Secondary structure and small RNA-seq evidence for dme-mir-4974

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mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:21263917-21264049 +	GCATTGACTTCTTTTGTTCTT---TGTTTTTATTCCCTGTCAG--AGAGTATATT--GATTTTAGGTGG-----------------------AC-------ATTTGCGACCATATAAAATAT-ATATATTCCTGATAAAGAATATTTA--------ATATATCTTCTTTTTCGGTATAC
droSim1	chr2L:20861453-20861585 +	GCACTGACTTCTTTTGTTCTT---TGTTTTTATTCCCTAGCAG--AGAGTATATT--GATTTTAGGCGG-----------------------TC-------ATTTGCGACCATATAAAGTAT-ACATATTCCTGATCAGAACTATTTA--------ATATATCTTTTTTTTCGGTACAC
droSec1	super_18:1195266-1195398 +	GCACTGACTTCTTTTGTTCTT---TGTTTTTATTCCCTAGCAG--AGAGTATATT--GATTTTAGGCGG-----------------------TC-------ATTTGCGACCATATAAAGTAT-ACATATTCCTGATCAGAACTATTTA--------ATATATCTTTTTTTTCGGTATAC
droYak2	chrU:19793626-19793766 +	GAACTTAATTATATCGTTCTC---T-CTCTTACACCCTTAAAG--AGGGTGTATT--GATTTTAACCGGAAAAAC-----GCAAAAAAGGAGAC-------ATTTGCGGCCATATAAAGTAA-ATATATTCTTAATCAGTATCAA-----------------CGTCAGTTTTAAGATCC
droEre2	scaffold_4784:24793627-24793751 +	TAATTGAATTTCTTTGGTTTT---T-TTACCATTTACTTTTAG--AGAATATACTAGAATTTC--TGAGAAGTGTGTAACAGGCAGAAGGAAAC-------GTTTTCGACCATATAAATTAT-ATATATTCTTGATCAGGA--------------------------------------
droAna3	scaffold_13499:388035-388162 -	TTATT----TCCTTTGTTCTT---CGTTTTTATACCCTTGCAG--AGGGTATTAT--AATTTTGGTCAAAAGTGTGCAACGCAGAGAAGGAGAC-------ATCTCCGACCCTATAAAGTAT-ATATATTCTTGATCAGGATCACCT--------------------------------
dp4	chr2:13223937-13224089 -	CCGTTCGCCTTTTTGGTTCTTTATTGTTTTTATACCCTTCTAG--AGAGTATTAC--GATTTTGGGCTAATGTCTGCAAGACTGGAAC--------CTGCAACATAGAATCCCATAGGGTATTATATAT-----ATGAGGATCGGTAG--------CCATCTCT-CTTTTTCTATACAC
droPer1	super_0:7229185-7229317 +	CCGTTCGCCTTTTTGGTTCTTTATTGTTTTTATACCCTTCTAG--AGAGTATTAT--GATTTTGGGCTGCTGTCTGCAAGGCTGAAAT--------CTATTGCATAGAATCCTATAGGGTATTATATAT-----GTCAGGA-----------------------------TCGGTAGCC
droWil1	scaffold_181150:776667-776791 -	T--------TTTTTTGATTTT---CTTTTTTATAACCTTGCAAAAAGGGTATATT--CATTTTGGTCAAAGGAAT-----------------GC-------ATCTCCGACCATGTAAATTAT-ATATATTCTTGATTAGCACGACGAGACGAGTTCATATAG----------------C
droVir3	scaffold_12963:16876342-16876466 -	GAACTCGTTTCTGGTGTACGT-CGTGTTTTTATACCCTTGTAG--AGAGTATTTT--AATTTTGTCGTGGAATGTGCAACGCATGGATGGAGAC-------ATTTGGGACCCCATAAAGTAT-ATGTATTCTAGATAA-----------------------------------------
droMoj3	Unknown	GGTTTCAGTTCTTTTGTTTTT---TTTTG--ATATCCCAAA-------------------------------TGTGAAGTGCTAAAGAGTTGAAATTCGGAATGTAGATTGGCAT-----------------TGAGTTCAATAAGATA--------TGGCGGATATATTGTATAC---A
droGri2	scaffold_3049:4191-4318 -	ATTGACAAAT---TTATTTTT---AATTCTTCTTTTGTTCGAG--TGGGTATAAC--AGGTAGAAGGAA-----------------------GC-------ATCTCCGACGCCATAAAGTAT-ATATGTTTCTGAGAAGGATCAATTG--------AGGAGTCGATGTAGTTCGT---C

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:21263917-21264049 +	GCATTGACTTCTTTTGTTCTTTGTTTTTATTCCCTGTCAGAGAGTATATTGATTTTAGGTGGACATTTGCGACCATATAAAATATATATATTCCTGATAAAGAATATTTAATATATCTTCTTTTTCGGTATAC
droSim1	chr2L:20861453-20861585 +	GCACTGACTTCTTTTGTTCTTTGTTTTTATTCCCTAGCAGAGAGTATATTGATTTTAGGCGGTCATTTGCGACCATATAAAGTATACATATTCCTGATCAGAACTATTTAATATATCTTTTTTTTCGGTACAC
droSec1	super_18:1195266-1195398 +	GCACTGACTTCTTTTGTTCTTTGTTTTTATTCCCTAGCAGAGAGTATATTGATTTTAGGCGGTCATTTGCGACCATATAAAGTATACATATTCCTGATCAGAACTATTTAATATATCTTTTTTTTCGGTATAC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

GCACTGACTTCTTTTGTTCTT---TGTTTTTATTCCCTAGCAGAGAGTATATTGATTTTAGGCGGTCATTTGCGA----------------------CCATATAAAGTAT-ACATATTCCTGATCAGAACTATTTAATATATCTTTTTTTTCGGTACAC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

CCGTTCGCCTTTTTGGTTCTTTATTGTTTTTATACCCTTCTAGAGAGTATTACGATTTTGGGCTAATGTCTGCAAGACTGGAACCTGCAACATAGAATCCCATAGGGTATTATATAT-----ATGAGGATCGGTAGCCATCTC-TCTTTTTCTATACAC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

dG=-21.5, p-value=0.009901	dG=-20.7, p-value=0.009901

droSim1

dG=-16.4, p-value=0.009901	dG=-15.5, p-value=0.009901

droSec1

dG=-16.4, p-value=0.009901	dG=-15.5, p-value=0.009901

droYak2

dG=-15.2, p-value=0.009901	dG=-15.0, p-value=0.009901	dG=-14.8, p-value=0.009901	dG=-14.6, p-value=0.009901	dG=-14.6, p-value=0.009901

droEre2

dG=-11.0, p-value=0.009901	dG=-10.8, p-value=0.009901	dG=-10.6, p-value=0.009901	dG=-10.6, p-value=0.009901	dG=-10.6, p-value=0.009901	dG=-9.8, p-value=0.009901

droAna3

dG=-17.2, p-value=0.009901	dG=-17.2, p-value=0.009901	dG=-17.2, p-value=0.009901	dG=-17.2, p-value=0.009901	dG=-17.2, p-value=0.009901	dG=-14.6, p-value=0.009901

dp4

dG=-14.7, p-value=0.009901	dG=-14.7, p-value=0.009901	dG=-14.3, p-value=0.009901	dG=-14.3, p-value=0.009901	dG=-14.1, p-value=0.009901

droPer1

dG=-16.7, p-value=0.009901	dG=-16.6, p-value=0.009901	dG=-16.2, p-value=0.009901	dG=-16.1, p-value=0.009901	dG=-16.1, p-value=0.009901	dG=-15.7, p-value=0.009901

droWil1

dG=-13.5, p-value=0.009901	dG=-13.5, p-value=0.009901	dG=-13.3, p-value=0.009901	dG=-12.9, p-value=0.009901	dG=-12.9, p-value=0.009901

droVir3

dG=-13.4, p-value=0.009901	dG=-13.3, p-value=0.009901	dG=-13.3, p-value=0.009901	dG=-13.2, p-value=0.009901	dG=-13.2, p-value=0.009901	dG=-12.6, p-value=0.009901

droMoj3

dG=-7.0, p-value=0.009901	dG=-6.3, p-value=0.009901	dG=-6.0, p-value=0.009901	dG=-6.0, p-value=0.009901

droGri2

dG=-8.6, p-value=0.009901	dG=-7.7, p-value=0.009901	dG=-7.4, p-value=0.009901

Generated: 03/07/2013 at 06:22 PM