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

-46.3 -46.3 -46.0 -46.0 -46.0 -46.0

droSim1

-48.4 -48.4 -48.1 -48.1 -48.0 -48.0

droSec1

-48.4 -48.4 -48.1 -48.1 -48.0 -48.0

droYak2

-48.9 -48.9 -48.9 -48.9 -48.5 -48.5

droEre2

-47.2 -47.2 -46.9 -46.9 -46.6 -46.6

droAna3

-39.8 -39.4 -39.4 -39.4 -39.1 -39.0

dp4

-54.0 -53.8 -53.4 -53.4 -53.3 -53.2

droPer1

-52.6 -52.2 -52.2 -52.1 -52.1 -52.1

droWil1

-47.3 -47.0 -46.7 -46.5 -46.5 -46.4

droVir3

-26.6 -26.0 -25.9 -25.8 -25.6

droMoj3

-26.3 -25.9 -25.7 -25.6 -25.6 -25.5

droGri2

-30.1 -29.6 -29.5 -29.3 -29.1

Generated: 01/05/2013 at 05:31 PM