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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatctcactttcaaaactataccaataatttggatccatcgtctctacttaattttttcttttgtacgtcttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTGTGATCAACGGAGCATTGAGTTACACCACTCTCCCT

Basic information

species Vitis vinifera
transcript Vv05s0049g01780.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|30305618|gb|CB982412.1|CB982412
EST:     CTTTGACCAAGACGACAATGGGGTCGTTTACCCTTGGGAGACCTATACCG                         GCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
genomic: CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCGgtaccatctc ... ttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
EST: gi|27581814|gb|CB004509.1|CB004509
EST:     CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCG                         GCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
genomic: CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCGgtaccatctc ... ttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
EST: gi|30305765|gb|CB982559.1|CB982559
EST:     CTTTGACCTAGACGACAATGGGGTCGTTTACCCTTGGGAGACCTATACCG                         GCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
genomic: CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCGgtaccatctc ... ttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
EST: gi|29783233|gb|CB349272.2|CB349272
EST:     CTTTGACCAAGACGACAATGGGGTCGTTTACCCTTGGGAGACCTATACCG                         GCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
genomic: CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCGgtaccatctc ... ttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
EST: gi|110400288|gb|EC966846.1|EC966846
EST:     CTTTGACCAAGACGACAATGGGGTCGTTTACCCTTGGGAGACCTATACCG                         GCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
genomic: CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCGgtaccatctc ... ttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
EST: gi|30135359|gb|CB920697.1|CB920697
EST:     CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCG                         GCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
genomic: CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCGgtaccatctc ... ttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
EST: gi|29782913|gb|CB348630.2|CB348630
EST:     CTTTGACCAAGACGACAATGGGGTCGTTTACCCTTGGGAGACCTATACCG                         GCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
genomic: CTTTGACCAAGACGACAATGGGATCGTTTACCCTTGGGAGACCTATACCGgtaccatctc ... ttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
EST: gi|29783277|gb|CB349356.2|CB349356
EST:     TTTACCCTTGGGAGACCTATACCG                         GCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG
genomic: TTTACCCTTGGGAGACCTATACCGgtaccatctc ... ttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttggatccatcgtctctacttaattttttcttttgtacgtcttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTGTGATCAACGGAGCATTGAGTTACACCACTCTCCCT
                     acttaat  putative branch site (score: 4)
                    tacttaattttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccatctcactttcaaaactataccaataatttggatccatcgtctctacttaattttttcttttgtacgtcttggaaacagGCCTGCGTGCTGTTGGTTTTAACACGATTGCCTCACTTATTATGGCGATTGTGATCAACGGAGCATTGAGTTACACCACTCTCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA