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

Legend:maturestarmismatch

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-ATTGCTAAATATTTTCTTTGTATAAATGACTTTTAACATTTGTACAATATTAATATTTAAACATTTCTCGAATCAAAGTATGCCACATCAGCTTTGCAAGCCAAASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
--------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-24.8

droSim1

-19.0

droSec1

-17.4

droYak2

No secondary structure predictions returned

droEre2

-22.1 -21.4

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

-3.1 -3.1 -3.1 -3.1 -2.9 -2.4

droVir3

-13.0 -12.4 -12.4 -12.1 -12.0

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:33 PM