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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatcgtagagaaatttaaacgacgtgatggttttttagtttgtcgccattgttaatcgctgttttatgagaattttgggcttattattgttttgtttgtttggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAGAATGGTGAGCAGTATGGGGCGCCGTTCGTTGAGGAGGAGTGGGATGAGG

Basic information

species Vitis vinifera
transcript Vv13s0019g05240.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05240.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G10500.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagatcgtagagaaatttaaacgacgtgatggttttttagtttgtcgccattgttaatcgctgttttatgagaattttgggcttattattgttttgtttgtttggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAGAATGGTGAGCAGTATGGGGCGCCGTTCGTTGAGGAGGAGTGGGATGAGG
                             |   |  ||| |  || | |     |||  | | ||||| ||| ||  |||| | |  | | | | ||||    |||   | ||||||||| |||||  | ||| | || ||||| ||||||||||| || || || ||||| |||||||| || || ||||| ||||||||||||||||| ||||
-----------------------------gtaagactttgatctttttga----gttccttgttgtttaatggga--tttgtgttgttgactttgttgtggaattg--tgggaagGATGCGTTTGTGCTTTGTAGGATTTTTCAGAAGAGTGGCTCCGGACCTAAAAATGGAGAGCAGTACGGTGCTCCGTTTGTTGAGGAGGAGTGGGAGGAGG
















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|110687443|gb|EE064856.1|EE064856
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|71857288|gb|DT006343.1|DT006343
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGACGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAA
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAA
EST: gi|30327358|gb|CD010620.1|CD010620
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|32269108|gb|CD718267.1|CD718267
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|161718084|gb|FC067601.1|FC067601
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|30302696|gb|CB979490.1|CB979490
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|294966128|gb|GW837495.1|GW837495
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGNNNNNNNCAGGCGTGGCGCAG                         GATGCATTTGTA
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTA
EST: gi|71870084|gb|DT019139.1|DT019139
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|161720867|gb|FC070982.1|FC070982
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|32248038|gb|CD713857.1|CD713857
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|32269553|gb|CD718712.1|CD718712
EST:     ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: ATGAGTACAGGCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
EST: gi|161705821|gb|FC057098.1|FC057098
EST:     GCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAG                         GATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG
genomic: GCTTATGGATGAAGAATTGAAGAAAACAGGCGTGGCGCAGgtgagatcgt ... ggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctgttttatgagaattttgggcttattattgttttgtttgtttggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAGAATGGTGAGCAGTATGGGGCGCCGTTCGTTGAGGAGGAGTGGGATGAGG
                        ttattattgttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatcgtagagaaatttaaacgacgtgatggttttttagtttgtcgccattgttaatcgctgttttatgagaattttgggcttattattgttttgtttgtttggtcgagaagGATGCATTTGTATTGTGTCGAATCTTTCAAAAGAGTGGCTCAGGTCCAAAGAATGGTGAGCAGTATGGGGCGCCGTTCGTTGAGGAGGAGTGGGATGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG