Secondary structure and small RNA-seq evidence for dme-mir-1005

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:4343681-4343771 +	CCACCATTCTGACCTGTGAGTTGAT-CGA----TTTCGAGGTTTTG--------------------------------GCACAC------GAATA-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droSim1	chr2L:4265544-4265633 +	CTACCATTCTGACCTGTGAGTTGAT-CGA----TTTCGAGTTTTTG--------------------------------GC-CAC------AAATA-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droSec1	super_5:2441095-2441185 +	CCACCATTCTGACCTGTGAGTTGAT-CGA----TTTCGAGGTTTTG--------------------------------GCACAC------AAATG-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droYak2	chr2L:4375638-4375728 +	CCACCATTCTGACCTGTGAGTTGAT-CGA----TTTCGAGGTTTTG--------------------------------GCAGCC------AAAAA-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droEre2	scaffold_4929:4420541-4420630 +	CCACCATTCTGACCTGTGAGTTCAT-CGA----TTTCGAGGTTT-G--------------------------------CCAGCC------AAAAA-------------TAATCTGGAATC-TTTAATTCGCAGTTCCCACCGAAATGT
droAna3	scaffold_12916:13781299-13781395 -	TAACGGTTTTGACTTGTAAGAACCA-AAACTACTTTCT--GTAT-C--------------------------------AAAGCC------AGAAA---CTAATCG---TAA--TTGAAAT-TATCTTAACCAGTCCCCATTGAGCTGT
dp4	chr4_group2:339129-339252 +	CCACCATTTTGACATGTAAGTGTCC-ATA---TCCTCGAGGCTCCTGCAATGCACTGCAATGCACTGCAATGACCGCAATGCTG------ACGTA-------------TTATTTATGTTC-TCCGATCCCCAGTTCCCACTGAAATGT
droPer1	super_8:3550415-3550538 -	CCACCATTTTGACATGTAAGTGTCC-ATA---TCCTCGAGGCTCCTGCAATGCACTGCAATGCACTGCAATGACCGCAATGCTG------ACGTA-------------TTATTTATGTTC-TCCGATCCCCAGTTCCCACTGAAATGT
droWil1	scaffold_180772:1844874-1844969 -	TTACAATTCTATCATGTAAGTTAAAACGA----TTAAGTAATTTC---------------------------------ACACTT------ACATATATT---------TATTTAACTTTCTCTTGTCTCCTAGTCCCACTTGAAATGC
droVir3	Unknown	CAGTGGTATTGACCTGTAAGTATG-----------------------------------------------------------------------------------------TTGAATT-TTCTTACTGCAGTTCCGCTGGAGATCG
droMoj3	scaffold_6500:22625692-22625724 +	CCTCCATATTGCTCTGCGTGCAAGA-TGC----GCCCG--------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15252:16827853-16827948 -	CCACCATTCTGACATGTAACC--AC-TGA----TCCTGATCCTT-G--------------------------------ATTG-CACTGCCCATTT---TGAATGCGTTTTC-------TT-TCTGCTTTGCAGTTCCCACGGAAATGG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:4343681-4343771 +	CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGGTTTTGGCACACGAATATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT
droSim1	chr2L:4265544-4265633 +	CTACCATTCTGACCTGTGAGTTGATCGATTTCGAGTTTTTGGC-CACAAATATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT
droSec1	super_5:2441095-2441185 +	CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGGTTTTGGCACACAAATGTAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT
droYak2	chr2L:4375638-4375728 +	CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGGTTTTGGCAGCCAAAAATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT
droEre2	scaffold_4929:4420541-4420630 +	CCACCATTCTGACCTGTGAGTTCATCGATTTCGAGGTT-TGCCAGCCAAAAATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

CTACCATTCTGACCTGTGAGTTGATCGAT-TTCGAGTTTTTGGC-CACA---------------------------------AATATAATCTGGAATCTTTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
.........................................................................................TCTGGAATCTTTAATTCGCAG...............	21	1	5.00	5	5
...............GTGAGTTGATCGAT-TTCGAGTT.......................................................................................	22	1	1.00	1	1

dp4

CCACCATTTTGACATGTAAGTGTCCATATCCTCGAGGCTCCTGC-AATGCACTGCAATGCACTGCAATGACCGCAATGCTGACGTATTATTTATGTTCTCCGATCCCCAGTTCCCACTGAAATGT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-16.7	-16.7	-16.0	-16.0	-15.9	-15.8

droSim1

-16.1	-16.0	-15.5

droSec1

-17.0	-17.0	-16.9	-16.3	-16.3	-16.2

droYak2

-18.5	-18.1	-18.1	-17.6

droEre2

-12.3	-11.6

droAna3

-4.0	-3.6	-3.5	-3.3	-3.2	-3.2

dp4

-14.5	-14.5	-14.5	-14.3	-13.8	-13.7

droPer1

-14.5	-14.5	-14.5	-14.3	-13.8	-13.7

droWil1

-5.5	-5.5	-5.4	-4.8	-4.8	-4.8

droVir3

-1.9	-1.1	-1.0

droMoj3

-4.2	-3.8	-3.3

droGri2

-6.2	-6.0	-5.6	-5.5	-5.4	-5.3

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