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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactggaataataaggtatcctatttgagatcaagagctaatctatcttgattttggggtcaaaactgcaaccgcctagtataacacaagttcaatgcagATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAAGGAGTCACTACCAACCGTCTTTTTATTGGGATAGTGGGAATAACTCTCG

Basic information

species Vitis vinifera
transcript Vv11s0052g00320.t01
intron # 32
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 32
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 31
tactggaataataaggtatcctatttgagatcaagagctaatctatcttgattttggggtcaaa--actgcaaccgcctagtataacacaagttcaatgcagATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAAGGAGTCACTACCAACCGTCTTTTTATTGGGATAGTGGGAATAACTCTCG
                             |  |    || |  | |||  ||     ||  |    ||  ||     | |    |     |  |   |  || ||||||| ||||| |||||||||||||| |||||||| ||  | |||  ||||||    |  || |  |||||| | || ||  |    || ||  | |
---------------------------gtaaaagatactgacttctctgtataaaaaggctaggggacgacagaaaacaaactgattgttaaatttgt-tagGTATTCAACGAGTTCAATGCACGGAAGCCAGATGAAATAAACATTTTCCGAGGAGTTCTCAGGAATCACCTTTTTGTGGGCATCATCTCTATCACCATTG
















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|110426116|gb|EC992513.1|EC992513
EST:     CTAGCAAAGAGAAGAATACAGTGATATTCAATGCTTTTGTTCTTTGTCAG                         ATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAA
genomic: CTAGCAAAGAGAAGAATACAGTGATATTCAATGCTTTTGTTCTTTGTCAGgtatatttaa ... ttcaatgcagATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAA
EST: gi|110727598|gb|EE104541.1|EE104541
EST:     CTAGCAAAGAGAAGAATACAGTGATATTCAATGCTTTTGTTCTTTGTCAG                         ATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAA
genomic: CTAGCAAAGAGAAGAATACAGTGATATTCAATGCTTTTGTTCTTTGTCAGgtatatttaa ... ttcaatgcagATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAA
EST: gi|71883815|gb|DT032870.1|DT032870
EST:     CTAGCAAAGAGAAGAATACAGTGATATTCAATGCATTTGTTCTTTGTCAG                         ATATTCAATGAGTTTAATGCACGGAAGCCAGATGAAATTAATGTATTCAAA
genomic: CTAGCAAAGAGAAGAATACAGTGATATTCAATGCTTTTGTTCTTTGTCAGgtatatttaa ... ttcaatgcagATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgattttggggtcaaaactgcaaccgcctagtataacacaagttcaatgcagATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAAGGAGTCACTACCAACCGTCTTTTTATTGGGATAGTGGGAATAACTCTCG
                                 gtataac  putative branch site (score: 3)
                               tagtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactggaataataaggtatcctatttgagatcaagagctaatctatcttgattttggggtcaaaactgcaaccgcctagtataacacaagttcaatgcagATATTCAATGAGTTTAATGCACGGAAGCCGGATGAAATTAATGTATTCAAAGGAGTCACTACCAACCGTCTTTTTATTGGGATAGTGGGAATAACTCTCG

- - ggaataa
- - - - - - - - - - - - - - - - - - - - - - - - - -ttttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaag