Secondary structure and small RNA-seq evidence for dme-mir-956

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3L:11766816-11766993 - ATGAGC-ACTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCA-CTGGCCC---------------------AAATGCAGTTTGCC-C-GGAGA--------------CGCCGGT---------------TAACCCAG--------------CACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCAACAATATGCAAA
droSim1 chr3L:11132280-11132457 - ATGTGC-TCTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCA-CTGGCCC---------------------AAATGCAGTTTGCC-C-GGAGA--------------CGCCGGT---------------TGCCCAAG--------------CACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCCACAATATGCAAA
droSec1 super_0:3951754-3951931 - ATGAGC-TCTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCA-CTGGCCC---------------------AAATGCAGTTTGCC-C-GGAGA--------------CGCCGGT---------------TGCCCAAG--------------CACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCCACAATATGCTAA
droYak2 chr3L:11795661-11795838 - ATGTGC-ACTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCA-CTGGCCC---------------------AAATGCAGTTTGCC-C-GGAGG--------------AGCCGGT---------------TTACCCAG--------------CACTCAAGTGTGTAGTTTCGAGACCACTCTAATCCATTGCACCATTTTCCACTATATGCAAA
droEre2 scaffold_4784:11744386-11744563 - ATGTGC-ACTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCTAGTGCTCG-GCTCA-CCGGCCC---------------------AAATGCAGTTTGCC-C-GGAGA--------------TGCCGGT---------------TTCCTCAG--------------CACTCAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCCACAATATGCAAA
droAna3 scaffold_13337:6020232-6020390 - ATGTGC-ACTTTTCTAGATCGTTATCGCGTTTGGAATGGTCTCGTTAGCTAACGAATGGACTA------------------------------------------AAATGCAATTTGCA-A-TTCGG--------------CGCCAAT---------------TATCCAGG--------------CGCCAAAAAGTTTAGTTTCGAGACCACTCTAATCCATTGCATGATCTTCACTTGTATGCAAA
dp4 chrXR_group8:4341287-4341484 + ATGTGC-ACTTCTACTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAACTGCTTGCGCGCA-TTGGCC----------------------AAATGCATTTCGCA-C-CGGGATGGATGTG--GATG-------TGGCTGGATGTGGTGTCCCCAAG--------------CACAGCCAGGTGTAGTTTCGAGACCACTCTAATCCATTGCACCGCCCACCCATTTATGCAAA
droPer1 gnl|ti|732454354:721-914 + ATGTGC-ACTTCTACTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAACTGCTTGCGCGCA-TTGGC-----------------------AAATGCATTTCGCA-CCGGA--TGGATGTG--GATG-------TGGCTGGATGTG-TGTTCCCAAG--------------CACAGCC-AGTGTAGTTTCGAGACCACTCTA-TCCATTGCACCGCCCACCCATTTATGCAAA
droWil1 scaffold_180949:2569086-2569314 + ATGTGC-AATTATACTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAACAAGTGCTTG-GGGCAATTGAGCCAAAAACAAAACAGAAAAAAGAAAATGCACTTTGCCAT-CAAAACGAATGTGCGAATATGCAATT---------------TGGCCAGGCTCCTCGAACATAACACTAAGAGGTGTAGTTTCGAGACCACTCTAATCCATTGCCACATTTTTCACAATATGCAAA
droVir3 scaffold_13049:23989392-23989532 - ATGCGCGAAATTTAACGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAACA---------------TTGACCA---------------------AAGCGCACCTT----------------------------------------------------------------------ACAGCGTAGTGTAGTTTCGAGACCACTCTAATCCATTGCATCGTTTCTGGGCATATGCAAA
droMoj3 scaffold_6680:18620871-18621011 - ATGTGCGAAATTCAACGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAACA---------------TTAACCA---------------------AAGCGCACCTT----------------------------------------------------------------------ACGGCGTAGTGTAGTTTCGAGACCACTCTAATCCATTGCACCGTTTCTTTCCATATGCAAA
droGri2 scaffold_15110:9704256-9704382 + ATGTGCGAATCTAAGCGATCGTTATCGCGTTTGGAATGGTCTCGTTAGCTAACCAAAGCGCT--------------------------------------------------CGTT----------------------------------------------------------------------ACAGCGTAGTGTAGTTTCGAGACCACTCTAATCCATTCCATCGCTTTTCATTGTATGCAAA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3L:11766816-11766993 - ATGAGC-ACTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCA-CTGGCCC---------------------AAATGCAGTTTGCC-C-GGAGA--------------CGCCGGT---------------TAACCCAG--------------CACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCAACAATATGCAAA
droSim1 chr3L:11132280-11132457 - ATGTGC-TCTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCA-CTGGCCC---------------------AAATGCAGTTTGCC-C-GGAGA--------------CGCCGGT---------------TGCCCAAG--------------CACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCCACAATATGCAAA
droSec1 super_0:3951754-3951931 - ATGAGC-TCTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCA-CTGGCCC---------------------AAATGCAGTTTGCC-C-GGAGA--------------CGCCGGT---------------TGCCCAAG--------------CACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCCACAATATGCTAA
droYak2 chr3L:11795661-11795838 - ATGTGC-ACTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCA-CTGGCCC---------------------AAATGCAGTTTGCC-C-GGAGG--------------AGCCGGT---------------TTACCCAG--------------CACTCAAGTGTGTAGTTTCGAGACCACTCTAATCCATTGCACCATTTTCCACTATATGCAAA
droEre2 scaffold_4784:11744386-11744563 - ATGTGC-ACTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCTAGTGCTCG-GCTCA-CCGGCCC---------------------AAATGCAGTTTGCC-C-GGAGA--------------TGCCGGT---------------TTCCTCAG--------------CACTCAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCCACAATATGCAAA
droAna3 scaffold_13337:6020232-6020390 - ATGTGC-ACTTTTCTAGATCGTTATCGCGTTTGGAATGGTCTCGTTAGCTAACGAATGGACTA------------------------------------------AAATGCAATTTGCA-A-TTCGG--------------CGCCAAT---------------TATCCAGG--------------CGCCAAAAAGTTTAGTTTCGAGACCACTCTAATCCATTGCATGATCTTCACTTGTATGCAAA
dp4 chrXR_group8:4341287-4341484 + ATGTGC-ACTTCTACTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAACTGCTTGCGCGCA-TTGGCC----------------------AAATGCATTTCGCA-C-CGGGATGGATGTG--GATG-------TGGCTGGATGTGGTGTCCCCAAG--------------CACAGCCAGGTGTAGTTTCGAGACCACTCTAATCCATTGCACCGCCCACCCATTTATGCAAA
droPer1 gnl|ti|732454354:721-914 + ATGTGC-ACTTCTACTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAACTGCTTGCGCGCA-TTGGC-----------------------AAATGCATTTCGCA-CCGGA--TGGATGTG--GATG-------TGGCTGGATGTG-TGTTCCCAAG--------------CACAGCC-AGTGTAGTTTCGAGACCACTCTA-TCCATTGCACCGCCCACCCATTTATGCAAA
droWil1 scaffold_180949:2569086-2569314 + ATGTGC-AATTATACTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAACAAGTGCTTG-GGGCAATTGAGCCAAAAACAAAACAGAAAAAAGAAAATGCACTTTGCCAT-CAAAACGAATGTGCGAATATGCAATT---------------TGGCCAGGCTCCTCGAACATAACACTAAGAGGTGTAGTTTCGAGACCACTCTAATCCATTGCCACATTTTTCACAATATGCAAA
droVir3 scaffold_13049:23989392-23989532 - ATGCGCGAAATTTAACGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAACA---------------TTGACCA---------------------AAGCGCACCTT----------------------------------------------------------------------ACAGCGTAGTGTAGTTTCGAGACCACTCTAATCCATTGCATCGTTTCTGGGCATATGCAAA
droMoj3 scaffold_6680:18620871-18621011 - ATGTGCGAAATTCAACGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAACA---------------TTAACCA---------------------AAGCGCACCTT----------------------------------------------------------------------ACGGCGTAGTGTAGTTTCGAGACCACTCTAATCCATTGCACCGTTTCTTTCCATATGCAAA
droGri2 scaffold_15110:9704256-9704382 + ATGTGCGAATCTAAGCGATCGTTATCGCGTTTGGAATGGTCTCGTTAGCTAACCAAAGCGCT--------------------------------------------------CGTT----------------------------------------------------------------------ACAGCGTAGTGTAGTTTCGAGACCACTCTAATCCATTCCATCGCTTTTCATTGTATGCAAA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATGTGCTCTTTTCCTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAAGTGCTCG-GCTCACTGGCCCAAATGCAGTTTGCCCGGAGACGCCGGT--------------------TGCCCAAGCACTGAAATGTGTAGTTTCGAGACCACTCTAATCCATTGCAGCATTTTCCACAATATGCAAASizeHit CountTotal NormTotalGSM343915
Embryo
........................................................................................................................................................TTTCGAGACCACTCTAATCCATT........................231158.00158158
.........................................................................................................................................................TTCGAGACCACTCTAATCCATT........................221128.00128128
........................................................................................................................................................TTTCGAGACCACTCTAATCCAT.........................22156.005656
........................................................................................................................................................TTTCGAGACCACTCTAATCCA..........................2116.0066
.........................GTGTTTGGAATGGTCTCGTTAGC.......................................................................................................................................................2313.0033
.........................................................................................................................................................TTCGAGACCACTCTAATCCAT.........................2112.0022
.........................GTGTTTGGAATGGTCTCGTTAGCT......................................................................................................................................................2411.0011
dp4
ATGTGCACTTCTACTGATCGTTATCGTGTTTGGAATGGTCTCGTTAGCTAACGGATGAGCAACTGCTTGCGCGCATTGGC-CAAATGCATTTCGCACCGGGATGGATGTGGATGTGGCTGGATGTGGTGTCCCCAAGCACAGCCAGGTGTAGTTTCGAGACCACTCTAATCCATTGCACCGCCCACCCATTTATGCAAASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
........................................................................................................................................................TTTCGAGACCACTCTAATCCATT........................2311562.0015622931269
.........................................................................................................................................................TTCGAGACCACTCTAATCCATT........................2211051.001051212839
........................................................................................................................................................TTTCGAGACCACTCTAATCCAT.........................221403.0040338365
........................................................................................................................................................TTTCGAGACCACTCTAATCCA..........................21186.0086482
.........................................................................................................................................................TTCGAGACCACTCTAATCCAT.........................21157.0057156
........................................................................................................................................................TTTCGAGACCACTCTAATCC...........................20113.0013013
.........................................................................................................................................................TTCGAGACCACTCTAATCCA..........................2019.00909
.........................GTGTTTGGAATGGTCTCGTTAGCT......................................................................................................................................................2415.00514
............................................................................................................................................................GAGACCACTCTAATCCATT........................1914.00413
........................................................................................................................................................TTTCGAGACCACTCTAATC............................1914.00404
.........................GTGTTTGGAATGGTCTCGTT..........................................................................................................................................................2012.00202
.........................GTGTTTGGAATGGTCTCGTTA.........................................................................................................................................................2112.00202
.........................GTGTTTGGAATGGTCTCGTTAGC.......................................................................................................................................................2312.00202
.........................GTGTTTGGAATGGTCTCGTTAG........................................................................................................................................................2212.00202
...........................GTTTGGAATGGTCTCGTTAGCT......................................................................................................................................................2212.00211
............................................................................................................................................AGCCAGGTGTAGTTTCGAGAC......................................2111.00110
.............................TTGGAATGGTCTCGTTAGCT......................................................................................................................................................2011.00110
.........................................................................................................................................................TTCGAGACCACTCTAATCC...........................1911.00101
..........................TGTTTGGAATGGTCTCGTTAGC.......................................................................................................................................................2211.00101
............................................................................................................................................AGCCAGGTGTAGTTTCGAGA.......................................2011.00110
.........................................................................................................................................................TTCGAGACCACTCTAATC............................1811.00101
................................GAATGGTCTCGTTAGCTAA....................................................................................................................................................1911.00110
................................................TAACGGATGAGCAACTGCTTGCGCGC.............................................................................................................................2611.00110
..........................................................................................................................................................TCGAGACCACTCTAATCCATT........................2111.00101
.....................................................................................TGCATTTCGCACCGGGATGGATGTGGA.......................................................................................2711.00110

Secondary Structure

dm3

dG=-45.7,  p-value=0.009901 dG=-45.7,  p-value=0.009901 dG=-45.4,  p-value=0.009901 dG=-45.4,  p-value=0.009901 dG=-45.3,  p-value=0.009901

droSim1

dG=-47.8,  p-value=0.009901 dG=-47.8,  p-value=0.009901 dG=-47.4,  p-value=0.009901 dG=-47.4,  p-value=0.009901 dG=-47.2,  p-value=0.009901

droSec1

dG=-47.8,  p-value=0.009901 dG=-47.8,  p-value=0.009901 dG=-47.4,  p-value=0.009901 dG=-47.4,  p-value=0.009901 dG=-47.2,  p-value=0.009901

droYak2

dG=-48.9,  p-value=0.009901 dG=-48.9,  p-value=0.009901 dG=-48.9,  p-value=0.009901 dG=-48.9,  p-value=0.009901 dG=-48.5,  p-value=0.009901

droEre2

dG=-46.6,  p-value=0.009901 dG=-46.6,  p-value=0.009901 dG=-46.0,  p-value=0.009901 dG=-46.0,  p-value=0.009901 dG=-45.9,  p-value=0.009901

droAna3

dG=-34.4,  p-value=0.009901 dG=-34.3,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-34.0,  p-value=0.009901 dG=-31.0,  p-value=0.009901

dp4

dG=-54.0,  p-value=0.009901 dG=-53.4,  p-value=0.009901 dG=-53.4,  p-value=0.009901 dG=-53.2,  p-value=0.009901 dG=-51.9,  p-value=0.009901

droPer1

dG=-52.2,  p-value=0.009901 dG=-52.2,  p-value=0.009901 dG=-51.7,  p-value=0.009901 dG=-51.7,  p-value=0.009901 dG=-51.7,  p-value=0.009901

droWil1

dG=-47.3,  p-value=0.009901 dG=-47.0,  p-value=0.009901 dG=-46.5,  p-value=0.009901 dG=-46.4,  p-value=0.009901 dG=-46.4,  p-value=0.009901

droVir3

dG=-25.8,  p-value=0.009901 dG=-25.1,  p-value=0.009901 dG=-25.1,  p-value=0.009901

droMoj3

dG=-26.3,  p-value=0.009901 dG=-25.7,  p-value=0.009901 dG=-25.6,  p-value=0.009901 dG=-25.5,  p-value=0.009901 dG=-25.4,  p-value=0.009901

droGri2

dG=-27.7,  p-value=0.009901 dG=-27.0,  p-value=0.009901 dG=-26.7,  p-value=0.009901

Generated: 03/07/2013 at 07:13 PM