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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaaagaccttgaatcataattggttgctccttaataagttagccatgtcttaacctcccaccttaagatgatccaaggtcaaatgcttttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTTGAAGAGTATGATGGCAAGTCTTTGAGCTTCAAGCAAATTATCAGGTCAA

Basic information

species Vitis vinifera
transcript Vv11s0052g01380.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|110712895|gb|EE088351.1|EE088351
EST:     TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAGAAG                         GTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
genomic: TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAAAAGgttggtatcg ... ttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
EST: gi|161709162|gb|FC061372.1|FC061372
EST:     TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAGAAG                         GTCTATGTCGATAACTTGGTTAAGACAGCATACGACAACTGGAATCAAGTT
genomic: TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAAAAGgttggtatcg ... ttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
EST: gi|27581990|gb|CB004685.1|CB004685
EST:     TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAAAAG                         GTCTATGTCAATAACTTGGTTAAGAAAGCATACAAAAACTGGAATCAAGTT
genomic: TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAAAAGgttggtatcg ... ttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
EST: gi|26263708|gb|CA814771.1|CA814771
EST:     TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAGAAG                         GTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
genomic: TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAAAAGgttggtatcg ... ttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
EST: gi|71883679|gb|DT032734.1|DT032734
EST:     TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAGAAG                         GTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
genomic: TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAAAAGgttggtatcg ... ttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
EST: gi|110719043|gb|EE096564.1|EE096564
EST:     TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAGAAG                         GTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT
genomic: TTGCTGGGGAGCAGTATTTCTCTGCTGATTCTCTTTCTGAGAGCCAAAAGgttggtatcg ... ttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtcttaacctcccaccttaagatgatccaaggtcaaatgcttttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTTGAAGAGTATGATGGCAAGTCTTTGAGCTTCAAGCAAATTATCAGGTCAA
    tcttaac  putative branch site (score: 2)
                                          cttttactt  putative PPT
                                           ttttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaaagaccttgaatcataattggttgctccttaataagttagccatgtcttaacctcccaccttaagatgatccaaggtcaaatgcttttacttgcagGTCTATGTCGATAACTTGGTTAAGAAAGCATACGAAAACTGGAATCAAGTTGAAGAGTATGATGGCAAGTCTTTGAGCTTCAAGCAAATTATCAGGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- -aaagacc
- - - - - - - - - - - - - tgctcct
- - - - - - - - - - - - - - - - - - - - - - ccatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaatgc