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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggatgatttgatctttagctcggttacatctctttagtgacatttattggttcacattatttattagttaattgatttgtatttcatttcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGAGTTTCTCTTGATTCTAAGGATTCACAAGGGAGAACAG

Basic information

species Vitis vinifera
transcript Vv06s0009g03440.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|110367982|gb|EC931941.1|EC931941
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
EST: gi|110702003|gb|EE080223.1|EE080223
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
EST: gi|28959189|gb|CB339596.1|CB339596
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
EST: gi|110398850|gb|EC965326.1|EC965326
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
EST: gi|110382025|gb|EC938279.1|EC938279
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
EST: gi|110398949|gb|EC965433.1|EC965433
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
EST: gi|28958619|gb|CB339304.1|CB339304
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
EST: gi|71888016|gb|DT037071.1|DT037071
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA
EST: gi|28959022|gb|CB339512.1|CB339512
EST:     AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAA                         GCTGCTAGATATGATGCCATTGATGATGTTAAAATCATAGCTTCTGCTGGA
genomic: AAGCTTCAGCCGAAACGGCGTCGCAGGAGAACGTAGAGGCCTTGCTTGAAgtacaagaaa ... tcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattggttcacattatttattagttaattgatttgtatttcatttcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGAGTTTCTCTTGATTCTAAGGATTCACAAGGGAGAACAG
                          aattgat  putative branch site (score: 4)
                                    tatttcatttctttt  putative PPT
            attatttattagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggatgatttgatctttagctcggttacatctctttagtgacatttattggttcacattatttattagttaattgatttgtatttcatttcttttacagGCTGCTAGATATGATGACATTGATGATGTTAAAATCATAGCTTCTGCTGGAGTTTCTCTTGATTCTAAGGATTCACAAGGGAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - catctct