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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcagttatagagattccagccataatttcttgatgatatgatttatcatattcataaacataacttttttccttgtactttatgcctcatccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT

Basic information

species Vitis vinifera
transcript Vv05s0029g00060.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|77578980|gb|DV218321.1|DV218321
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|349807865|gb|FQ402256.1|FQ402256
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71890565|gb|DT039620.1|DT039620
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|349812708|gb|FQ409867.1|FQ409867
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71873838|gb|DT022893.1|DT022893
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|110372532|gb|EC936708.1|EC936708
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71871639|gb|DT020694.1|DT020694
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|352786484|gb|FQ479093.1|FQ479093
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71890799|gb|DT039854.1|DT039854
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|110381320|gb|EC946647.1|EC946647
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACTGT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAAC--T
EST: gi|351039396|gb|FQ461263.1|FQ461263
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|349823439|gb|FQ423250.1|FQ423250
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACC
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71864683|gb|DT013738.1|DT013738
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71868560|gb|DT017615.1|DT017615
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACTGT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAAC--T
EST: gi|351046057|gb|FQ441440.1|FQ441440
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCCTCAG                         AAATACCGGTTGGGGAGGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|161713162|gb|FC062502.1|FC062502
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71877393|gb|DT026448.1|DT026448
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|349820030|gb|FQ404752.1|FQ404752
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|110374025|gb|EC938502.1|EC938502
EST:     CAATGGGGGTAAAAGGCCTCACCC-TTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACTGT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAAC--T
EST: gi|33401619|gb|CF207246.1|CF207246
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACTGT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAAC--T
EST: gi|351046098|gb|FQ442476.1|FQ442476
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|351045231|gb|FQ451679.1|FQ451679
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|110427496|gb|EC993936.1|EC993936
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACTGT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAAC--T
EST: gi|71871109|gb|DT020164.1|DT020164
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACTGT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAAC--T
EST: gi|71871652|gb|DT020707.1|DT020707
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71867598|gb|DT016653.1|DT016653
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACTGT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAAC--T
EST: gi|351043504|gb|FQ428976.1|FQ428976
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|352790540|gb|FQ478180.1|FQ478180
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|351055909|gb|FQ453370.1|FQ453370
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|71873299|gb|DT022354.1|DT022354
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
EST: gi|110358181|gb|EC922212.1|EC922212
EST:     CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAG                         AAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
genomic: CAATGGGGGTAAAAGGCCTCACCCTTTATCATTTGAAGTCGCATCTTCAGgtttgttgtt ... atccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatattcataaacataacttttttccttgtactttatgcctcatccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT
              acataac  putative branch site (score: 3)
                                         cctcatcctt  putative PPT
     tattcataaacataac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcagttatagagattccagccataatttcttgatgatatgatttatcatattcataaacataacttttttccttgtactttatgcctcatccttgcagAAATACCGGTTGGGGAAGCAATCATGCAAGGAGTTAACTGACAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - atagaga
- - - - - - - - -ccagcca
- - - - - - - - - - - - - - - cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - cataaac