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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatatggtattcccatattacttggtttttatgctgtgtgactatttcttggaactccaaaacctttgaccctttttttgcagTGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGGAGATGCCCAGAGAAAACAGCGGCGTGCAAAG

Basic information

species Vitis vinifera
transcript Vv09s0002g07530.t01
intron # 21
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|34543430|gb|CF511662.1|CF511662
EST:     GAACTCCAAAGCCAGATGCATCTATTGCAAGCAAAGGCCACCTTAG                         TGTATCAGATCTCCTTGATTACATTAGTCCAGATCAAGATTCAAAGGGGGG
genomic: GAACTCCAAAGCCAGATGCATCTATTGCAAGCAAAGGCCACCTTAGgtattgatat ... ttttttgcagTGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGG
EST: gi|110698822|gb|EE076760.1|EE076760
EST:     AATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCAAAGGCCACCTTAG                         TGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGG
genomic: AATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCAAAGGCCACCTTAGgtattgatat ... ttttttgcagTGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGG
EST: gi|30132945|gb|CB918284.1|CB918284
EST:     GCCAGATGCATCTATTGCAAGCAAAGGCCACCTTAG                         TGTATCAGATCTCCTTGATTACATTAGTCCAGATCAAGATTCAAANNNNNN
genomic: GCCAGATGCATCTATTGCAAGCAAAGGCCACCTTAGgtattgatat ... ttttttgcagTGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGG
EST: gi|110698721|gb|EE076539.1|EE076539
EST:     AATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCAAAGGCCACCTTAG                         TGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGG
genomic: AATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCAAAGGCCACCTTAGgtattgatat ... ttttttgcagTGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgctgtgtgactatttcttggaactccaaaacctttgaccctttttttgcagTGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGGAGATGCCCAGAGAAAACAGCGGCGTGCAAAG
                                   ctttgac  putative branch site (score: 4)
                                  cctttgaccctttttt  CT-rich tract
                                            ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgatatggtattcccatattacttggtttttatgctgtgtgactatttcttggaactccaaaacctttgaccctttttttgcagTGTATCAGATCTCCTTGATTACATTAGTCCGGATCAAGATTCAAAGGGGGGAGATGCCCAGAGAAAACAGCGGCGTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG