Secondary structure and small RNA-seq evidence for dme-mir-993

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:2602040-2602188 + GG-GATCTC---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTT-CGG-CA-CATTGTCGGACTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACC--TCAA--------TATG
droSim1 chr3R:2632916-2633065 + GG-GATCTC---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTT-CGG-CG-CATTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACC--TCAAT-------GAAA
droSec1 super_6:2693177-2693327 + GG-GATCTC---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTTTCGG-CG-CATTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACC--TCAAT-------GAAA
droYak2 chr3R:7811352-7811500 - GG-GATCTC---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTT-CGA-CG-CATTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAATAAACC--TCAA--------GACA
droEre2 scaffold_4770:2845885-2846032 + GG-GATCTT---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTT-CGA-CG-C-TTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAATAAACC--TCAA--------GCCA
droAna3 scaffold_13340:5446725-5446870 - AC-GATCTT---------------------------CAATTGA--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATATTGCGTT-CGA-TG-CATTGTCGGACTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAAC--AT-----------T
dp4 chr2:19773774-19773922 - CG-GATCTT---------------------------TGATTGC--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATATTGCGCC-CGA-TG-TATTTTCGAGTGTTTGTGTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAAC--TC--------TGAA
droPer1 super_3:2522178-2522326 - CG-GATCTT---------------------------TGATTGC--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATATTGCGCT-CGA-TG-TATTTTCGAGTGTTTGTGTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAAC--TC--------TGAA
droWil1 scaffold_181089:11961167-11961347 + GATAATTTT---------------------------CATTTGTTTTTATTCAAGTTACACCGAAACAAAAAAGAAAACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTTTAAAGTGCATTTCCGATGCCATTG-------------TCAATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAAC--AATGACGACATAAA
droVir3 scaffold_13047:6141838-6142002 - GT-GGTCTCGTACTGGGTGAAGTGGGGGTCAGTGAATAACAGA--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATAGTGCATT-CAAATGCCATT-------------CTCAATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAACTCA----------AAA
droMoj3 scaffold_6540:16546170-16546300 - -------------------------------------AACAGA--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATAGTGCATA-CGAATGCCATTG-------------TCAATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAACTCAA--------ACTC
droGri2 scaffold_14906:11483329-11483464 - GT-GATATT---------------------------CA---GA--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-TTAGTGCATT-CAAATGCCATTG-------------TCAATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAACG-AA--------TAAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:2602040-2602188 + GG-GATCTC---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTT-CGG-CA-CATTGTCGGACTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACC--TCAA--------TATG
droSim1 chr3R:2632916-2633065 + GG-GATCTC---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTT-CGG-CG-CATTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACC--TCAAT-------GAAA
droSec1 super_6:2693177-2693327 + GG-GATCTC---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTTTCGG-CG-CATTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACC--TCAAT-------GAAA
droYak2 chr3R:7811352-7811500 - GG-GATCTC---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTT-CGA-CG-CATTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAATAAACC--TCAA--------GACA
droEre2 scaffold_4770:2845885-2846032 + GG-GATCTT---------------------------CAATTGT--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-AAATGGCGTT-CGA-CG-C-TTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAATAAACC--TCAA--------GCCA
droAna3 scaffold_13340:5446725-5446870 - AC-GATCTT---------------------------CAATTGA--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATATTGCGTT-CGA-TG-CATTGTCGGACTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAAC--AT-----------T
dp4 chr2:19773774-19773922 - CG-GATCTT---------------------------TGATTGC--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATATTGCGCC-CGA-TG-TATTTTCGAGTGTTTGTGTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAAC--TC--------TGAA
droPer1 super_3:2522178-2522326 - CG-GATCTT---------------------------TGATTGC--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATATTGCGCT-CGA-TG-TATTTTCGAGTGTTTGTGTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAAC--TC--------TGAA
droWil1 scaffold_181089:11961167-11961347 + GATAATTTT---------------------------CATTTGTTTTTATTCAAGTTACACCGAAACAAAAAAGAAAACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTTTAAAGTGCATTTCCGATGCCATTG-------------TCAATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAAC--AATGACGACATAAA
droVir3 scaffold_13047:6141838-6142002 - GT-GGTCTCGTACTGGGTGAAGTGGGGGTCAGTGAATAACAGA--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATAGTGCATT-CAAATGCCATT-------------CTCAATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAACTCA----------AAA
droMoj3 scaffold_6540:16546170-16546300 - -------------------------------------AACAGA--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-ATAGTGCATA-CGAATGCCATTG-------------TCAATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAACTCAA--------ACTC
droGri2 scaffold_14906:11483329-11483464 - GT-GATATT---------------------------CA---GA--------------------------------AACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTT-TTAGTGCATT-CAAATGCCATTG-------------TCAATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAACG-AA--------TAAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGGATCTCCAATTGTAACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTTAAATGGCGTTCGGCGCATTGTCGGATTGCTGGCTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACCTCAATGAAASizeHit CountTotal NormTotalGSM343915
Embryo
...................................................................................................GAAGCTCGTCTCTACAGGTATCT............................231350.00350350
.............................CTACCCTGTAGTTCCGGGCTTTTG.................................................................................................24115.001515
..............................TACCCTGTAGTTCCGGGCTTTTG.................................................................................................2319.0099
...................................................................................................GAAGCTCGTCTCTACAGGTATC.............................2219.0099
....................................................................................................AAGCTCGTCTCTACAGGTATCT............................2216.0066
...................................................................................................GAAGCTCGTCTCTACAGGTAT..............................2114.0044
.............................CTACCCTGTAGTTCCGGGCTTTTGT................................................................................................2511.0011
..............................TACCCTGTAGTTCCGGGCTTTT..................................................................................................2211.0011
...................................................................................................GAAGCTCGTCTCTACAGGTATCTC...........................2411.0011
.............................CTACCCTGTAGTTCCGGGCTTTT..................................................................................................2311.0011
dp4
CGGATCTTTGATTGCAACGCTCCCGTGACCTACCCTGTAGTTCCGGGCTTTTGTTTATATTGCGCCCGATGTATTTTCGAGTGTTTGTGTCGATTATCAGAAGCTCGTCTCTACAGGTATCTCACAGGGTAGAAAGAAACAACTCTGAA-SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
...................................................................................................GAAGCTCGTCTCTACAGGTATCT............................231678.00678314364
...................................................................................................GAAGCTCGTCTCTACAGGTATC.............................22162.00621151
.............................CTACCCTGTAGTTCCGGGCTTTTG.................................................................................................24154.00542529
..............................TACCCTGTAGTTCCGGGCTTTTG.................................................................................................23148.00481236
....................................................................................................AAGCTCGTCTCTACAGGTATCT............................22132.00321418
...................................................................................................GAAGCTCGTCTCTACAGGTAT..............................21118.0018315
.............................CTACCCTGTAGTTCCGGGCTT....................................................................................................2118.00808
..............................TACCCTGTAGTTCCGGGCTTTT..................................................................................................2217.00725
.............................CTACCCTGTAGTTCCGGGCTTTT..................................................................................................2314.00404
..............................TACCCTGTAGTTCCGGGCTT....................................................................................................2013.00303
.............................CTACCCTGTAGTTCCGGGCTTT...................................................................................................2212.00202
..............................TACCCTGTAGTTCCGGGCTTTTGT................................................................................................2412.00202
..................................................................................................AGAAGCTCGTCTCTACAGGTATCT............................2411.00110
.............................CTACCCTGTAGTTCCGGGCT.....................................................................................................2011.00101
...............................ACCCTGTAGTTCCGGGCTTTTG.................................................................................................2211.00101
.............................CTACCCTGTAGTTCCGGGC......................................................................................................1911.00101
..............................TACCCTGTAGTTCCGGGCTTT...................................................................................................2111.00101
...................................................................................................GAAGCTCGTCTCTACAGGT................................1911.00101
...................................................................................................GAAGCTCGTCTCTACAGGTA...............................2011.00101

Secondary Structure

dm3

-46.3 -46.3 -46.3 -45.9 -45.9 -45.9

droSim1

-44.1 -44.1 -44.1 -44.1 -44.1 -44.1

droSec1

-45.3 -45.3 -45.3 -45.0 -45.0 -45.0

droYak2

-44.7 -44.7 -44.7 -44.7 -44.7 -44.7

droEre2

-44.8 -44.8 -44.8 -44.8 -44.8 -44.8

droAna3

-42.9 -42.9 -42.9 -42.8 -42.8 -42.8

dp4

-41.6 -41.6 -41.6 -41.3 -41.3 -41.3

droPer1

-46.4 -46.4 -46.4 -46.1 -46.1 -46.1

droWil1

-37.9 -37.9 -37.9 -37.9 -37.9 -37.9

droVir3

-36.1 -36.1 -36.1 -35.9 -35.9 -35.9

droMoj3

-38.6 -38.6 -38.6 -38.6 -38.6 -38.6

droGri2

-37.3 -37.3 -37.3 -37.3 -37.3 -37.3

Generated: 01/05/2013 at 05:36 PM