Secondary structure and small RNA-seq evidence for dme-mir-4987

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:10840329-10840491 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAAAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droSim1 chr2L:10648081-10648243 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droSec1 super_3:6258415-6258577 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droYak2 chr2L:7248063-7248225 - AACAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAGAAGAAAATGAT-------
droEre2 scaffold_4929:14589948-14590110 + ACCAGTCGT---CTGTTGGTGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGAT-------
droAna3 scaffold_12916:14695622-14695781 - ACCAATCGT---CCGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAAAAGAAGAT----------
dp4 chr4_group4:3045338-3045500 - AACAATCGT---CTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGAT-------
droPer1 super_10:2060188-2060350 - AACAATCGT---CTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGAT-------
droWil1 scaffold_180703:3531157-3531322 + AACATTCGAGTAGTGTTGGCGGTGCCGTTGACGATGACTCAGCGCGTTTGCAACAGCGTGCGGCACGATTCTCTCAGCAGGGCTCTGGTTCGGCTAAGAAATCGGTCGTTGCGATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATGTT-------
droVir3 scaffold_12963:15772752-15772915 + ATTCGTCGT---CGGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGTCTAAGAAATCTGTCGTCGCAATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------
droMoj3 scaffold_6500:18770378-18770547 + ATTCGTCGT---CGGTTGGCGGTGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGACGAGCGGTGGCTCGGCTAAGAAATCTGTCGTCGCAATTGTAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAGGCCTCG
droGri2 scaffold_15126:2074135-2074298 - ATTCGTCGT---CGGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:10840329-10840491 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAAAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droSim1 chr2L:10648081-10648243 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droSec1 super_3:6258415-6258577 - ATCAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGT-------
droYak2 chr2L:7248063-7248225 - AACAGTCGT---CTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAAAACAAGAAGAAAATGAT-------
droEre2 scaffold_4929:14589948-14590110 + ACCAGTCGT---CTGTTGGTGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGAT-------
droAna3 scaffold_12916:14695622-14695781 - ACCAATCGT---CCGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGAGCGGCACGTTTCTCGCAGCAGAGCTCCGGCTCAGCCAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAAAAGAAGAT----------
dp4 chr4_group4:3045338-3045500 - AACAATCGT---CTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGAT-------
droPer1 super_10:2060188-2060350 - AACAATCGT---CTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGAT-------
droWil1 scaffold_180703:3531157-3531322 + AACATTCGAGTAGTGTTGGCGGTGCCGTTGACGATGACTCAGCGCGTTTGCAACAGCGTGCGGCACGATTCTCTCAGCAGGGCTCTGGTTCGGCTAAGAAATCGGTCGTTGCGATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAATAAGAAGAAAATGTT-------
droVir3 scaffold_12963:15772752-15772915 + ATTCGTCGT---CGGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGTCTAAGAAATCTGTCGTCGCAATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------
droMoj3 scaffold_6500:18770378-18770547 + ATTCGTCGT---CGGTTGGCGGTGCTGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGACGAGCGGTGGCTCGGCTAAGAAATCTGTCGTCGCAATTGTAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAGGCCTCG
droGri2 scaffold_15126:2074135-2074298 - ATTCGTCGT---CGGTGGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGTTTCTCACAGTCGAGCAGCGGCTCGGCAAAGAAATCTGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGCACAAGAAGAGATTGCAG------

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATCAGTCGTCTGTTGGCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAGAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGAACAAGAAGAAAATGGTSizeHit CountTotal NormTotalGSM343915
Embryo
.............................GATGACACAGCGCGCTTGC...................................................................................................................1911.0011
dp4
AACAATCGTCTGTGGGTGGGGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGGGCGGCACGTTTCTCGCAGCAGGGCTCCGGCTCGGCTAAGAAATTTGTCGTCGCCATTGCAAGTTCGCCTTTTGGTCTCACCACGGCCAAAAACCGGAAGAAACTGATSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.............................................TGCAACAGCGGGCGGCACGTTTCTC.............................................................................................2511.00110

Secondary Structure

dm3

-51.8 -51.1 -50.9

droSim1

-53.2 -52.5 -52.5 -52.5 -52.5 -52.3

droSec1

-53.2 -52.5 -52.5 -52.5 -52.5 -52.3

droYak2

-53.4 -53.2 -52.7 -52.7 -52.7 -52.5

droEre2

-51.6 -51.0 -51.0 -50.9 -50.9 -50.9

droAna3

-56.4 -55.8 -55.7 -55.5

dp4

-61.0 -61.0 -61.0 -60.1 -60.1 -60.1

droPer1

-61.0 -61.0 -61.0 -60.1 -60.1 -60.1

droWil1

-52.1 -51.8 -51.4 -51.2 -51.1

droVir3

-58.0 -57.4 -57.4 -57.2 -57.1 -57.1

droMoj3

-56.4 -55.6 -55.4 -55.4

droGri2

-59.1 -58.5 -58.5 -58.3 -58.2 -58.2

Generated: 01/05/2013 at 05:29 PM