Secondary structure and small RNA-seq evidence for dme-mir-958

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:22662374-22662495 - GGATT-TTCC-------------------------ACGATCGGCGTGTCTATGGCAAGTAGAATAGCAGGCTTATCACATGTTTAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCACACCCG---------A
droSim1 chr3L:21947666-21947787 - GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCACACCCG---------A
droSec1 super_11:2578674-2578788 - GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCA----------------
droYak2 chr3L:23128644-23128763 - GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTTAACTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCGAACCC-----------
droEre2 scaffold_4784:22312266-22312387 - GGATT-GTCT-------------------------ACGATCGGCGTGGCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTTACATCAAACCCG---------A
droAna3 scaffold_13337:22380395-22380515 - GAATA-TTCCA------------------------ACGACCGGTGGGTTTTTAGCAAGTAGAATAGCAGGCTTATCACAGGTTCC-TTTA-ACCCACTGTGAGATTCTTCTATTCTACTTTCGAGAAACACCCGTAAACACCGATCTC-----------
dp4 chrXR_group8:344159-344293 - GGATA-TGGC-------------------T--AGCACGATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATCTAATAGAGC-AGCCCTC
droPer1 super_96:132292-132395 + G-------------------------------------ATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATC-----------------
droWil1 scaffold_180698:7060886-7061014 + TGAGTTTTGA--------------CTATGACT--ATCTAACGGTGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCCTTTACAACCGGTGTGAGATTCTTCTATTCTACTTTCGAAAAGCACCCGATAACAACAAA--------------
droVir3 scaffold_13049:17089392-17089522 + TGTTT-TTTTA------ATGTTCTCTATAT--ATTTTGATCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTACAATTCA-ACCTAGTGTGAGATTCTTCTATTCTACTTTCGACAAACACCAGCTAGCGTC-----------------
droMoj3 scaffold_6680:22084806-22084935 + GTGTT-TTCC--------------CTGTGATT--CTCAGTCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTACCATTTG-ACCGAGTGTGAGATTCTTCTATTCTACTTTCGACAAGCACCAGTCAGCGTCGTTTTCG----------
droGri2 scaffold_15110:15103971-15104124 - GTGTG-TGCAGGTTTTATGGTTTTTGTTTT--ACTCTGATCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTAACATTCG-ACATGGTGTGAGATTCTTCTATTCTACTTTCGACAAACACCAGCTAGCGTCACATTCAGTTAAGTTTA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:22662374-22662495 - GGATT-TTCC-------------------------ACGATCGGCGTGTCTATGGCAAGTAGAATAGCAGGCTTATCACATGTTTAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCACACCCG---------A
droSim1 chr3L:21947666-21947787 - GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCACACCCG---------A
droSec1 super_11:2578674-2578788 - GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCA----------------
droYak2 chr3L:23128644-23128763 - GGATT-TTCC-------------------------ACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTTAACTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTAACATCGAACCC-----------
droEre2 scaffold_4784:22312266-22312387 - GGATT-GTCT-------------------------ACGATCGGCGTGGCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCTGCTGTGAGATTCTTCTATTCTACTTTCGACAA-CACCCGTTTACATCAAACCCG---------A
droAna3 scaffold_13337:22380395-22380515 - GAATA-TTCCA------------------------ACGACCGGTGGGTTTTTAGCAAGTAGAATAGCAGGCTTATCACAGGTTCC-TTTA-ACCCACTGTGAGATTCTTCTATTCTACTTTCGAGAAACACCCGTAAACACCGATCTC-----------
dp4 chrXR_group8:344159-344293 - GGATA-TGGC-------------------T--AGCACGATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATCTAATAGAGC-AGCCCTC
droPer1 super_96:132292-132395 + G-------------------------------------ATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCA-ATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATC-----------------
droWil1 scaffold_180698:7060886-7061014 + TGAGTTTTGA--------------CTATGACT--ATCTAACGGTGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCCTTTACAACCGGTGTGAGATTCTTCTATTCTACTTTCGAAAAGCACCCGATAACAACAAA--------------
droVir3 scaffold_13049:17089392-17089522 + TGTTT-TTTTA------ATGTTCTCTATAT--ATTTTGATCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTACAATTCA-ACCTAGTGTGAGATTCTTCTATTCTACTTTCGACAAACACCAGCTAGCGTC-----------------
droMoj3 scaffold_6680:22084806-22084935 + GTGTT-TTCC--------------CTGTGATT--CTCAGTCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTACCATTTG-ACCGAGTGTGAGATTCTTCTATTCTACTTTCGACAAGCACCAGTCAGCGTCGTTTTCG----------
droGri2 scaffold_15110:15103971-15104124 - GTGTG-TGCAGGTTTTATGGTTTTTGTTTT--ACTCTGATCGGTGTGGAT-TGGCAAGTAGAATAGCAGGCTTATCACATGTAACATTCG-ACATGGTGTGAGATTCTTCTATTCTACTTTCGACAAACACCAGCTAGCGTCACATTCAGTTAAGTTTA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GGATT----TTCCACGATCGGCGTGTCTTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCAATTCAATCTGCTGTGAGATTCTTCTATTCTACTTTCGACA-ACACCCGTTAACATCACA--------CCCGASizeHit CountTotal NormTotalGSM343915
Embryo
..................................AGTAGAATAGCAGGCTTATCACA..............................................................................2312335.0023352335
............................................................................TGAGATTCTTCTATTCTACTTT.....................................221564.00564564
..................................AGTAGAATAGCAGGCTTATCAC...............................................................................221510.00510510
....................................TAGAATAGCAGGCTTATCACA..............................................................................211172.00172172
....................................TAGAATAGCAGGCTTATCAC...............................................................................20170.007070
............................................................................TGAGATTCTTCTATTCTACTT......................................21139.003939
.........................................................TGTTCAATTCAATCTGCTG...........................................................19117.001717
..................................AGTAGAATAGCAGGCTTATCA................................................................................2119.0099
....................................TAGAATAGCAGGCTTATCACATG............................................................................2319.0099
..................................AGTAGAATAGCAGGCTTATC.................................................................................2018.0088
............................................................................TGAGATTCTTCTATTCTACT.......................................2017.0077
.................................AAGTAGAATAGCAGGCTTATCAC...............................................................................2314.0044
............................................................................TGAGATTCTTCTATTCTACTTTC....................................2312.0022
..................................AGTAGAATAGCAGGCTTAT..................................................................................1912.0022
...................................GTAGAATAGCAGGCTTATCACA..............................................................................2212.0022
..........................................................................TGTGAGATTCTTCTATTCTACT.......................................2212.0022
.............................................................................GAGATTCTTCTATTCTACTTT.....................................2111.0011
.................................AAGTAGAATAGCAGGCTTATCACA..............................................................................2411.0011
....................................................................ATCTGCTGTGAGATTCTTCT...............................................2011.0011
......................................GAATAGCAGGCTTATCACA..............................................................................1911.0011
..................................AGTAGAATAGCAGGCTTATCACAT.............................................................................2411.0011
dp4
GGATATGGCTAGCACGATCGGTGTGTATTTGGCAAGTAGAATAGCAGGCTTATCACATGTTCCATTCAATCCGCTGTGAGATTCTTCTATTCTACTTTCGACAAACACCCGTTGACATCTAATAGAGCAGCCCTCSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
..................................AGTAGAATAGCAGGCTTATCACA..............................................................................2311985.001985192659
............................................................................TGAGATTCTTCTATTCTACTTT.....................................2211302.0013021099203
..................................AGTAGAATAGCAGGCTTATCAC...............................................................................221440.004404346
.........................................................TGTTCCATTCAATCCGCTG...........................................................19176.0076751
............................................................................TGAGATTCTTCTATTCTACTT......................................21169.00694524
..................................AGTAGAATAGCAGGCTTATCA................................................................................21160.00604020
..................................AGTAGAATAGCAGGCTTATC.................................................................................20131.0031283
....................................TAGAATAGCAGGCTTATCACA..............................................................................21129.0029290
............................................................................TGAGATTCTTCTATTCTACT.......................................20119.0019118
....................................TAGAATAGCAGGCTTATCAC...............................................................................2018.00880
..................................AGTAGAATAGCAGGCTTAT..................................................................................1918.00880
.............................................................................GAGATTCTTCTATTCTACTTT.....................................2116.00660
....................................TAGAATAGCAGGCTTATCACATG............................................................................2314.00440
............................................................................TGAGATTCTTCTATTCTAC........................................1914.00440
..................................AGTAGAATAGCAGGCTTA...................................................................................1813.00330
............................................................................TGAGATTCTTCTATTCTACTTTC....................................2313.00330
................................................................................ATTCTTCTATTCTACTTT.....................................1811.00110
.....................................AGAATAGCAGGCTTATCACA..............................................................................2011.00110
......................................GAATAGCAGGCTTATCACA..............................................................................1911.00110
.......................................AATAGCAGGCTTATCACA..............................................................................1811.00110
............................................................................TGAGATTCTTCTATTCTA.........................................1811.00110
....................................TAGAATAGCAGGCTTATCACATGT...........................................................................2411.00110
.....................................AGAATAGCAGGCTTATCAC...............................................................................1911.00110
...................................GTAGAATAGCAGGCTTATCACA..............................................................................2211.00110

Secondary Structure

dm3

dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droSim1

dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droSec1

dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droYak2

dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droEre2

dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.7,  p-value=0.009901 dG=-19.6,  p-value=0.009901

droAna3

dG=-22.4,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.8,  p-value=0.009901 dG=-21.7,  p-value=0.009901

dp4

dG=-19.3,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.8,  p-value=0.009901

droPer1

dG=-19.3,  p-value=0.009901 dG=-19.3,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.9,  p-value=0.009901 dG=-18.8,  p-value=0.009901

droWil1

dG=-20.9,  p-value=0.009901 dG=-20.9,  p-value=0.009901 dG=-20.6,  p-value=0.009901 dG=-20.6,  p-value=0.009901 dG=-20.5,  p-value=0.009901

droVir3

dG=-20.5,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.0,  p-value=0.009901

droMoj3

dG=-20.5,  p-value=0.009901 dG=-20.5,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.1,  p-value=0.009901 dG=-20.0,  p-value=0.009901

droGri2

dG=-23.7,  p-value=0.009901 dG=-23.3,  p-value=0.009901 dG=-23.2,  p-value=0.009901 dG=-23.2,  p-value=0.009901 dG=-22.8,  p-value=0.009901

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