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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccctaattgcagcactttctctcctttttttccctcttttaaattcttcatatctttttggacagtttcctttgaagtccttcaattattttttcactatatagtattctataacatttggttatttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG

Basic information

species Vitis vinifera
transcript Vv18s0041g01360.t01
intron # 12
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|30133605|gb|CB918944.1|CB918944
EST:     ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGAT                         TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
genomic: ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGATgtatgcccta ... atttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
EST: gi|352769084|gb|FQ471032.1|FQ471032
EST:     ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGAT                         TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
genomic: ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGATgtatgcccta ... atttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
EST: gi|110369051|gb|EC933194.1|EC933194
EST:     ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGAT                         TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
genomic: ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGATgtatgcccta ... atttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
EST: gi|37183876|gb|CF603230.1|CF603230
EST:     ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGAT                         TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
genomic: ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGATgtatgcccta ... atttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
EST: gi|46918636|gb|CN547965.1|CN547965
EST:     ATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGAT                         TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
genomic: ATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGATgtatgcccta ... atttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
EST: gi|32268986|gb|CD718145.1|CD718145
EST:     ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGAT                         TGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
genomic: ATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCATGGATgtatgcccta ... atttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcaattattttttcactatatagtattctataacatttggttatttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG
                              ctataac  putative branch site (score: 3)
                                           ttatttct  putative PPT
     aattattttttcacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccctaattgcagcactttctctcctttttttccctcttttaaattcttcatatctttttggacagtttcctttgaagtccttcaattattttttcactatatagtattctataacatttggttatttctgcagTGTTCTCAGAACCCTCTGAGTATTGCAAAGTATCAAAATGACAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG