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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattcaatcctcctgaatgcaacaacttggtaaccaacacaacttttgcttatactgctagctctttttgtccttagagcctaagtataggaactt...

Basic information

species Vitis vinifera
transcript Vv05s0077g00690.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA17G03990.1 (Glycine max), 5'ss of exon 11
TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgta--aaatt--------caatcctcctgaat-----------gcaacaacttggtaaccaacacaacttttgctt-atactgc-tagctctttttgt-----ccttagagcctaagtataggaactt------------------------------------------------------------------------
||| || ||||||||||||||||| ||||||||||||||| |||| ||  | |||||||| |||||||| || ||||||||   | ||        || | ||| | |||            |||    |||||  ||   | ||   ||| || |||  || |   |  |  |||       ||  | | | |  |||| |   |                                                                        
TGACGAGGACATGCTAAAGAAGCTTGGTGACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagacaacagtactcttaaattgtatgcatagtcaatcgtttggttccctctagaaggattgttttataaggcatgatttgtcatgtgagctttttcaaccttgaaaatagcagaatgaagaatacttgtaaaatttagtttccttgttcagcacttaaaattgatatattctttattcatggaatcag

upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA07G36610.1 (Glycine max), 5'ss of exon 11
TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgta---aaattcaatcctcctgaatgcaacaacttggtaaccaacacaactttt-------gcttatactgctag-ctctttttgtccttagagcct----aagtataggaactt----------------------------------------------------------------------------
 || || ||||||||||||||||| || |||||||||||| | || ||  | |||||||| |||||||| || ||||||||   |  | || | ||| | ||    |    |||  ||           | |       | ||||  |   || |    |||||| |  |||| |    ||   ||  ||                                                                               
CGACGAGGACATGCTAAAGAAGCTTGGCGACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAGgtattgacttacagtactcttaaaatgtatgcattgtcaattgtttggttctgtctggaaggattattttataaggcatgatttgtcatgtgagcttttccaaccttaaaaatagcagaatgaagcatacttccttgtaaaatgtagtttcctttgtatgcactattgatattctttattaatggaatcag

upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA08G47350.1 (Glycine max), 5'ss of exon 11
TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgta--------aaattcaatcctcctgaatgcaacaacttg---gtaaccaaca--caacttt------tgctt-atactgctagctctttttgtccttagagcctaagt------ataggaactt--------------------------------------------------------------------
    || || |||||||||||||| ||||||||| ||||  |||| ||  | ||||| |||||| ||||||| ||||||||        |||| |     |   |||| |       ||    |||  ||||  ||| |||      || || | | ||     |  || | |  |||| || | | |      ||| || ||                                                                     
---TGAGGAAATGCTAAAGAAGCTTGGTGACCTTTTGAATGAGAGTCATTATAGCTGTAGTGTTCTATACGAATGCAGgtattaataccaaatactgggttttagaattctgtcttctgtttataaagaacatgcaattttattgtgtgtttgacagtgtctagtggttgtatatttagtgcttgatttgtgttatatgatctctttcaatcttcaaatcactaatattgcgtgtacaatgtcattttttttttctttttactttgaatcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110410868|gb|EC976562.1|EC976562
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTGTACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|30299412|gb|CB976206.1|CB976206
EST:     GACCTTATGAACAAGAGCCCCGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|27583346|gb|CB006041.1|CB006041
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|33406611|gb|CF212238.1|CF212238
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|33407058|gb|CF212685.1|CF212685
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|110392261|gb|EC957554.1|EC957554
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTGTACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|110430378|gb|EC996932.1|EC996932
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTGTACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|30137246|gb|CB922584.1|CB922584
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|110392865|gb|EC957405.1|EC957405
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTGTACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|27585689|gb|CB008384.1|CB008384
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|27585107|gb|CB007802.1|CB007802
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|32246094|gb|CD711913.1|CD711913
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|30299334|gb|CB976128.1|CB976128
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCNGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|110406864|gb|EC972451.1|EC972451
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTGTACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|33406531|gb|CF212158.1|CF212158
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
EST: gi|110732746|gb|EE108300.1|EE108300
EST:     GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTGTACGAGTGCAG                         CTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT
genomic: GACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattca ... ctgtgattagCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAGgtaaaattcaatcctcctgaatgcaacaacttggtaaccaacacaacttttgcttatactgctagctctttttgtccttagagcctaagtataggaactt

- - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacaa