTCGTTGGCAATTAATTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAGAGCAA----------CTTA------
dp4	chr2:5019555-5019683 -	AAATCCA-GAAAAT------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAAAT--ATTGC-CTTTGACCA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCCATAACAA----------CG-ATAA---
droPer1	super_19:724982-725124 -	AAATCCA-GAAAAT------TCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAAAT--ATTGC-CTTTGACCA----TTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCCATAACAACGATAAGCAACATATAATCG
droWil1	scaffold_181089:11166523-11166648 -	TAAC------AT--------TCTATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TTAAATTGC-CAA-AACAA-TAAACCACAGCCACTATCTTCACTGCCGCCGCGACAGGCCATGACAA----------CAATCGG---
droVir3	scaffold_12855:2682541-2682664 -	AAAAAAA-ATTACCTTAAATCCGATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCAA-T------------TGACAA----ATCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTATGACAG----------CAAA--A---
droMoj3	scaffold_6540:11883356-11883481 -	CGAAAAA-ATACCCTTTAATCCGATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCAC-T------------TGAAAA----ATCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTATGACAC----------CGAGAGA---
droGri2	scaffold_14624:2267430-2267555 +	AAACCAA-ATTCCAT-----TGAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCAA-C------------TGACAA----ATCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTATGACACCAATAA-----ATATAA---

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CAATCAAAGTATTCTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAA-TTATTGCCGTTGACAATTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCTAAAGCAACTTATGG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
................................TGGCAGTGTGGTTAGCTGGTTGTG...........................................................................	24	1	936.00	936	936
................................TGGCAGTGTGGTTAGCTGGTTG.............................................................................	22	1	261.00	261	261
....................................................................................CAGCCACTATCTTCACTGCCGCC........................	23	1	112.00	112	112
................................TGGCAGTGTGGTTAGCTGGTT..............................................................................	21	1	64.00	64	64
................................TGGCAGTGTGGTTAGCTGGTTGT............................................................................	23	1	53.00	53	53
................................TGGCAGTGTGGTTAGCTGGT...............................................................................	20	1	12.00	12	12
....................................................................................CAGCCACTATCTTCACTGCCGC.........................	22	1	7.00	7	7
................................TGGCAGTGTGGTTAGCTGG................................................................................	19	1	3.00	3	3
................................TGGCAGTGTGGTTAGCTGGTTGTGT..........................................................................	25	1	2.00	2	2
........................................................TAGCCAA-TTATTGCCGTTGACAATTCA...............................................	27	1	2.00	2	2
................................................................TTATTGCCGTTGACAATTCA...............................................	20	1	1.00	1	1
................................TGGCAGTGTGGTTAGCTGGTTGTGTA.........................................................................	26	1	1.00	1	1
.................................GGCAGTGTGGTTAGCTGGTTGTG...........................................................................	23	1	1.00	1	1
........................................................TAGCCAA-TTATTGCCGTTGACAATT.................................................	25	1	1.00	1	1

dp4

AAATCC-AGAAAATTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAAATATTGCCTTTGACCATTCACAGCCACTATCTTCACTGCCGCCGCGACAAGCCATAACAACG-ATAA	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
................................TGGCAGTGTGGTTAGCTGGTT..............................................................................	21	1	160061.00	160061	36	160025
................................TGGCAGTGTGGTTAGCTGGTTG.............................................................................	22	1	57618.00	57618	69	57549
................................TGGCAGTGTGGTTAGCTGGT...............................................................................	20	1	49111.00	49111	11	49100
................................TGGCAGTGTGGTTAGCTGGTTGTG...........................................................................	24	1	33773.00	33773	289	33484
................................TGGCAGTGTGGTTAGCTGG................................................................................	19	1	22823.00	22823	4	22819
................................TGGCAGTGTGGTTAGCTGGTTGT............................................................................	23	1	9297.00	9297	12	9285
................................TGGCAGTGTGGTTAGCTGGTTGTGT..........................................................................	25	1	763.00	763	4	759
................................TGGCAGTGTGGTTAGCTG.................................................................................	18	1	462.00	462	0	462
....................................................................................CAGCCACTATCTTCACTGCCGCC........................	23	1	450.00	450	53	397
.................................GGCAGTGTGGTTAGCTGGTT..............................................................................	20	1	160.00	160	0	160
..................................GCAGTGTGGTTAGCTGGTT..............................................................................	19	1	84.00	84	0	84
....................................................................................CAGCCACTATCTTCACTGCCGC.........................	22	1	62.00	62	7	55
.................................GGCAGTGTGGTTAGCTGGTTG.............................................................................	21	1	57.00	57	0	57
.................................GGCAGTGTGGTTAGCTGGT...............................................................................	19	1	51.00	51	0	51
.................................GGCAGTGTGGTTAGCTGGTTGTG...........................................................................	23	1	34.00	34	1	33
..................................GCAGTGTGGTTAGCTGGTTG.............................................................................	20	1	27.00	27	0	27

Secondary Structure

dm3

-37.2	-36.5	-36.2

droSim1

-37.2	-36.5	-36.2

droSec1

-37.2	-36.5	-36.2

droYak2

-37.2	-36.5	-36.2

droEre2

-40.2	-39.5	-39.2

droAna3

-41.6	-40.9	-40.7	-40.6

dp4

-37.6	-36.9	-36.6

droPer1

-37.6	-36.9	-36.6

droWil1

-34.9	-34.7	-34.5	-34.3	-34.1	-33.9

droVir3

-36.4	-36.3	-35.7	-35.6	-35.4

droMoj3

-36.4	-35.7	-35.4

droGri2

-36.4	-36.3	-35.7	-35.6	-35.4

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