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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtaactctactttctctctctcttttttttttctctctctcatatctcactttctctctcggttaacttttttctgtatctttctgtgtcgattttgtttttgacttcagGGGAGCCTTGCCCGCTCAGAATCTTGAAGCTAGG

Basic information

species Vitis vinifera
transcript Vv14s0030g01260.t01
intron # 1
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|71862308|gb|DT011363.1|DT011363
EST:     TTGTTTCTCTCTCTAGAATTCCTCAGATTCAATCAA                         GGGAGCCTTGCCCGCTCAGAATCTTGAAGCTA-G
genomic: TTGTTTCTCTCTCTAGAATTCCTCAGATTCAATCAAgtagtaactc ... ttgacttcagGGGAGCCTTGCCCGCTCAGAATCTTGAAGCTAGG
EST: gi|71862261|gb|DT011316.1|DT011316
EST:     TTGTTTCTCTCTCTAGAATTCCTCAGATTCAATCAA                         GGGAGCCTTGCCCGCTCAGAATCTTGGAGCTA-G
genomic: TTGTTTCTCTCTCTAGAATTCCTCAGATTCAATCAAgtagtaactc ... ttgacttcagGGGAGCCTTGCCCGCTCAGAATCTTGAAGCTAGG
EST: gi|71861054|gb|DT010109.1|DT010109
EST:     TTGTTTCTCTCTCTAGAATTCCTCAGATTCAATCAA                         GGGAGCCTTGCCCGCTCAGAATCTTGAAGCTA-G
genomic: TTGTTTCTCTCTCTAGAATTCCTCAGATTCAATCAAgtagtaactc ... ttgacttcagGGGAGCCTTGCCCGCTCAGAATCTTGAAGCTAGG
EST: gi|71864831|gb|DT013886.1|DT013886
EST:     TTGTTTCTCTCTCTAGAATTCCTCAGATTCAATCAA                         GGGAGCCTTGCCCGCTCAGAATCTTGAAGCTA-G
genomic: TTGTTTCTCTCTCTAGAATTCCTCAGATTCAATCAAgtagtaactc ... ttgacttcagGGGAGCCTTGCCCGCTCAGAATCTTGAAGCTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctcggttaacttttttctgtatctttctgtgtcgattttgtttttgacttcagGGGAGCCTTGCCCGCTCAGAATCTTGAAGCTAGG
                                           ttttgac  putative branch site (score: 3)
                                     ttttgttttt  CT-rich tract
       ttaactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtaactctactttctctctctcttttttttttctctctctcatatctcactttctctctcggttaacttttttctgtatctttctgtgtcgattttgtttttgacttcagGGGAGCCTTGCCCGCTCAGAATCTTGAAGCTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC