Secondary structure and small RNA-seq evidence for dme-mir-983-2

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:4262501-4262629 - ATTATATGCATATGCTATTATATTGCAATAATTAAATAATACGTTTCGAACTAATGATTTTCAGTTCATTCATTAGGTAGTTACGCATTATCTAGTTGTT--------GTAAACATTCAACTCG---ATGGCGGATGAGA
droSim1 chrX:3277361-3277447 - ------TGCATATGAT---ATCTTGCAGTAATTTAGTAATACCTTTCGAACACATGATTTTCAG-TCATTCATGAGTTCGTCAGGTATTATCTAGTT-------------------------------------------
droSec1 super_4:2462215-2462301 + ------TGCATATGAT---ATGTTGCAGTAATTTAGTAATACCTTTCGAACATATGATTTTCAG-TCATTCATGAGTTCGTTAGGTATTATCTAGTT-------------------------------------------
droYak2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------
droEre2 scaffold_4690:1633107-1633226 - ------GTGTGATATT---ATGTTACAGTGATTTAATAATTCGATTCGAAGTTATGTGCTTTAA-TCATTCATAAATGCGAAACGGATTATTAAGTTATT--------GTTAACATTCAACTCG---TTGGCGTGTGAGA
droAna3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------
dp4 Unknown --------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------
droWil1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6540:31110074-31110202 - A-----CGTCTGTGTTATTTTTTTGAAGAGAACCAATTAAACAGTTCTCAGTTAAA-----TAA-ACATTTGAGTATTTATTACCTATTTTAAAGTTAATTAAATGTTCCATATAATTAACTACCATTTTACAGCTGATA
droGri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:4262501-4262629 - ATTATATGCATATGCTATTATATTGCAATAATTAAATAATACGTTTCGAACTAATGATTTTCAGTTCATTCATTAGGTAGTTACGCATTATCTAGTTGTTGTAAACATTCAACTCGATGGCGGATGAGA
droSim1 chrX:3277361-3277447 - ------TGCATATGA---TATCTTGCAGTAATTTAGTAATACCTTTCGAACACATGATTTTCAG-TCATTCATGAGTTCGTCAGGTATTATCTAGTT--------------------------------
droSec1 super_4:2462215-2462301 + ------TGCATATGA---TATGTTGCAGTAATTTAGTAATACCTTTCGAACATATGATTTTCAG-TCATTCATGAGTTCGTTAGGTATTATCTAGTT--------------------------------
droEre2 scaffold_4690:1633107-1633226 - ------GTGTGATAT---TATGTTACAGTGATTTAATAATTCGATTCGAAGTTATGTGCTTTAA-TCATTCATAAATGCGAAACGGATTATTAAGTTATTGTTAACATTCAACTCGTTGGCGTGTGAGA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
------TGCATATGAT---ATCTTGCAGTAATTTAGTAATACCTTTCGAACACATGATTTTCAG-TCATTCATGAGTTCGTCAGGTATTATCTAGTT--------------------------------SizeHit CountTotal NormTotalGSM343915
Embryo
..................................AGTAATACCTTTCGAACACATG.........................................................................2232.6788
dp4
---------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-23.0

droSim1

-22.8 -22.5 -22.4 -22.4 -22.3

droSec1

-22.8 -22.5 -22.4 -22.4 -22.3

droYak2

No secondary structure predictions returned

droEre2

-31.0 -31.0

droAna3

No secondary structure predictions returned

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

-13.1 -13.1 -12.7 -12.7 -12.6 -12.6

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:34 PM