Secondary structure and small RNA-seq evidence for dme-mir-4916

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:9130478-9130566 - AAGTACTCAAGATAAG--TGGGT-GTTCTTG--GAAATTCGCC-TCGATCGGTAGCTAAA---------------------------------TTTCTGATTACTCCTAAAAGCCT-TTTGGATTGAGC
droSim1 chrX:7292594-7292672 - A---------GATAAG--TGGGT-GTTCTTG--GAAATTCGCC-TCGATCGGTA-CTAAA---------------------------------TTTCTGATTACTCCTAAAAGCCT-TTTGGATTGAGC
droSec1 super_68:18213-18301 - AAGTACTCAAGATAAG--TGGGT-GTTCTTG--GAAATTCGCC-TCGATCGGTAGCTAAA---------------------------------TTTCTGATTACTCCTAAAAGCCT-TTTGGATTGAGC
droYak2 chrX:17726636-17726725 - AAGTTCTCAAGATAAG--TGGGT-GTTCTTG--GAAATTCGCCTTCGATCGGTTGCTAAA---------------------------------TTTCTGATTACCCCTAAAAGCCT-TTTGGATTGAGC
droEre2 scaffold_4690:5984818-5984906 + AAGTTCTCAAGATAAG--TGGGT-GTTCTTG--GAAATTCGCC-TCGTTCGGTAGCTAAA---------------------------------TTTCTAATTACTCCCAAAAGCCT-TTTGGATTGAGC
droAna3 scaffold_13047:993021-993104 - AAAACCTGAGAATAAG--TGGGTAGTTCCGAGCGAAAGACTCC-TCCATCTTAA---------------------------------------CATCCATTT--CCCGTTCAGCCT-TTTGGATTGAGC
dp4 chrXL_group1e:1170761-1170857 + AGCTGCTCAAGATAAG--TGGGT----TCCG--CAGATACGTTTTTCCTCTGCAG-----------------------ACTCGAGAGTCTCTTTTTTTGGCTTTCGCCCACAGCCT-TTTGGATAGAGC
droPer1 super_30:24276-24372 - AGCTGCTCAAGATAAG--TGGGT----TCCG--CAGATTCGTGTTTCCCCTACAG-----------------------ACTCGTGAGTCTCTTTTTTTGGCTTTCGCCCACAGCCT-TTTGGATAGAGC
droWil1 scaffold_181096:7487008-7487059 + TTGATTACTACAT--------------------------------------------TGATTTCAACTTTCA---------------------T-----------TTGATAAGCCT-TTTGGATTGAGC
droVir3 scaffold_13052:1731753-1731829 + AAAATTTAAATAAATA--TATGT-GTAATTT--GAATACTGCC-TCGATGGTTAGCTACG---------------------------------TTTTTTA------------TTCT-TATGTACCTCTT
droMoj3 scaffold_6498:2397368-2397459 + TAATATTTGAAATTAGGCTTATT-GTTATTAA-TAAAGCCTCA-TTTTTCTGCA-CTTGG---------------------------------CTTTAAATTATTTTTCAAAATTTGGAGATATTGAGC
droGri2 scaffold_15203:7061820-7061918 + AAGAGCTTAAGATAAG--TATGT-GTTCCGT--GTGATAAAAG--GAATCTTCAG----A------------CAGCGAACT-GA---TCGCC-TTACTGAATCCG-CTTGCAGTCT-TTTGGATTGAGC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:9130478-9130566 - AAGTACTCAAGATAAGTGGGTGTTCTTGGAAATTCGCC-TCGATCGGTAGCTAAATTTCTGATTACTCCTAAAAGCCTTTTGGATTGAGC
droSim1 chrX:7292594-7292672 - A---------GATAAGTGGGTGTTCTTGGAAATTCGCC-TCGATCGGTA-CTAAATTTCTGATTACTCCTAAAAGCCTTTTGGATTGAGC
droSec1 super_68:18213-18301 - AAGTACTCAAGATAAGTGGGTGTTCTTGGAAATTCGCC-TCGATCGGTAGCTAAATTTCTGATTACTCCTAAAAGCCTTTTGGATTGAGC
droYak2 chrX:17726636-17726725 - AAGTTCTCAAGATAAGTGGGTGTTCTTGGAAATTCGCCTTCGATCGGTTGCTAAATTTCTGATTACCCCTAAAAGCCTTTTGGATTGAGC
droEre2 scaffold_4690:5984818-5984906 + AAGTTCTCAAGATAAGTGGGTGTTCTTGGAAATTCGCC-TCGTTCGGTAGCTAAATTTCTAATTACTCCCAAAAGCCTTTTGGATTGAGC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
A---------GATAAGTGGGTGTTCTTGGAAATTCGCCTC-GATCGGTA-----------CTAAATTTCTGATTACTCCTAAAAGCCTTTTGGATTGAGCSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AGCTGCTCAAGATAAGTGGGTTC---CGCAGATACGTTTTTCCTCTGCAGACTCGAGAGTCTCTTTTTTTGGCTTTCGCCCACAGCCTTTTGGATAGAGCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-12.9

droSim1

-13.5 -12.5

droSec1

-12.9

droYak2

-12.4 -12.4 -12.1 -12.0 -12.0 -11.8

droEre2

-16.1

droAna3

-7.6 -7.0

dp4

-22.5 -21.6

droPer1

-16.1

droWil1

0.0 0.4

droVir3

-3.0 -3.0 -2.4 -2.3 -2.1

droMoj3

-7.5 -7.2 -6.9

droGri2

-12.1 -11.8 -11.6 -11.6 -11.4 -11.4

Generated: 01/05/2013 at 05:20 PM