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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaattctaggttatttagttcgattatcatcagttttaataggtaatcttgaatttattttgcgtgattaaagctctctgtttttaatgatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCCTAGAGTTGGATACACTTGAAGCTCTACATATGTAGTAACTGAGAATCCT

Basic information

species Vitis vinifera
transcript Vv03s0038g04500.t01
intron # 12
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|33405951|gb|CF211578.1|CF211578
EST:     CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAG                         GCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAACTCC
genomic: CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAGgcaagtacat ... gatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCC
EST: gi|352776732|gb|FQ472619.1|FQ472619
EST:     CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAG                         GCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCC
genomic: CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAGgcaagtacat ... gatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCC
EST: gi|33401638|gb|CF207265.1|CF207265
EST:     CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAG                         GCACGGCTACTGGAAGTTAATGTTGATAGTTATATACAAATAAAAAACTCC
genomic: CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAGgcaagtacat ... gatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCC
EST: gi|45770374|gb|CN006226.1|CN006226
EST:     CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAG                         GCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAACTCC
genomic: CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAGgcaagtacat ... gatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCC
EST: gi|110361466|gb|EC924940.1|EC924940
EST:     CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAG                         GCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAACTCC
genomic: CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAGgcaagtacat ... gatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCC
EST: gi|110381698|gb|EC935151.1|EC935151
EST:     CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAG                         GCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAACTCC
genomic: CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAGgcaagtacat ... gatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCC
EST: gi|33407075|gb|CF212702.1|CF212702
EST:     CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAG                         GCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAACTCC
genomic: CATGGAGACTCTTCCTCCCCTTTCAGGCAATATATGCTTGTAGTTTTGAGgcaagtacat ... gatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcttgaatttattttgcgtgattaaagctctctgtttttaatgatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCCTAGAGTTGGATACACTTGAAGCTCTACATATGTAGTAACTGAGAATCCT
                                      ttttaat  putative branch site (score: 3)
     ttgaatttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggaattctaggttatttagttcgattatcatcagttttaataggtaatcttgaatttattttgcgtgattaaagctctctgtttttaatgatgttgcagGCACGGCTAATGGAAGTTAATGTTGATAGTTATATACAAATAAAAAATTCCTAGAGTTGGATACACTTGAAGCTCTACATATGTAGTAACTGAGAATCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcgtga