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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggcatttgtgttacagtctgtttgttgtgatattttttttgtttggaggctttcttgttcacttgtggtgctttcaactttgattggtgtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG

Basic information

species Vitis vinifera
transcript Vv14s0006g01660.t01
intron # 4
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|110380611|gb|EC945891.1|EC945891
EST:     AGCAGGCCTGGAAGAGAATAGCTTATTATACTATACCCATTTGTTAACAG                         GTTATATTGGTTCTGTTTCTTTTTTGAACGCAGTATTAGAAGTTGTCCATA
genomic: AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAGgtatgtttat ... gtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
EST: gi|110715098|gb|EE092763.1|EE092763
EST:     AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAG                         GTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
genomic: AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAGgtatgtttat ... gtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
EST: gi|71859315|gb|DT008370.1|DT008370
EST:     AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAG                         GTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
genomic: AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAGgtatgtttat ... gtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
EST: gi|294966903|gb|GW839778.1|GW839778
EST:     AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAG                         GTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
genomic: AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAGgtatgtttat ... gtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
EST: gi|37186505|gb|CF605858.1|CF605858
EST:     AGCAGGCCTGGAAGAGAATAGCTTATTATACTATACCCATTTGTTAACAG                         GTTATATTGGTTCTGTTTCTTTTTTGAACGCAGTATTAGAAGTTGTCCATA
genomic: AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAGgtatgtttat ... gtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
EST: gi|71863971|gb|DT013026.1|DT013026
EST:     AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAG                         GTTATATTGGTTCTGTTTCTTTTTTGAACGCAGTATTAGAAGTTGTCCATA
genomic: AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAGgtatgtttat ... gtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
EST: gi|71859789|gb|DT008844.1|DT008844
EST:     AGCAGGCCTGGAAGAGAATAGCTTATTATACTATACCCATTTGTTAACAG                         GTTATATTGGTTCTGTTTCTTTTTTGAACGCAGTATTAGAAGTTGTCCATA
genomic: AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAGgtatgtttat ... gtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA
EST: gi|161712131|gb|FC061503.1|FC061503
EST:     AGCAGGCCTGGAAGAGAATAGCTTATTATACTATACCCATTTGTTAACAG                         GTTATATTGGTTCTGTTTCTTTTTTGAACGCAGTATTAGAAGTTGTCCATA
genomic: AGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTTAACAGgtatgtttat ... gtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaggctttcttgttcacttgtggtgctttcaactttgattggtgtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG
                                  ctttgat  putative branch site (score: 5)
                                              tattttc  putative PPT
                                            tgtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggcatttgtgttacagtctgtttgttgtgatattttttttgtttggaggctttcttgttcacttgtggtgctttcaactttgattggtgtattttcagGTTATATTGGTTCTGTTTCTTTTTTGAACGCGGTATTAGAAGTTGTCCATAAACTCCGTTCTGTTAATCCAAAGCTGACATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- -gcatttg
- - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - -tgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgg