Secondary structure and small RNA-seq evidence for dme-mir-4971

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:3463274-3463415 -	GGAAG-GGCCAACTTCT---CGGCCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCATTCACTGTTCGAGGAGATCATGTCGG--------GCTCGGATG
droSim1	wop21h10.b1:281-423 +	GGAAG-GGCCAATTTCT---CGGCTCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCAGTCACTGTTCGAGGAGATTATGTCGG--------GCTCGGATG
droSec1	super_129:25371-25512 -	GGAAG-GGCCAACTTCT---CGGCCCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCAGTCACTGTTCGAGGAGATCATGTCGG--------GCTCGGATG
droYak2	chrU:14964015-14964156 +	GGAAG-GGCCAACTTCT---CGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCACTCACTGTTCGAGGAGATCATGTCGG--------GCTCGGATG
droEre2	scaffold_4929:3498112-3498253 -	GGAAG-GGCCAACTTCA---CGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGTGGATC------CAGGAGCAATTCTGCCGC-------TGGCGACAG--ATCATCGGCCA--CTGACAATGC----------------------CCACTCGCTGTTCGAGGAGATCATGTCGG--------GCTCGGATG
droAna3	scaffold_12943:2497935-2498076 +	GGCAG-AGCCAACTTCG---GAGCCCT--------TGAAACGGTCGACGAGCTTGTCAGTGGCGGCTC------CATAAAGAATCCTGCCGC-------TGGCGACAG--ACAGTCGGCCA--CTGACAACGC----------------------GCACTCGCTGTTCGAGGAAATAATGTCTG--------GCTCCGACG
dp4	chr4_group3:936699-936854 -	GGAGT-GCTCGTCTACG---TGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGC-------TGGCGACAG--ATTGTCGGCCA--CTGACAATGC----------------------CCATTCACTGTTCGAGGAGATCATGTCGG--------GCTCTGATG
droPer1	super_1:2415168-2415323 -	GGAGT-GCTCGTCTACG---TGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGC-------TGGCGACAG--ATTGTCGGCCA--CTGACAATGC----------------------CCATTCACTGTTCGAGGAGATCATGTCGG--------GCTCTGATG
droWil1	scaffold_189765:461-602 -	GTAAC-GATAGACGGAG---ATACCTT--------CGAGGTGGTGGACGAGTTCGTCTACCTCGGATC------CTTGTTGATGGCTGACAA-------CAATG----------TTAGTCG--GGAAATACGA----------------------AGGCGCATTATCAGCGGAAGTCGTGCCTACTATTGGCTCCAGAAGA
droVir3	scaffold_12963:15952027-15952160 -	ATTAGATGCCGATTGCGGTTCGTCCAT--------CAAGTCTGCGGCTGAGCTTGTCAGCGCCGT---------------CAATGCTGCCGC-------TGGCGACAG----CCTCGGC-G--CTGACAAGGA----------------------GCATGCCATGTTTGAGTATTTCCTCAACG--------AAGATGACG
droMoj3	scaffold_6473:12510219-12510341 +	GGTTT-G----------------------------------------TGTGTGTGTGTGTGGTGGAACTTC---AATGCGAACCT------CTTGCCACAATCGAGTGCAATTAACTGCCA--TGATATATGGCCAATCCCA-------------------TATGCAGACGGCGACCGAGTCGAA-------GTTCGGCTG
droGri2	scaffold_14853:4216060-4216150 -	------------------------------------------------------------------------------------TCGACCGC-------TGGCCACAA--ATGGCCGGACAGACAGACA-------GACAGACAGACAGACAGACAGACTCACTGACATAATTGATCATATC----------GCTTATACG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:3463274-3463415 -	GGAAGGGCCAACTTCTCGGCCCTCGACACGGTGGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droSim1	wop21h10.b1:281-423 +	GGAAGGGCCAATTTCTCGGCTCTCGACACGGTTGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCAGTCACTGTTCGAGGAGATTATGTCGGGCTCGGATG
droSec1	super_129:25371-25512 -	GGAAGGGCCAACTTCTCGGCCCTCGACACGGTTGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCAGTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droYak2	chrU:14964015-14964156 +	GGAAGGGCCAACTTCTCGGGCCTCGACACGGTGGATGAGCTTGTCAGTGGCGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCACTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droEre2	scaffold_4929:3498112-3498253 -	GGAAGGGCCAACTTCACGGGCCTCGACACGGTGGATGAGCTTGTCAGTGGTGGATCCAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCACTCGCTGTTCGAGGAGATCATGTCGGGCTCGGATG
droAna3	scaffold_12943:2497935-2498076 +	GGCAGAGCCAACTTCGGAGCCCTTGAAACGGTCGACGAGCTTGTCAGTGGCGGCTCCATAAAGAATCCTGCCGCTGGCGACAGACAGTCGGCCACTGACAACGCGCACTCGCTGTTCGAGGAAATAATGTCTGGCTCCGACG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GGAAGGGCCAATTTCTCGGCTCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCAGTCACTGTTCGAGGAGATTATGTCGGGCTCGGATG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.......................................TTGATGAGCTTGTCAGTGGCG................................................................................................	21	1	1.00	1	1

dp4

GGAGTGCTCGTCTACGTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGCTGGCGACAGATTGTCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCTGATG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
..............................................................................................CAGATTGTCGGCCACTGAC...........................................	19	1	1.00	1	1	0

Secondary Structure

dm3

-58.8	-57.9

droSim1

-48.7	-48.7	-48.7	-48.7	-48.6	-48.6

droSec1

-50.9	-50.9	-50.8	-50.8	-50.4	-50.0

droYak2

-54.9	-54.0

droEre2

-53.6	-52.7

droAna3

-43.9	-43.9	-43.9	-43.0	-43.0	-43.0

dp4

-42.8	-42.1	-42.1	-42.0	-42.0	-41.9

droPer1

-42.8	-42.1	-42.1	-42.0	-42.0	-41.9

droWil1

-33.6	-33.4	-33.2	-33.1	-33.0	-32.9

droVir3

-40.7	-40.6	-40.5	-40.4	-40.4	-40.2

droMoj3

-23.6	-23.6	-23.3	-23.3	-23.3	-23.1

droGri2

-12.6	-12.6	-12.1	-12.1	-11.9	-11.9

Generated: 01/05/2013 at 05:26 PM