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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtaacatcacattaagatgcttgttttttgtattgatgatacttatttaagatgaattttcaagttgtgaagaacttttgtcatttacactattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGGGACCAAATAGATCCAAGAACCCAGAGTTTTCTCACATGGGAAAGTCTAG

Basic information

species Vitis vinifera
transcript Vv08s0040g01700.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------------------------tagtaa-catcacattaagatgcttgtttt-ttgtattgatgatacttatttaagatgaattttcaagtt-gtgaagaacttttgtcatttacactattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGGGACCAAATAGATCCAAGAACCCAGAGTTTTCTCACATGGGAAAGTCTAG
                                          | | |  |||       ||||  ||||||  ||| |||    |   | ||||  |   | |   ||| || ||  | |  |||||   |||  |||  | ||||| |||| | ||||||  || |||||||| ||||| ||||||||||| |||    | |||||||| ||||| ||||||||  | |||||||||||||| |
gtccctcatcctaatctcttttctgcgcagaatttcgagttctggaagtcatagttacgagataattgtttgattgaattttgtacgataatttgtgggaattcggcaattttgttgatagtttttgcgttttgtactgatccagGTGTTTACAACAGCTGGTGTACCAATTGAGTGGGAAGAACACTATGTTGGGACTGAGATAGATCCGAGAACACAGAGTTTCTTGACATGGGAAAGTCTCG
















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|110685854|gb|EE062936.1|EE062936
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|110687099|gb|EE064211.1|EE064211
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|71860684|gb|DT009739.1|DT009739
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|161709349|gb|FC059678.1|FC059678
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|46917993|gb|CN547322.1|CN547322
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|71861005|gb|DT010060.1|DT010060
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|33406750|gb|CF212377.1|CF212377
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|294964824|gb|GW838627.1|GW838627
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|71861425|gb|DT010480.1|DT010480
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|161716798|gb|FC067212.1|FC067212
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|71861392|gb|DT010447.1|DT010447
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|71860905|gb|DT009960.1|DT009960
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAAGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|71869279|gb|DT018334.1|DT018334
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG
EST: gi|71861610|gb|DT010665.1|DT010665
EST:     TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAG                         GTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAAGAACACTATGTGGGG
genomic: TTTTCCCCGGCGATGGAATCGGGCCCGAGATCGCTGAGGCCGTCAAACAGgtttttccat ... actattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttaagatgaattttcaagttgtgaagaacttttgtcatttacactattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGGGACCAAATAGATCCAAGAACCCAGAGTTTTCTCACATGGGAAAGTCTAG
        atgaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtaacatcacattaagatgcttgttttttgtattgatgatacttatttaagatgaattttcaagttgtgaagaacttttgtcatttacactattacagGTATTTAGAGCAGCTGACGTGCCAATTGAATGGGAGGAACACTATGTGGGGGACCAAATAGATCCAAGAACCCAGAGTTTTCTCACATGGGAAAGTCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - catcaca
- - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - aagatgaa