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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagtttagaacttgctttagaagaaacttctaaaaatatagctgtgacttttgaaatatttttgtcagatcattaattatatgtaatttcatctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCAGTTGTATACTACAACCTACCTGAGGTTCAACAGGCACTTCATGTTTATA

Basic information

species Vitis vinifera
transcript Vv11s0037g00740.t01
intron # 6
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|110384773|gb|EC949233.1|EC949233
EST:     CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATT                         AGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
genomic: CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATTgtgagttgca ... catctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
EST: gi|351015461|gb|FQ447290.1|FQ447290
EST:     CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATT                         AGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
genomic: CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATTgtgagttgca ... catctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
EST: gi|110419335|gb|EC985553.1|EC985553
EST:     CAAAGTTGGCTTTTC-AATCAGCTAATGAAAAGATTGATT                         AGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
genomic: CAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATTgtgagttgca ... catctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
EST: gi|29785466|gb|CB342476.2|CB342476
EST:     CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATT                         AGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
genomic: CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATTgtgagttgca ... catctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
EST: gi|351022774|gb|FQ428683.1|FQ428683
EST:     CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATT                         AGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
genomic: CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATTgtgagttgca ... catctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
EST: gi|110361863|gb|EC925365.1|EC925365
EST:     CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATT                         AGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA
genomic: CTTGCAGTGTCAAAGTTGGCTTTTCAAATCAGCTAATGAAAAGATTGATTgtgagttgca ... catctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacttttgaaatatttttgtcagatcattaattatatgtaatttcatctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCAGTTGTATACTACAACCTACCTGAGGTTCAACAGGCACTTCATGTTTATA
                          cattaat  putative branch site (score: 3)
                                          tttcatct  putative PPT
         aaatatttttgtcaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagtttagaacttgctttagaagaaacttctaaaaatatagctgtgacttttgaaatatttttgtcagatcattaattatatgtaatttcatctgatagAGGGTTGGTCGCATCAGCGAGAGGTATGATCCATGCACAGAGCAGCACTCAGTTGTATACTACAACCTACCTGAGGTTCAACAGGCACTTCATGTTTATA

- - - - - -cttgctt
- - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - tgaaata