Secondary structure and small RNA-seq evidence for dme-mir-972

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chrX:19445170-19445290 +	TGCAAATAGCTAAAGAGAATGATAGGGAA----ATTGCT--AAATATTTTTTTTGTATAAATAACTTTT---AACTTTTGTACAATA------CG-AATATTTAGGCATTTCTCAAATCA------------------------------AA------------------------GATTTGCAAGCC-----------------AAA
droSim1	chrX:15010925-15011057 +	ATAAAAAAGCTGAAGAGAATGATAGTG-----AATTGCT--AAATATTTTCTTTGTATAAATGACTTTT---AACATTTGTACAATA------TT-AATATTTAAACATTTCTCGAATCA------------------------------AAGTA-----------TGCCACATCAGCTTTGCAAGCC-----------------AAA
droSec1	super_8:1727594-1727726 +	ATAAAAAAGCTGAAAAGAATGATAGTG-----AATTGCT--AAATATTTTCTTTGTATAAATAACTTTT---AATATTTGTACAATA------TT-AATATTTAAACATTTCTCGAATCA------------------------------AAGTA-----------TGCGACATCAGCTTTGCAAGCC-----------------AAA
droYak2	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:9681872-9682038 +	-TGAAATAGCTGAATATAATGCTAGTGAA----ATTGTT--AAATATTTACTTTGTATAAATGACCTTCATAAACATTTATACAATT------TCAAATATTTTGCCATTTCTCAATCCAATTCAATTTTGCCACACAGAAGTGTCCAAAAAGTA-----------TGCTACATCATATTTGCAATCC-----------------AGA
droAna3	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7946002-7946145 +	CTTAAATATTCGAAACGTGTACTAAGA-----TTCTACT--TCTTGCT------------------------AGCTTATTTTG--TAAACTAATG-AATAATTAAATGACAATGAAAACG------------------------------AAGTAAATTAGTTAATTAAGACAGCTGCTTAACATATAAAATAATTGAAAATATTCAA
droVir3	scaffold_13042:918660-918775 -	CTGAAAGAACTATAGATATTATTAATAATAGGAACTGCTTCAGATATTTTGTTTGCAGT-----GTCTT---AGCTTTTGTTT--TA------TG-ATGTTTTATATATTCCGAATATTA------------------------------AA------------------------GCTTCAAA---------------------AAA
droMoj3	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chrX:19445170-19445290 +	TGCAAATAGCTAAAGAGAATGATAGGGAAATTGCTAAATATTTTTTTTGTATAAATAACTTTTAACTTTTGTACAATACGAATATTTAGGCATTTCTCAAATCAAA-------------GATTTGCAAGCCAAA
droSim1	chrX:15010925-15011057 +	ATAAAAAAGCTGAAGAGAATGATAGTGA-ATTGCTAAATATTTTCTTTGTATAAATGACTTTTAACATTTGTACAATATTAATATTTAAACATTTCTCGAATCAAAGTATGCCACATCAGCTTTGCAAGCCAAA
droSec1	super_8:1727594-1727726 +	ATAAAAAAGCTGAAAAGAATGATAGTGA-ATTGCTAAATATTTTCTTTGTATAAATAACTTTTAATATTTGTACAATATTAATATTTAAACATTTCTCGAATCAAAGTATGCGACATCAGCTTTGCAAGCCAAA

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

ATAAAAAAGCTGAAGAGAATGATAGTGA-ATTGCTAAATATTTTCTTTGTATAAATGACTTTTAACATTTGTACAATATTAATATTTAAACATTTCTCGAATCAAAGTATGCCACATCAGCTTTGCAAGCCAAA	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

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

Secondary Structure

dm3

dG=-15.0, p-value=0.009901	dG=-15.0, p-value=0.009901	dG=-14.9, p-value=0.009901	dG=-14.7, p-value=0.009901	dG=-14.0, p-value=0.009901

droSim1

dG=-14.7, p-value=0.009901

droSec1

dG=-13.1, p-value=0.009901

droYak2

No secondary structure predictions returned

droEre2

dG=-13.6, p-value=0.009901	dG=-12.6, p-value=0.009901

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

dG=-0.2, p-value=0.029703	dG=-0.1, p-value=0.029703	dG=-0.1, p-value=0.009901	dG=0.0, p-value=0.029703	dG=0.1, p-value=0.009901

droVir3

dG=-7.0, p-value=0.009901	dG=-7.0, p-value=0.009901	dG=-7.0, p-value=0.009901	dG=-6.7, p-value=0.009901	dG=-6.5, p-value=0.009901

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 07:16 PM