Secondary structure and small RNA-seq evidence for dme-mir-4965

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chrX:16500125-16500242 + GTATTCGCAGTAC-AAGCACAAGGTGATCGATGGGAGATGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCAC--ACACTCACTCA--------------------------CCCAGGTTTCATCCATACAAATGTGTTTG
droSim1 chrX_random:4339044-4339160 + GTATTCGCAATAC-AAGCACAAGGTGATCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCAC--ACACTCACTCA--------------------------CCCA-GTTTCATCCATGCAAATGTGTTTG
droSec1 super_17:323461-323577 + GTATTCGCAATAC-AAGCACAAGGTGATCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCAC--ACACTCACTCA--------------------------CCCA-GTTTCATCCATGCAAATGTGTTTG
droYak2 chrX:10606276-10606397 + GAATTTAGAATAA-AAACAAAAGGTGATCGATGGGAGCTGACCTTGAGCCTGAGCTGAGATGATGAAGTAGATCGATCACAC-AC--TCACTCACTCA--------------------------CTCA-GTTTCATCCATGCAAATTTGTTTG
droEre2 scaffold_4690:6858711-6858812 + CCC-----AATAA-AACCAAAAGGTGATCGATGGGAGCTGA----G--CCTGA--AGTGATGATGAAGTAAATCGATCACA-------CACTCACT------------------------------CA-GATTCATCCATGCAAATTTGTTTG
droAna3 scaffold_13337:17013621-17013746 + GAAATCTCAGCAGCAAGCTCAG-CGGATCG---GGTGTTGG----A--GGTGG--TCTGCCATTGACGAAGAGCAACAGCACCAA--TTCCTTCC---AGGAGCATAGCGCTCCCAAGC----------GTCGTCCCAGTATGGGTGCCTTGG
dp4 chrXL_group1a:8134511-8134553 - ACT------------------------------------------------------------------------------CCAC--ACACACACACA--------------------------CACA---GACAGACATATAAAGGA-CATG
droPer1 super_5:779941-779973 + ACACTCGCACTCC-C---ACAAGAAGAGCAGCAGTAG--------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_180698:6476640-6476654 + ATTT------------------------------------------------------------------------------------------------------------------------------------------GAATGTGTGTG
droVir3 scaffold_13042:4246856-4246902 - CAC-----------------------------------------------------------------------------AC-ACACACACACACATG--------------------------TACAGCTTTCACTCATGCATATTTGTT--
droMoj3 scaffold_6500:26586811-26586907 + GCATTTGCACTG------------------CTCGAAAATGA----GCAATTGC--AAAGATCATTG-----------CACA---A--TACATTGC---AGAGAAATACTGCACAAAATAATTTAGTTA-ATTT------------TAAGTTGA
droGri2 scaffold_15245:5234538-5234618 - GCAAAATGAACAC-----AAAAACTGTTG------------------------------------------------CATACCAC--ACACTAACTG--T--AAATATCA--------------CATTTTTATTATTCTTATAATTATTAATA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chrX:16500125-16500242 + GTATTCGCAGTACAAGCACAAGGTGATCGATGGGAGATGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCAGGTTTCATCCATACAAATGTGTTTG
droSim1 chrX_random:4339044-4339160 + GTATTCGCAATACAAGCACAAGGTGATCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCA-GTTTCATCCATGCAAATGTGTTTG
droSec1 super_17:323461-323577 + GTATTCGCAATACAAGCACAAGGTGATCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCA-GTTTCATCCATGCAAATGTGTTTG
droYak2 chrX:10606276-10606397 + GAATTTAGAATAAAAACAAAAGGTGATCGATGGGAGCTGACCTTGAGCCTGAGCTGAGATGATGAAGTAGATCGATCACAC-ACTCACTCACTCACTCA-GTTTCATCCATGCAAATTTGTTTG
droEre2 scaffold_4690:6858711-6858812 + -----CCCAATAAAACCAAAAGGTGATCGATGGGAGCTGA----G--CCTGA--AGTGATGATGAAGTAAATCGATCACAC-----AC----TCACTCA-GATTCATCCATGCAAATTTGTTTG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GTATTCGCAATACAAGCACAAGGTGATCGATGGGAGCTGAGCGCCTGATGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCAG-TTTCATCCATGCAAATGTGTTTGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
-----------------------------------------------------------------------ACTCCACACACACACACACACAG---ACAGACATATAAAGGA-CATGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-26.0 -25.6

droSim1

-24.0 -23.7 -23.6 -23.6 -23.4 -23.3

droSec1

-24.0 -23.7 -23.6 -23.6 -23.4 -23.3

droYak2

-22.9 -22.9 -22.9 -22.5 -22.5 -22.5

droEre2

-16.5 -16.4 -16.4 -16.4 -16.2 -16.1

droAna3

-27.8 -27.0

dp4

0.0

droPer1

0.0

droWil1

No secondary structure predictions returned

droVir3

0.0 0.9 1.0

droMoj3

-9.8 -9.4 -9.3 -9.1 -9.0 -8.9

droGri2

-0.5 0.0 0.3 0.5 0.5

Generated: 01/05/2013 at 05:25 PM