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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgggtatcagcataataatttcttgttttttctaaaagcaatctccaaatatttgacagtataatttattttattttataattttgtggaattgcagAGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAGAAACTTCTCAG

Basic information

species Vitis vinifera
transcript Vv01s0127g00720.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|110384872|gb|EC949339.1|EC949339
EST:     GGAATCCTCCTCAAAGCGCGGCAGCCAAACTGTAAAAGTTTCAGAAAAAG                         AGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
genomic: GGAATCCTCCTCAAAGCGCGGCAGCCAAACTGTAAAAGTTTCAGAAAAAGgttcgtacgg ... ggaattgcagAGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
EST: gi|34547687|gb|CF515919.1|CF515919
EST:     GGAATCCTCCTCAAAGCGCGGCAGCCAAACTGTATGAGTCTCAGAAAAAG                         AGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
genomic: GGAATCCTCCTCAAAGCGCGGCAGCCAAACTGTAAAAGTTTCAGAAAAAGgttcgtacgg ... ggaattgcagAGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
EST: gi|34548812|gb|CF517044.1|CF517044
EST:     GGAATCCTCCTCAAAGCGCGGCAGCCAAACTGTATAAGTTTCAGAAAAAG                         AGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
genomic: GGAATCCTCCTCAAAGCGCGGCAGCCAAACTGTAAAAGTTTCAGAAAAAGgttcgtacgg ... ggaattgcagAGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
EST: gi|71859278|gb|DT008333.1|DT008333
EST:     AAGTTTCAGAAAAAG                         AGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
genomic: AAGTTTCAGAAAAAGgttcgtacgg ... ggaattgcagAGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
EST: gi|161715637|gb|FC066795.1|FC066795
EST:     GGAATCCTCCTCAAAGCGCGGCAGCCAAACTGTATAAGTTTCAGAAAAAG                         AGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG
genomic: GGAATCCTCCTCAAAGCGCGGCAGCCAAACTGTAAAAGTTTCAGAAAAAGgttcgtacgg ... ggaattgcagAGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccaaatatttgacagtataatttattttattttataattttgtggaattgcagAGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAGAAACTTCTCAG
        atttgac  putative branch site (score: 4)
     aatatttgacagtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgggtatcagcataataatttcttgttttttctaaaagcaatctccaaatatttgacagtataatttattttattttataattttgtggaattgcagAGTAAAGATATGGCGACTGATTCATGCGAGGACGCCATTGCAGAACTGCAGAAACTTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - -aaagcaa
- - - - - - - - - - - - - - - - - - - - - - -ctccaaa