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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattctagtgcttttgaagaacatagttgaaaatttgtcagatttggggatcattgtgcagtattaaatggaacttaatgggagttcacttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCGGTTGGATTGGTGACAGGAGTACCTGCAATGGACTGGTGTGCTGATGCCT

Basic information

species Vitis vinifera
transcript Vv14s0066g01410.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|351015151|gb|FQ444440.1|FQ444440
EST:     TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAG                         AAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
genomic: TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAGgtttgagctt ... ttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
EST: gi|110372810|gb|EC937002.1|EC937002
EST:     TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAG                         AAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
genomic: TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAGgtttgagctt ... ttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
EST: gi|351034441|gb|FQ463254.1|FQ463254
EST:     TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAG                         AAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
genomic: TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAGgtttgagctt ... ttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
EST: gi|351013037|gb|FQ433764.1|FQ433764
EST:     TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAG                         AAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
genomic: TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAGgtttgagctt ... ttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
EST: gi|161706998|gb|FC055106.1|FC055106
EST:     TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAG                         AAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
genomic: TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAGgtttgagctt ... ttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
EST: gi|349826215|gb|FQ416020.1|FQ416020
EST:     TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAG                         AAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
genomic: TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAGgtttgagctt ... ttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
EST: gi|110395323|gb|EC960981.1|EC960981
EST:     TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAG                         AAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
genomic: TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAGgtttgagctt ... ttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
EST: gi|77580476|gb|DV219125.1|DV219125
EST:     TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAG                         AAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG
genomic: TCGGACCCAGATGTTTTTCCCAATACCCACCCCCATTTCAGAATCAAAAGgtttgagctt ... ttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggggatcattgtgcagtattaaatggaacttaatgggagttcacttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCGGTTGGATTGGTGACAGGAGTACCTGCAATGGACTGGTGTGCTGATGCCT
                            acttaat  putative branch site (score: 4)
                                        ttcactttt  putative PPT
               agtattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattctagtgcttttgaagaacatagttgaaaatttgtcagatttggggatcattgtgcagtattaaatggaacttaatgggagttcacttttgagcagAAAGCGAAGTCCTTTTCCTTGAAGGAATGTGCAATTTCTATAGCTTTGGCGGTTGGATTGGTGACAGGAGTACCTGCAATGGACTGGTGTGCTGATGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - gaagaac
- - - - - - - - - - - - - - -gaaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgga