Secondary structure and small RNA-seq evidence for dme-mir-4976

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mature

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mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:2723022-2723155 -	ACATCATCGATTATTGTCGATGCCGGCGTT---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTC---CGCG---TCTGGTCCACG
droSim1	chr2R:1535693-1535826 -	ACATCATCGATTATTGTCGATGCCGGCGTT---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTC---CGCG---TCTGGTCCACG
droSec1	super_1:401443-401575 -	ACATCATCGATTATTGTCGATGCCGGCGTT---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAA-GCGTCGTCTCGCTT---CGCG---TCTGGTCCACG
droYak2	chr2L:15457678-15457811 -	ACATCATCGATTATTGTCGATGCCGGCGTT---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCATTGAGTTTGTGTTGTCTGCATTCAGCTCGGTGGATGTCAGCCATCGGTGGAAGGCGTCGTCGCGCTC---CGCG---TCTGGTCCACG
droEre2	scaffold_4929:19824507-19824640 +	ACATCATCGATTATGGTCGATGGCGGCGTC---TCCCG---CTC------------------------------------------------------------------------------CAGGCTGTCGTCCACGGAGTTCGTGTTGTCGGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCGCGCTC---CGCG---TCCGGTCCACG
droAna3	scaffold_13266:9050244-9050380 -	ACATCATCGATTATTGTCGATGTTGGCGTT---TCCTG---CTC------------------------------------------------------------------------------CAAGTTATCGTCAAGCGGGTTTGTGTTGTCGCCATTTAGCTCCGTAGATGTCAGCCACCGGTGGAAGGCGTCATCCAGCTC---CTCGGGGTCATGTCCACT
dp4	chr3:994566-994696 -	ACATCATCGATTATTGTCGATGCTGCTGTT---TCCTG---CTC------------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTC---CTTG---CC---ACCGCT
droPer1	super_2:1175582-1175712 -	ACATCATCGATTATTGTCGATGCTGCTGTT---TCCTG---CTC------------------------------------------------------------------------------CGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTC---CTTG---CC---ACCGCT
droWil1	scaffold_180745:52392-52526 +	ACATCATCGATTATCGTTGATGCTGATGTTTTTTCCTG---CTC------------------------------------------------------------------------------CAAGCTAACGTCCAGTGTATTGGTATTTTCAACATTCAGCTCTGTGGATGTTAGCCAACGATGAAATGCATCATCATCTTGTTCCA-----TC---ATCTTC
droVir3	scaffold_12875:15675057-15675224 -	ACATCATCGATTATTGTTGATGCTGGCGTT---TCCTG---TTCGACAGCAACTGCTGCTGCTGCTGC---------------------------------------TGCCGCAGCTGCTGCCAAGCTATCGTCGAGCGTGTTTGTGCTGTCAACATTCAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCGTCAGCTTC---CTCA--------ATTTCC
droMoj3	scaffold_6496:8124753-8124946 +	ACATCATCGATTATTGTTGATGCTGGTGTT---TCCTGCTGCTGAACGGCAAgTGtTGgTGgTGgTggGtgGGgTggGGgTGtTGgTGgTGgTGgTTgTGgTTgTGgTTgTGgTGgTGgTGTCAAGCTATCGTCGAGCGTGTTTGTGCTGTCAACATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCGTC---------------------------
droGri2	scaffold_15245:12478490-12478641 -	ACATCATCGATTATTGTTGATGCTGATGTT---TCCTG---CTCAATTGTAGCTTCTGCTGCAGCTGC---------------------------------------AGCTGCTGCTGCTGCCAAGTTATCGTCAAACATATTTGTACTGTCAATATTGAGTTCCGTCGATGTCAGCCAGCGATGAAATGCATCATC---------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:2723022-2723155 -	ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGCGTCTGGTCCACG
droSim1	chr2R:1535693-1535826 -	ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGCGTCTGGTCCACG
droSec1	super_1:401443-401575 -	ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAA-GCGTCGTCTCGCTTCGCGTCTGGTCCACG
droYak2	chr2L:15457678-15457811 -	ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATTGAGTTTGTGTTGTCTGCATTCAGCTCGGTGGATGTCAGCCATCGGTGGAAGGCGTCGTCGCGCTCCGCGTCTGGTCCACG
droEre2	scaffold_4929:19824507-19824640 +	ACATCATCGATTATGGTCGATGGCGGCGTCTCCCGCTCCAGGCTGTCGTCCACGGAGTTCGTGTTGTCGGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCGCGCTCCGCGTCCGGTCCACG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ACATCATCGATTATTGTCGATGCCGGCGTTTCCCGCTCCAGGCTGTCGTCCATGGAGTTTGTGTTGTCAGCATTCAGCTCGGTGGATGTCAGCCAGCGGTGGAAGGCGTCGTCTCGCTCCGCGTCTGGTCCACG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

ACATCATCGATTATTGTCGATGCTGCTGTTTCCTGCTCCGAGGCATCGTCCGGCGTGTTTGTGCTGTCAGCATTCAGCTCCGTCGATGTCAGCCACCGATGGAACGCATCATCCAGGTCCTTGCC---ACCGCT	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-38.5, p-value=0.009901	dG=-38.3, p-value=0.009901	dG=-37.8, p-value=0.009901	dG=-37.6, p-value=0.009901

droSim1

dG=-38.5, p-value=0.009901	dG=-38.3, p-value=0.009901	dG=-37.8, p-value=0.009901	dG=-37.6, p-value=0.009901

droSec1

dG=-38.5, p-value=0.009901	dG=-38.3, p-value=0.009901	dG=-37.8, p-value=0.009901	dG=-37.6, p-value=0.009901

droYak2

dG=-38.8, p-value=0.009901

droEre2

dG=-38.5, p-value=0.009901	dG=-38.4, p-value=0.009901	dG=-37.8, p-value=0.009901	dG=-37.7, p-value=0.009901	dG=-37.6, p-value=0.009901

droAna3

dG=-14.9, p-value=0.009901	dG=-14.7, p-value=0.009901	dG=-14.2, p-value=0.009901	dG=-14.0, p-value=0.009901

dp4

dG=-21.7, p-value=0.009901	dG=-21.7, p-value=0.009901	dG=-21.2, p-value=0.009901	dG=-21.1, p-value=0.009901	dG=-20.8, p-value=0.009901

droPer1

dG=-21.7, p-value=0.009901	dG=-21.7, p-value=0.009901	dG=-21.2, p-value=0.009901	dG=-21.1, p-value=0.009901	dG=-20.8, p-value=0.009901

droWil1

dG=-17.6, p-value=0.009901	dG=-17.0, p-value=0.009901	dG=-16.8, p-value=0.009901

droVir3

dG=-34.5, p-value=0.009901	dG=-34.3, p-value=0.009901	dG=-34.2, p-value=0.009901	dG=-34.1, p-value=0.009901	dG=-34.0, p-value=0.009901	dG=-28.1, p-value=0.009901

droMoj3

dG=-39.6, p-value=0.009901	dG=-39.6, p-value=0.009901	dG=-39.4, p-value=0.009901	dG=-39.4, p-value=0.009901	dG=-39.3, p-value=0.009901	dG=-33.6, p-value=0.009901

droGri2

dG=-31.5, p-value=0.009901	dG=-30.9, p-value=0.009901	dG=-30.7, p-value=0.009901	dG=-30.6, p-value=0.009901	dG=-30.6, p-value=0.009901

Generated: 03/07/2013 at 06:41 PM