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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctaatatgatgaacttgcttgtgtacaaatttttccaattatgttcttaaagtttggttggtgtctacttcttttgcaactctgattaatggtctatgttatattcttccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATTATGTGCATATCCGCATACAGCAACGGAACGGAAGGAAAAGCCTGACAAC

Basic information

species Vitis vinifera
transcript Vv19s0177g00100.t01
intron # 2
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|22011062|gb|BQ796096.1|BQ796096
EST:     ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|32457673|gb|CD798847.1|CD798847
EST:     AGCCAAGTTTCATGTCTGTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGAGTCAAAAGATT
genomic: AGCCAAGTTTCATGTC--TGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|34414969|gb|CF413723.1|CF413723
EST:     TTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: TTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|22010321|gb|BQ795355.1|BQ795355
EST:     AACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: AACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|27586671|gb|CB009366.1|CB009366
EST:     ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|110397208|gb|EC962936.1|EC962936
EST:     ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|22013158|gb|BQ798207.1|BQ798207
EST:     GATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: GATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|110408072|gb|EC973693.1|EC973693
EST:     TCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: TCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|30296517|gb|CB973311.1|CB973311
EST:     TCATGTCTGAACTCGANATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: TCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|110375483|gb|EC940472.1|EC940472
EST:     ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|110402223|gb|EC959593.1|EC959593
EST:     ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|30296476|gb|CB973270.1|CB973270
EST:     ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|22011007|gb|BQ796041.1|BQ796041
EST:     ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|22010208|gb|BQ795242.1|BQ795242
EST:     AAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: AAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|22008034|gb|BQ793068.1|BQ793068
EST:     ACAGCCAAGTTTCATGTTTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|110402090|gb|EC968723.1|EC968723
EST:     ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: ACAGCCAAGTTTCATGTCTGAACTCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
EST: gi|110407800|gb|EC973415.1|EC973415
EST:     TCGACATCCAGATCCCCACTGCTTTTG                         ATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT
genomic: TCGACATCCAGATCCCCACTGCTTTTGgtatgctaat ... ccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacttcttttgcaactctgattaatggtctatgttatattcttccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATTATGTGCATATCCGCATACAGCAACGGAACGGAAGGAAAAGCCTGACAAC
                    gattaat  putative branch site (score: 3)
                                      tattcttcc  putative PPT
                               tatgttatattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctaatatgatgaacttgcttgtgtacaaatttttccaattatgttcttaaagtttggttggtgtctacttcttttgcaactctgattaatggtctatgttatattcttccaatattagATCCGTTTGCTGAGGCAAATGCTGAGGACTCAGGTGCTGGGTCAAAAGATTATGTGCATATCCGCATACAGCAACGGAACGGAAGGAAAAGCCTGACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA