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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggagtccattaaaataatcttgaatgacaaatgcttttggtttggtctttcagtcatgtcttgttttcttacataaggatgggtgtttttttttccagCTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGGGAGAATGAGAGTCAAGAAAATGGGAATGTTCCAACTCAACATGCGGCAA

Basic information

species Vitis vinifera
transcript Vv16s0098g00320.t01
intron # 5
splice site 3'
intron type U2

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|351040645|gb|FQ438189.1|FQ438189
EST:     TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAG                         CTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
genomic: TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAGgtttgcttta ... ttttttccagCTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
EST: gi|351026899|gb|FQ436552.1|FQ436552
EST:     TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAG                         CTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
genomic: TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAGgtttgcttta ... ttttttccagCTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
EST: gi|351028525|gb|FQ444806.1|FQ444806
EST:     TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAG                         CTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
genomic: TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAGgtttgcttta ... ttttttccagCTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
EST: gi|351021577|gb|FQ429681.1|FQ429681
EST:     TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAG                         CTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
genomic: TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAGgtttgcttta ... ttttttccagCTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
EST: gi|161715191|gb|FC066437.1|FC066437
EST:     TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAG                         CTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG
genomic: TTTTCGAGCGGACAGAGCCATTGCAAGATCTCGATAGAATATTTACAAAGgtttgcttta ... ttttttccagCTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtctttcagtcatgtcttgttttcttacataaggatgggtgtttttttttccagCTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGGGAGAATGAGAGTCAAGAAAATGGGAATGTTCCAACTCAACATGCGGCAA
                      ttcttac  putative branch site (score: 2)
                                        tgtttttttttcc  putative PPT
                                        tgttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggagtccattaaaataatcttgaatgacaaatgcttttggtttggtctttcagtcatgtcttgttttcttacataaggatgggtgtttttttttccagCTTGCAACCGATTTTGAAGAGCAATGGGCAAATGGAATGGTAGAGGGGTGGGAGAATGAGAGTCAAGAAAATGGGAATGTTCCAACTCAACATGCGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - aaaataa
- - - - - - - - - - - - - - -caaatgc
- - - - - - - - - - - - - - - - - - - - ggtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatggg