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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccttttctctcattcctcgtctccttcttctccttcttctccttcttcttttctgagtgaatctgaatcgtctatggtgctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGAAGAAGAATTCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAG

Basic information

species Vitis vinifera
transcript Vv09s0002g02560.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|71877453|gb|DT026508.1|DT026508
EST:     GCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: GCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|30126857|gb|CB912196.1|CB912196
EST:     CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|30137111|gb|CB922449.1|CB922449
EST:     AGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: AGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|71866381|gb|DT015436.1|DT015436
EST:     CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|30127339|gb|CB912678.1|CB912678
EST:     GAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: GAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|77581630|gb|DV219763.1|DV219763
EST:     CAGCAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|110365315|gb|EC928109.1|EC928109
EST:     CTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|30136063|gb|CB921401.1|CB921401
EST:     CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|71869153|gb|DT018208.1|DT018208
EST:     CAGCAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|37187689|gb|CF607042.1|CF607042
EST:     CGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|71855040|gb|DT004095.1|DT004095
EST:     CAGCAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|71871612|gb|DT020667.1|DT020667
EST:     CAGCAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|71860821|gb|DT009876.1|DT009876
EST:     CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCTACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|71868068|gb|DT017123.1|DT017123
EST:     CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|110393499|gb|EC958782.1|EC958782
EST:     CCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|110707611|gb|EE084204.1|EE084204
EST:     CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|71866729|gb|DT015784.1|DT015784
EST:     GCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: GCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|30133884|gb|CB919223.1|CB919223
EST:     GCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: GCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
EST: gi|29782791|gb|CB348407.2|CB348407
EST:     CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAG                         GGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA
genomic: CAGCTCGCCTATTGCAGCCACAGAAAACCCTAGCAGgtccttttct ... gctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttctccttcttcttttctgagtgaatctgaatcgtctatggtgctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGAAGAAGAATTCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAG
            ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccttttctctcattcctcgtctccttcttctccttcttctccttcttcttttctgagtgaatctgaatcgtctatggtgctattgcagGGAAAGGTGAAATGGCGACAGTTCCAGGGCAGTTGATTTGGGAGATCGTGAAGAAGAATTCCTCCTTTCTCGTGAAGGAGTTCGGGAACGGCACCGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG