Secondary structure and small RNA-seq evidence for dme-mir-4956

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:6979754-6979901 -	GAGTGCCAACAATTTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACCTG
droSim1	chrX:5492772-5492919 -	GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACTTG
droSec1	super_24:199934-200081 -	GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCATG------AACGATCCTCGGGCAAGCAACACCAACTTG
droYak2	chrX:14374793-14374940 +	GAGTGCCAACAATCTGGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEre2	scaffold_4690:15890244-15890391 -	GAGTGCCAATAATCTTGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG------AACGATCCCCGGGCAAGCAACACCAACCTG
droAna3	scaffold_13117:2326296-2326455 -	CAGTGCCAATTCCCTTGGCGGCGGCGGTGGCGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACATGCTT---AATGACCAGCGGCCGAGCAACACCAACCTG
dp4	chrXL_group1a:6391512-6391662 -	CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCGAGCAACACCAATCTG
droPer1	super_25:931278-931428 +	CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCCAGCAACACCAATCTG
droWil1	scaffold_180777:2984533-2984680 +	CAGTGCCAATTCCCTTGGCG---------GTGGCAATATGTGCAATATGCCACCGATGGCCAGTAACAATTCATTGAACAACCTGTGCGGTCTATCATTGGGCAGCGGCGGCAGCGATGATCTTATG------AACGATCATCGTCCGAGTAATACCAATTTG
droVir3	scaffold_12928:60655-60799 -	CAGCGCCAATTCCCTTG------------GCGGCAACATCTGCAATATGCCGCCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATTGGCAGCGGCGGCAGCGATGATCACATG------AACGATCAGCGCAACAGCAACACCAATTTG
droMoj3	scaffold_6359:1380681-1380818 -	C-----CAATTCCCTCG------------GCGGCAACATCTGCAACATG---CCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATCGGCAGCGGCGGCAGCGATGATCTGATG------AACGATCAGCGCACAAGCAACACCAATTTG
droGri2	scaffold_14853:6692716-6692854 -	CAGCGCCAATTCACTCGGCG---------G---A---CTCTGCAACATG---CCGATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATAGGCAGCGGGGGCAGCGATGATCTTATG------AACGATCCACGCAACAGCAACACCAATTTG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:6979754-6979901 -	GAGTGCCAACAATTTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG---A---ACGATCCTCGGGCAAGCAACACCAACCTG
droSim1	chrX:5492772-5492919 -	GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATG---A---ACGATCCTCGGGCAAGCAACACCAACTTG
droSec1	super_24:199934-200081 -	GAGTGCCAACAATCTAGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCATG---A---ACGATCCTCGGGCAAGCAACACCAACTTG
droYak2	chrX:14374793-14374940 +	GAGTGCCAACAATCTGGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG---A---ACGATCCCCGGGCAAGCAACACCAACCTG
droEre2	scaffold_4690:15890244-15890391 -	GAGTGCCAATAATCTTGGGG---------GCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCATG---A---ACGATCCCCGGGCAAGCAACACCAACCTG
droAna3	scaffold_13117:2326296-2326455 -	CAGTGCCAATTCCCTTGGCGGCGGCGGTGGCGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACATGCTTA---ATGACCAGCGGCCGAGCAACACCAACCTG
dp4	chrXL_group1a:6391512-6391662 -	CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCGAGCAACACCAATCTG
droPer1	super_25:931278-931428 +	CAGTGCCAATAATCTTG------------GCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCCAGCAACACCAATCTG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GAGTGCCAACAATCTAGGGGGCGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCATGA------ACGATCCTCGGGCAAGCAACACCAACTTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

CAGTGCCAATAATCTT---GGCGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACATGATGATGCACGATCAGCGATCGAGCAACACCAATCTG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
...................................................................AGCAATCTATGCGGACTGTCGCT................................................................	23	1	2.00	2	2	0
............................................................................TGCGGACTGTCGCTGGGCAGC.........................................................	21	1	1.00	1	0	1
............................................................................TGCGGACTGTCGCTGGGCAGCG........................................................	22	1	1.00	1	0	1
..................................................................TAGCAATCTATGCGGACTGTCG..................................................................	22	1	1.00	1	1	0

Secondary Structure

dm3

-50.5	-50.4	-50.3	-50.0	-49.9	-49.9

droSim1

-50.5	-50.4	-50.3	-50.0	-49.9	-49.9

droSec1

-53.0	-52.8	-52.6	-52.5	-52.4	-52.2

droYak2

-55.4	-55.3	-55.1	-54.5

droEre2

-55.6	-55.1

droAna3

-53.8	-53.4	-53.3	-53.3	-53.1	-53.0

dp4

-51.0	-50.8	-50.6	-50.4

droPer1

-49.1	-48.9	-48.7	-48.5

droWil1

-42.5	-42.5	-42.3	-42.3	-42.1	-42.1

droVir3

-41.7	-41.7

droMoj3

-32.5	-32.5

droGri2

-34.3	-33.5	-33.4	-33.4

Generated: 01/05/2013 at 05:24 PM