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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctttttattttttaagcttctctctcattttcttaatttattaaatgtctttttctaaaaattaacttttttattttttatgttattcttaagcagAAGGTAAAATTGTCTGGGGTTTCTTGCTTGCATTTAAAAACTCTTTTTCGAGAGCATATTGGTGCAAAACTTGACGGGAATCAGATGCAATGGGAGCATC

Basic information

species Vitis vinifera
transcript Vv18s0001g04060.t01
intron # 1
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|110379274|gb|EC944459.1|EC944459
EST:     GCCGCTCACCGCCGCCAGAGTCATTCACCAAGGCAACGCACCATGTCGAG                         AAGGTAAAATTGTCTGGGGTTTCTTGCTTGCATTTAAAAACTCTTTTTCGA
genomic: GCCGCTCACCGCCGCCAGAGTCATTCACCAAGGCAACGCACCATGTCGAGgtaatttgtg ... tcttaagcagAAGGTAAAATTGTCTGGGGTTTCTTGCTTGCATTTAAAAACTCTTTTTCGA
EST: gi|110386605|gb|EC951218.1|EC951218
EST:     GCCGCTCACCGCCGCCAGAGTCATTCACCAAGGCAACGCACCATGTCGAG                         AAGGTAAAATTGTCTGGGGTTTCTTGCTTGCATTTAAAAACTCTTTTTCGA
genomic: GCCGCTCACCGCCGCCAGAGTCATTCACCAAGGCAACGCACCATGTCGAGgtaatttgtg ... tcttaagcagAAGGTAAAATTGTCTGGGGTTTCTTGCTTGCATTTAAAAACTCTTTTTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatgtctttttctaaaaattaacttttttattttttatgttattcttaagcagAAGGTAAAATTGTCTGGGGTTTCTTGCTTGCATTTAAAAACTCTTTTTCGAGAGCATATTGGTGCAAAACTTGACGGGAATCAGATGCAATGGGAGCATC
                  aattaac  putative branch site (score: 2)
                                         ttattctt  putative PPT
        tttttctaaaaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctttttattttttaagcttctctctcattttcttaatttattaaatgtctttttctaaaaattaacttttttattttttatgttattcttaagcagAAGGTAAAATTGTCTGGGGTTTCTTGCTTGCATTTAAAAACTCTTTTTCGAGAGCATATTGGTGCAAAACTTGACGGGAATCAGATGCAATGGGAGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - -ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaa