Secondary structure and small RNA-seq evidence for dme-mir-2b-1

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:8258601-8258707 - CAAAATAACT-------AAAAACTTCAACTGTCTTCA-----------------------------------------AAGTGGCAGTGACATGTTGTC----------------------------AACAATATTCATATCACAGCC-A-GCTTTGAGGAGCGTTGCGGTTTTTCT---------CGTCCGGC-----
droSim1 chr2L:8042700-8042806 - CAAAAGAACT-------GAAAACTTCAACTGTCTTCA-----------------------------------------AAGTGGCGGTGACATGTTGTC----------------------------AACAATATTCATATCACAGCC-A-GCTTTGAGGAGCGTTGCGGTTTTTCA---------CGCCCGAC-----
droSec1 super_3:3755253-3755359 - CAAAAGAACT-------GAAAACTTCAACTGTCTTCA-----------------------------------------AAGTGGCGGTGACATGTTGTC----------------------------AACAATATTCATATCACAGCC-A-GCTTTGAGGAGCGTTGTGGTTTTTCT---------CGCCCGCC-----
droYak2 chr2L:10894231-10894336 - GGAAAAAG-T-------GAAAACTTCAACTGTCTTCA-----------------------------------------AAGTGGCGGTGACATGTTGTC----------------------------AACAATATTCATATCACAGCC-A-GCTTTGAGGAGCGTTGCGGTTTTTCT---------CGCCAACC-----
droEre2 scaffold_4929:17167539-17167644 - CGCAATAG-T-------GAAAACTTCAACTGTCTTCA-----------------------------------------AAGTGGCGGTGACATGTTGTC----------------------------AGCAATATTCATATCACAGCC-A-GCTTTGAGGAGCGTTGCGGTTTTTCT---------CGCCCGCC-----
droAna3 scaffold_12916:6006043-6006142 + CAGATTTTTT----TA-GGGAACTGCGACCCTCCTTA-----------------------------------------AAGTGGCGGTGACATGTAGCT----------------------------TTC-ATATTCATATCACAGCTTT-GCTTTCAGGAGCGTTGAGGTTTCTC-----------------------
dp4 chr4_group3:3919027-3919154 + CCCATGGGATACTATAGGAAAGCTGCGACGCTCTTTA-----------------------------------------AAGTGGCGGTGACGTGTTGGT----------------------------AATAATATTCATATCACAGCC-A-GCTTTGAGGAGCGTTGCGGCCCTTCTGAAAATATGCGCCTCATTGGGG
droPer1 super_1:5401823-5401939 + CCCATGGGATACTATAGGAATGCTGCGACGCTCTTTA-----------------------------------------AAGTGGCGGTGACGTGTTGGT----------------------------AATAATATTCATATCACAGCC-A-GCTTTGA-GAGCGTTGCGGCCCTTCTGAA-A----TATGCGCC-----
droWil1 scaffold_180703:495398-495497 + TGTAAATTAT-------AGAATTTATGATAGATTTTT-----------------------------------------AATCATGGT-----------------------TTGAGTCAAAATTAAACAAAAATAGTTTAAATAAAAGC-AAA-TATA-GTAATATTTTTGTTT--------------------T-----
droVir3 Unknown -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6500:5445901-5446049 - TTAACTCCCG----AA-AGTAGGCTCTATT--ATCTAAAGTCGTACATTAAATTTTGTTTAGTATACCTAAATGAATTATATGAAAGTGAAATATTTCCTCAATATTGGCTCGAATC----------AATAGT----GTGTTGCGGTA-A-ACCTTAAAGAAAAATCTG----------------------GAA-----
droGri2 scaffold_15252:13434449-13434542 - TTCAATAGCA----AG-GAAATTCTTGGTTTTCTTTT-----------------------------------------GTTTATCGGGAAAATGTTATA----------------------------TAA-ACCTATATATCTTT----A-TCTC-----------TAGATCTCTCA---------CTATTTGC-----

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:8258601-8258707 - CAAA----ATAAC----TAAAAACTTCAACTGTCTTCAAAGTGGCAGTGACATGTTGTCAACAATATTCATATCACAGCC-AGCTTTGAGGAGCGTTGCGGTTTTTCT---------CGTCCGGC-----
droSim1 chr2L:8042700-8042806 - CAAA----AGAAC----TGAAAACTTCAACTGTCTTCAAAGTGGCGGTGACATGTTGTCAACAATATTCATATCACAGCC-AGCTTTGAGGAGCGTTGCGGTTTTTCA---------CGCCCGAC-----
droSec1 super_3:3755253-3755359 - CAAA----AGAAC----TGAAAACTTCAACTGTCTTCAAAGTGGCGGTGACATGTTGTCAACAATATTCATATCACAGCC-AGCTTTGAGGAGCGTTGTGGTTTTTCT---------CGCCCGCC-----
droYak2 chr2L:10894231-10894336 - GGAA----A-AAG----TGAAAACTTCAACTGTCTTCAAAGTGGCGGTGACATGTTGTCAACAATATTCATATCACAGCC-AGCTTTGAGGAGCGTTGCGGTTTTTCT---------CGCCAACC-----
droEre2 scaffold_4929:17167539-17167644 - CGCA----ATAG-----TGAAAACTTCAACTGTCTTCAAAGTGGCGGTGACATGTTGTCAGCAATATTCATATCACAGCC-AGCTTTGAGGAGCGTTGCGGTTTTTCT---------CGCCCGCC-----
droAna3 scaffold_12916:6006043-6006142 + CAGA----TTTTT-TTA-GGGAACTGCGACCCTCCTTAAAGTGGCGGTGACATGTAGCTTTC-ATATTCATATCACAGCTTTGCTTTCAGGAGCGTTGAGGTTTCTC-----------------------
dp4 chr4_group3:3919027-3919154 + CCCATGGGAT-ACTATAGGAAAGCTGCGACGCTCTTTAAAGTGGCGGTGACGTGTTGGTAATAATATTCATATCACAGCC-AGCTTTGAGGAGCGTTGCGGCCCTTCTGAAAATATGCGCCTCATTGGGG
droPer1 super_1:5401823-5401939 + CCCATGGGAT-ACTATAGGAATGCTGCGACGCTCTTTAAAGTGGCGGTGACGTGTTGGTAATAATATTCATATCACAGCC-AGCTTTGA-GAGCGTTGCGGCCCTTCTGAA-A----TATGCGCC-----

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CAAAAGAA-------CTGAAAACTTCAACTGTCTTCAAAGTGGCGGTGACATGTTGTCAACAATATTCATATCACAGCCAGCTTTGAGGAGCGTTGCGGTTTTTC--------------ACGCCCGACSizeHit CountTotal NormTotalGSM343915
Embryo
.....................................................................TATCACAGCCAGCTTTGAGGAGC....................................23215380.503076130761
.....................................................................TATCACAGCCAGCTTTGAGGAGCGT..................................25110655.001065510655
.........................................................................ACAGCCAGCTTTGAGGAGCG...................................202464.50929929
.......................................................................TCACAGCCAGCTTTGAGGAGCGT..................................231154.00154154
.........................................................................ACAGCCAGCTTTGAGGAG.....................................182122.50245245
.......................................................................TCACAGCCAGCTTTGAGGAGC....................................21286.50173173
.........................................................................ACAGCCAGCTTTGAGGAGCGT..................................21180.008080
.....................................................................TATCACAGCCAGCTTTGAGGAGCGTT.................................26180.008080
......................................................................ATCACAGCCAGCTTTGAGGAGC....................................2229.501919
..........................................................................CAGCCAGCTTTGAGGAGCG...................................1927.501515
......................................................................ATCACAGCCAGCTTTGAGGAGCGT..................................2417.0077
.....................................................................TATCACAGCCAGCTTTGAGG.......................................2026.001212
.......................................................................TCACAGCCAGCTTTGAGGA......................................1926.001212
..........................................................................CAGCCAGCTTTGAGGAGC....................................1824.5099
......................................................................ATCACAGCCAGCTTTGAGGAG.....................................2124.0088
....AGAA-------CTGAAAACTTCAACT..................................................................................................1914.0044
...........................................................................AGCCAGCTTTGAGGAGCGT..................................1913.0033
.......................................................................TCACAGCCAGCTTTGAGGAGCGTT.................................2413.0033
........................................................................CACAGCCAGCTTTGAGGAGCG...................................2123.0066
.........................................................................ACAGCCAGCTTTGAGGAGCGTT.................................2213.0033
dp4
CCCATGGGATACTATAGGAAAGCTGCGACGCTCTTTAAAGTGGCGGTGACGTGTTGGTAATAATATTCATATCACAGCCAGCTTTGAGGAGCGTTGCGGCCCTTCTGAAAATATGCGCCTCATTGGGGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.....................................................................TATCACAGCCAGCTTTGAGGAGCG...................................24247854.00957088337812330
.....................................................................TATCACAGCCAGCTTTGAGGAG.....................................22216749.0033498334980
.....................................................................TATCACAGCCAGCTTTGAGGAGCGT..................................2519711.00971180711640
.....................................................................TATCACAGCCAGCTTTGAGGAGC....................................2327169.0014338014338
.....................................................................TATCACAGCCAGCTTTGAGGA......................................2122620.00524052400
.......................................................................TCACAGCCAGCTTTGAGGAGCG...................................222302.0060456143
.........................................................................ACAGCCAGCTTTGAGGAG.....................................182302.00604251353
.......................................................................TCACAGCCAGCTTTGAGGAGC....................................212181.003623620
.....................................................................TATCACAGCCAGCTTTGAGGAGCGTT.................................261136.001369145
.......................................................................TCACAGCCAGCTTTGAGGAG.....................................202103.502072070
.........................................................................ACAGCCAGCTTTGAGGAGCGT..................................21179.00796415
.......................................................................TCACAGCCAGCTTTGAGGAGCGT..................................23158.0058553
......................................................................ATCACAGCCAGCTTTGAGGAGCG...................................23220.0040400
...........................................................................AGCCAGCTTTGAGGAGCG...................................18216.0032248
.......................................................................TCACAGCCAGCTTTGAGGA......................................19210.5021210
..........................................................................CAGCCAGCTTTGAGGAGCG...................................1929.0018162
......................................................................ATCACAGCCAGCTTTGAGGAGC....................................2228.5017170
........................................................................CACAGCCAGCTTTGAGGAG.....................................1928.5017413
......................................................................ATCACAGCCAGCTTTGAGGAGCGT..................................2417.00761
......................................................................ATCACAGCCAGCTTTGAGGAG.....................................2125.0010100

Secondary Structure

dm3

dG=-27.6,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.4,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-27.1,  p-value=0.009901

droSim1

dG=-28.0,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.5,  p-value=0.009901

droSec1

dG=-28.0,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.5,  p-value=0.009901

droYak2

dG=-28.0,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.5,  p-value=0.009901

droEre2

dG=-28.0,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.8,  p-value=0.009901 dG=-27.6,  p-value=0.009901 dG=-27.5,  p-value=0.009901

droAna3

dG=-22.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901

dp4

dG=-34.1,  p-value=0.009901 dG=-33.8,  p-value=0.009901 dG=-33.7,  p-value=0.009901 dG=-33.7,  p-value=0.009901 dG=-33.5,  p-value=0.009901

droPer1

dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.7,  p-value=0.009901 dG=-29.4,  p-value=0.009901 dG=-29.4,  p-value=0.009901

droWil1

dG=-3.7,  p-value=0.009901 dG=-3.3,  p-value=0.009901 dG=-3.3,  p-value=0.009901 dG=-3.2,  p-value=0.009901 dG=-3.1,  p-value=0.009901

droVir3

No secondary structure predictions returned

droMoj3

dG=-12.3,  p-value=0.009901 dG=-11.8,  p-value=0.009901 dG=-11.8,  p-value=0.009901 dG=-11.3,  p-value=0.009901 dG=-11.3,  p-value=0.009901

droGri2

dG=-4.3,  p-value=0.009901 dG=-4.1,  p-value=0.009901 dG=-4.0,  p-value=0.009901 dG=-3.5,  p-value=0.009901 dG=-3.4,  p-value=0.009901

Generated: 03/07/2013 at 05:08 PM