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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAGAAGCTTCTGGGAAGTCTTGGAGGAATCTTCTCGAAGACCTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttctttctatgctctatttgcctgatttttatttttattttatttttgtttccattccgtaaactcatactagcaaaaaaattagaggtgatgtgcctcgttcaccaagcattatgtatttatttattttgtgtgtttgacttggttggttttgcag

Basic information

species Vitis vinifera
transcript Vv17s0000g06860.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ31467 (Selaginella moellendorffii), 5'ss of exon 2
GGTGAGAAGCTTCTGGGAAGTCTTGGAGGAATCTTCTCGAAGACCTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttctttctatgctctatttgcctgatttttatttttattttatttttgtttccattccgtaaactcatactagcaaaaaaattagaggtgatgtgcctcgttcaccaagcattatgtatttatttattttgtgtgtttgacttggttggttttgcag
||||||||||| || || |||||||||||  |||| |||||||||||||||||||  ||| | |||   ||||| || || ||     |  ||||| |                                 |  ||||||| ||   || | || ||   |||| ||          ||||  || ||                                                                      
GGTGAGAAGCTCCTCGGCAGTCTTGGAGGCCTCTTTTCGAAGACCTGGAAGCCAAAGAAGGCTCGCAACATAACGGGACCGATGCTTTCTCGAGgtaag--------------------------------agctttatttcatggctgctaccgtttgctaaaatcgcg--gatggaaaatctacag----------------------------------------------------------------------

upper sequence: Vv17s0000g06860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ38682 (Selaginella moellendorffii), 5'ss of exon 2
GGTGAGAAGCTTCTGGGAAGTCTTGGAGGAATCTTCTCGAAGACCTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttctttctatgctctatttgcctgatttttatttttattttatttttgtttccattccgtaaactcatactagcaaaaaaattagaggtgatgtgcctcgttcaccaagcattatgtatttatttattttgtgtgtttgacttggttggttttgcag
||||||||||| || || |||||||||||  |||| |||||||||||||||||||  ||| | |||   ||||| || || ||     |  ||||| |                                 |  ||||||| ||   || | || ||   |||| ||      | ||||  |  ||                                                                        
GGTGAGAAGCTCCTCGGCAGTCTTGGAGGCCTCTTTTCGAAGACCTGGAAGCCAAAGAAGGCTCGCAACATAACGGGACCGATGCTTTCTCGAGgtaag--------------------------------agctttatttcatggctgctaccgtttgctaaaatcgcggatggaaaatcaacag------------------------------------------------------------------------
















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|110719867|gb|EE095367.1|EE095367
EST:     CTGGAAGCCA-TAAAGACCCGCC-AATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGGAAGG-CAGCCACATGGAAC
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGG-AAGGGCAGCCACATGGAAC
EST: gi|110690969|gb|EE068535.1|EE068535
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|71889052|gb|DT038107.1|DT038107
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|71885181|gb|DT034236.1|DT034236
EST:     TGGAAGCCAATAAAGACCCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: TGGAAGCCAATAAAGA-CCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|110418340|gb|EC984487.1|EC984487
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|56408671|gb|CX016923.1|CX016923
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|30330505|gb|CD013767.1|CD013767
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|27586846|gb|CB009541.1|CB009541
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|352773351|gb|FQ470938.1|FQ470938
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|110700186|gb|EE077934.1|EE077934
EST:     TGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTTAC-ACAAGAG                         ATGATCTGTCTTTACAGGAAGG-CAGCCACATGGAACAGAGAGAGAAAGT-
genomic: TGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATT-ACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTT-ACAGGAAGGGCAGCCACATGGAACAGAGAGAGAA-GTT
EST: gi|110701129|gb|EE078388.1|EE078388
EST:     TGNAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTTAC-ACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGGACAGAGAGAGAAATTAC
genomic: TGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATT-ACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|110430333|gb|EC996884.1|EC996884
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|110412633|gb|EC978388.1|EC978388
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|32269033|gb|CD718192.1|CD718192
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|110690996|gb|EE068594.1|EE068594
EST:     CTGGAAGCCCATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|110410237|gb|EC975915.1|EC975915
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
EST: gi|71890575|gb|DT039630.1|DT039630
EST:     CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAG                         ATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG
genomic: CTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttc ... ggttttgcagATGATCTGTCTTACAGGAAGGGCAGCCACATGGAACAGAGAGAGAAGTTAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAGAAGCTTCTGGGAAGTCTTGGAGGAATCTTCTCGAAGACCTGGAAGCCAATAAAGACCCGCCCAATAACAGGGCCTATTACCACAAGAGgttaattttctttctatgctctatttgcctgatttttatttttattttatttttgtttccattccgtaaactcatactagcaaaaaaattagaggtgatgtgcctcgttcaccaagcattatgtatttatttattttgtgtgtttgacttggttggttttgcag

- - - - - - - - - - - - - - - - - - - - - -  TGGAAG