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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccccagtagcactttcattctcatgtttgggctttccttagatgtgaatatatctcattaaaagtttccaaatctcaattttaagtcaatgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATTGAGAAG

Basic information

species Vitis vinifera
transcript Vv13s0019g03960.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03960.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G31830.1 (Glycine max), 3'ss of exon 10
atccccagtagcactttcattctcatgtttgggctttccttagatgtgaatatatctcattaaaagtt--tccaaat-ctcaattttaagt---caatgt-ttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATTGAGAAG
        | |  ||      ||||| || |     ||  |   | ||| | | ||   ||| |  ||  ||  | | | |  | ||||     |||||  || |||||||||||||  |||||||||||  | ||||||||||| || |||||||||||||||
----tattttgggctcaaggcctcattttagaatggtc--tgagtctga-tctctccatttacacattaatctgactgcactttcttaaacgcgcaatgaattccagGAAGCATTGTCTAAGAGCAATGAGATTTTTGAAACATTCAAACAAGAGATTGAGAAG
















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|71871908|gb|DT020963.1|DT020963
EST:     GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAG                         GAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
genomic: GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAGgttaactttg ... atgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
EST: gi|30326467|gb|CD009729.1|CD009729
EST:     GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAG                         GAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
genomic: GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAGgttaactttg ... atgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
EST: gi|110726208|gb|EE101788.1|EE101788
EST:     GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAG                         GAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
genomic: GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAGgttaactttg ... atgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
EST: gi|30255027|gb|CB971474.1|CB971474
EST:     GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAG                         GAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAGGAGATT
genomic: GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAGgttaactttg ... atgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
EST: gi|77586923|gb|DV222608.1|DV222608
EST:     GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAG                         GAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
genomic: GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAGgttaactttg ... atgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
EST: gi|110693582|gb|EE069938.1|EE069938
EST:     TGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAG                         GAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
genomic: TGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAGgttaactttg ... atgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
EST: gi|110727231|gb|EE103758.1|EE103758
EST:     GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAG                         GAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT
genomic: GCTTGCGCTTACAGTTAACAGCTGATGGAGAGAAGTTCCAACAATTCCAGgttaactttg ... atgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaatatatctcattaaaagtttccaaatctcaattttaagtcaatgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATTGAGAAG
     tatatctcattaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccccagtagcactttcattctcatgtttgggctttccttagatgtgaatatatctcattaaaagtttccaaatctcaattttaagtcaatgtttgcagGAAGCATTGTTAAAGAGCAATGAAGTCTTTGAAACATTTAAGCAAGAGATTGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
atcccca
- - - - - - - - -cattctc
- - - - - - - - - - - - -tgtttgg
- - - - - - - - - - - - - - - - gctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaatc