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 +	GCATTGACTTCTTTTGTTCTT---TGTTTTTATTCCCTGTCAG--AGAGTATATT--GATTTTAGGTGG-----------------------AC-------ATTTGCGACCATATAAAATAT-ATATATTCCTGATAAAGAATATTTA--------ATATATCTTCTTTTTCGGTATAC

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

-25.2	-25.1	-24.4	-24.3	-24.2

droSim1

-17.0	-16.4	-16.4	-16.1

droSec1

-17.0	-16.4	-16.4	-16.1

droYak2

-20.1	-19.4	-19.4	-19.4	-19.4	-19.2

droEre2

-14.0	-13.9	-13.7	-13.6	-13.5	-13.4

droAna3

-26.8	-26.0	-25.9	-25.9	-25.9	-25.8

dp4

-20.8	-20.8	-20.6	-20.6	-20.5	-20.5

droPer1

-24.7	-24.7	-24.3	-24.2	-24.1	-24.1

droWil1

-15.6	-15.6	-15.6	-15.4	-15.4	-15.4

droVir3

-14.4	-14.3	-14.2	-14.1	-14.1	-14.0

droMoj3

-11.9	-11.8	-11.7	-11.3	-11.2	-11.2

droGri2

-16.9	-16.5	-16.3	-16.2	-16.1	-16.1

Generated: 01/05/2013 at 05:27 PM