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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccctcacttggatctctatctatcactgaatttgtttagatttaaaagaattttaatattacctgaactcttactcagatttctataatgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTCTCAGAATCTAGTGTTGTTACCACATATTACTTCAATTGGTCCACGAGCA

Basic information

species Vitis vinifera
transcript Vv02s0025g04540.t01
intron # 8
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|30324077|gb|CD007339.1|CD007339
EST:     CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAG                         GTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
genomic: CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAGgtatgtattt ... atgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
EST: gi|32268084|gb|CD717243.1|CD717243
EST:     CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAG                         GTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
genomic: CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAGgtatgtattt ... atgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
EST: gi|77586359|gb|DV222293.1|DV222293
EST:     CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAG                         GTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
genomic: CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAGgtatgtattt ... atgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
EST: gi|110356940|gb|EC920131.1|EC920131
EST:     CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAG                         GTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
genomic: CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAGgtatgtattt ... atgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
EST: gi|110384571|gb|EC949018.1|EC949018
EST:     CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAG                         GTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
genomic: CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAGgtatgtattt ... atgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
EST: gi|71875070|gb|DT024125.1|DT024125
EST:     CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAG                         GTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
genomic: CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAGgtatgtattt ... atgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
EST: gi|34546746|gb|CF514978.1|CF514978
EST:     CCCTCTGTAAAG                         GTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
genomic: CCCTCTGTAAAGgtatgtattt ... atgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
EST: gi|30327947|gb|CD011209.1|CD011209
EST:     CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAG                         GTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC
genomic: CAGCCACTTCTATTGGTTCAGCATATAGATTACTTACTCCCTCTGTAAAGgtatgtattt ... atgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagaattttaatattacctgaactcttactcagatttctataatgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTCTCAGAATCTAGTGTTGTTACCACATATTACTTCAATTGGTCCACGAGCA
                         ctcttac  putative branch site (score: 3)
      aattttaatattacct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccctcacttggatctctatctatcactgaatttgtttagatttaaaagaattttaatattacctgaactcttactcagatttctataatgtaatcagGTTCAACTATTGATTTATTTCATGCTCAAATATGCAATGGAGATTTTACTCTCAGAATCTAGTGTTGTTACCACATATTACTTCAATTGGTCCACGAGCA

- -ccctcac
- - - - - - - - - - - - - cactgaa
- - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgaa