Secondary structure and small RNA-seq evidence for dme-mir-4984

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:8141524-8141677 - TTAAAATAGT-------------------------------------------CTCAACTTCG---------------C--TCGAGGTGTGAAAACCT--------------TTTGG----CCA--GCGA----A----TAC--GCCTCGGAT--------------CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGT----T-------------------------------------TTGCGGCCAA-------------------------------------------------------GTGCTTTC----------ATT
droSim1 chr2L:7922185-7922338 - TTAAAATAGT-------------------------------------------CTCCACTCCG---------------C--TCGAGGTGTGAAAACCT--------------TTTGG----CCA--GCGA----A----TGC--GCCTCGGAT--------------CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGT----T-------------------------------------TTGCGGCCAA-------------------------------------------------------GTGCTTTC----------ATT
droSec1 super_3:3638638-3638791 - TTAAAATAGT-------------------------------------------CTCCACTCCG---------------C--TCGAGGTGTGAAAACCT--------------TTTGG----CCA--GCGA----A----TAC--GCCTCGGAT--------------CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTCGCCATGT----T-------------------------------------TTGCGGCCAA-------------------------------------------------------GTGCTTTC----------ATT
droYak2 chr2L:10772572-10772720 - TTAAAATAGT-------------------------------------------CTCGAG----------------------ACGAGGTGTGAAAACCT--------------TTTGG----CCG--GCAA----A----TAC--GCCTCGGAT--------------CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTTGCCATGT----T-------------------------------------TTGCGGCCAT-------------------------------------------------------GTGCTTTC----------ATT
droEre2 scaffold_4929:17047208-17047355 - TTAAAATAGT-------------------------------------------CTCTAC----------------------TCGAGGTGTGAAAACCT--------------T-TGG----CCA--GCAA----A----TAC--GCCTCGGAT--------------CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----GGCCAAATGACACGTTTGCCATGT----T-------------------------------------TTGCTGCCAT-------------------------------------------------------GTGCTTTC----------ATT
droAna3 scaffold_12916:9486383-9486598 - TTTAAATAGT-------------------------------------------CTCTCG---------AGGGTC----T--TCGGGGTGTGAAAACCT--------------TTCGGTTAGCCA--GCCA---GCGA--GAC---ACTTAACTCACTTCGTGGCTTCCAAATCACGTTTCAAGATCGAGGTAAATTCTTTGACGTATTCGCT-----GGCGAAATGGCACGTCTGACATGG----AATGGCATGGCATGAGATGGGCATGGTATGGTTGGTTGGTGCGACTAA---------------------------------------------------ATA-ATGGTTTC----------ATT
dp4 chr4_group3:2877715-2877892 + TTAAAATAGTTGCAGCCCACAA-------GTCACATGCCGCCGCCGGCGCATT--GGACAT--------------------TGGAGGTGTGAAAACCA--------------AT--------------------A----TTC--GCTTCAGGT--------------CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----TGGCAAATGACACGTTTTGG---------------------------------------------------------------------------------ACCTGCAATTTCCAGCAT------------TTACTTTC----------ATT
droPer1 gnl|ti|733036400:69-254 + TTAAAATAGTTGCAGCCCACAAGTCACAAGTCACATGCCGCCGCCGGCGCATT--GGACAT--------------------TGGAGGTGTGAAAACCA--------------AT--------------------A----TTC--GCTTCAGGT--------------CCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCT-----TGGCAAATGACACGTTTTGG---------------------------------------------------------------------------------ACCTGCAATTTCCAGCAT------------TTACTTTC----------ATT
droWil1 scaffold_180703:2787401-2787579 - TCT-----------------------------------CTCCACCAACATAATATGGA------------------------CAAGGTGTTAAGGTCT------------CTTTTGG----ATG--GTAGTCAGT----TGC--TAGTTAACT--------------CAAATCACGTTTCAAGATCGAGGTGAATTCTTTGA-ATACTGTCA-----AGCGAAATGACACGTTTT----GT----C-------------------------------------TTA--------------------------------ACCCGCACCGGCCGGCCCCCACTTACATAGATATTTTT----------AGT
droVir3 scaffold_12963:13862249-13862454 + TTAAAGCGGC-------------------------------------------TTCAA------------------------CAAGGTGTTAAAATCG------------C-AAAGG----CCGTCACAG----CCA--CAG--TCCACAGTC--------------CGAATCACGTTTTAAGATCGAGGTGAATTCTT-AACACCGCCGCTTGCCCAGCCAAATGGCACGTTTTCAATGG----GCTGG----------------------------------------CAGCAGCCCCAAGCCCTCAGCCAGCTTCATCTGCAATTGCGACGAC------------TTTCTTTCTGGCCCAACGAAC
droMoj3 scaffold_6500:5788118-5788309 - TTGGAATACTTG--------------------------------------------AACACTGGTTACAGCGGCTAC---AACAAGGTGTTAAAAACAGAAAAAAGCGAACCAAAGG----CCG--GCACACAGCCACACAG--TCCACAGTT--------------CGAATCACGTTTTAAGATCGAGGTGAATTCTTA-CTACCGACGCTCAGCCAGCCAAATGGCACGTTTGCCATGG----C-------------------------------------AT-CGCTCAA-------------------------------------------------------CAGCTTTA----------AGC
droGri2 scaffold_15126:6028218-6028422 - TTTGAATACTTG--------------------------------------------AACACTGGTTACACCGACTTCAGCAACTAGGTGTTAAAGCCA------------CCAAAGG----CCT-TGCAG----A----CACAGTTCACAGTC--------------CGAATCACGTTTTATGATCGAGGTGAATTCTTTGGTAGAGCCGCTTACCCAGCCAAATGGCACGTTTGCTAAGCATGGACAG----------------------------------AT-C-CCCAAGAGCCCCAAGCTCTAAGCCA-----------------------------------GTTCCATC----------ATC

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:8141524-8141677 - TTAAAATAGTCTCAACTTCGCTCGAGGTGTGAAAACCTTTTGGCCAGCGAATACGCCTCGGATCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTGGCCAAATGACACGTTCGCCATGTTTTGCGGCCAAGTGCTTTCATT
droSim1 chr2L:7922185-7922338 - TTAAAATAGTCTCCACTCCGCTCGAGGTGTGAAAACCTTTTGGCCAGCGAATGCGCCTCGGATCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTGGCCAAATGACACGTTCGCCATGTTTTGCGGCCAAGTGCTTTCATT
droSec1 super_3:3638638-3638791 - TTAAAATAGTCTCCACTCCGCTCGAGGTGTGAAAACCTTTTGGCCAGCGAATACGCCTCGGATCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTGGCCAAATGACACGTTCGCCATGTTTTGCGGCCAAGTGCTTTCATT
droYak2 chr2L:10772572-10772720 - TTAAAATAGTCTCGAG-----ACGAGGTGTGAAAACCTTTTGGCCGGCAAATACGCCTCGGATCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTGGCCAAATGACACGTTTGCCATGTTTTGCGGCCATGTGCTTTCATT
droEre2 scaffold_4929:17047208-17047355 - TTAAAATAGTCTCTAC-----TCGAGGTGTGAAAACCT-TTGGCCAGCAAATACGCCTCGGATCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTGGCCAAATGACACGTTTGCCATGTTTTGCTGCCATGTGCTTTCATT

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TTAAAATAGTCTCC----------------------------------ACTCCGCTCGAGGTGTGAAAACCTTTTGGCCAGCGAATGCGCCTCGGATCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTGGCCAAATGACACGTTCGCCATGTTTT------------GCGGCCAAGTGCTTTCATTSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TTAAAATAGTTGCAGCCCACAAGTCACATGCCGCCGCCGGCGCATTGGA---CATTGGAGGTGTGAAAACCAAT----------ATTCGCTTCAGGTCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTTGGCAAATGACACGTTT---------TGGACCTGCAATTTCCAGCATTTACTTTCATTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-46.9 -46.9 -46.7 -46.7 -46.3 -46.3

droSim1

-49.0 -49.0 -48.4 -48.4 -48.4 -48.4

droSec1

-49.0 -49.0 -48.4 -48.4 -48.4 -48.4

droYak2

-36.0 -35.5 -35.4 -35.4 -35.1 -35.0

droEre2

-33.8 -33.7 -33.7 -33.6 -33.5 -33.4

droAna3

-49.2 -49.1 -49.0 -49.0 -49.0 -49.0

dp4

-20.6 -20.6 -20.3 -19.7 -19.7 -19.6

droPer1

-20.6 -20.6 -20.3 -19.7 -19.7 -19.6

droWil1

-18.9 -18.7 -18.6 -18.6 -18.5 -18.5

droVir3

-26.1 -26.1 -26.0 -26.0 -26.0 -26.0

droMoj3

-38.2 -38.2 -38.0 -38.0 -37.8 -37.8

droGri2

-35.8 -35.8 -35.5 -35.5 -35.1 -35.1

Generated: 01/05/2013 at 05:28 PM