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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaagtatgcatgccatgctaagactgcaggtccatagtttgaagccactgatcttcctcgagttataggatctaataagtaatttttattatgttgcagGAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTACAAGCTTTTATTTTTCTATTTAGTATTGGAGTCTATCAATAATATAGGAG

Basic information

species Vitis vinifera
transcript Vv11s0052g01710.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|351031975|gb|FQ460232.1|FQ460232
EST:     AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCCGCGAAGCAG                         GAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC
genomic: AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAGgtataacttg ... tatgttgcagGAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC
EST: gi|351032492|gb|FQ458857.1|FQ458857
EST:     AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCCGCGAAGCAG                         GAACTTGCGGAGATGATATTCCCATCTGCACTGTAGAAAGCAGCATGTTAC
genomic: AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAGgtataacttg ... tatgttgcagGAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC
EST: gi|349812955|gb|FQ411195.1|FQ411195
EST:     AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCCTCCGCGAAGCAN                         GAACTTGCGGAGA
genomic: AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAGgtataacttg ... tatgttgcagGAACTTGCGGAGA
EST: gi|351032512|gb|FQ458877.1|FQ458877
EST:     AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCCGCGAAGCAN                         GAACTTGCGGAGATGATATTCCA
genomic: AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAGgtataacttg ... tatgttgcagGAACTTGCGGAGATGATATTCCA
EST: gi|22015436|gb|BQ800470.1|BQ800470
EST:     AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAG                         GAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC
genomic: AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAGgtataacttg ... tatgttgcagGAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC
EST: gi|349820047|gb|FQ404769.1|FQ404769
EST:     AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCCGCGAAGCAG                         GAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC
genomic: AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAGgtataacttg ... tatgttgcagGAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC
EST: gi|29784962|gb|CB341547.2|CB341547
EST:     AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCCGCGAAGCAG                         GAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC
genomic: AGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAGgtataacttg ... tatgttgcagGAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccactgatcttcctcgagttataggatctaataagtaatttttattatgttgcagGAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTACAAGCTTTTATTTTTCTATTTAGTATTGGAGTCTATCAATAATATAGGAG
                         atctaat  putative branch site (score: 3)
 tttttatt  putative PPT
 ttataggatctaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaagtatgcatgccatgctaagactgcaggtccatagtttgaagccactgatcttcctcgagttataggatctaataagtaatttttattatgttgcagGAACTTGCGGAGATGATATTCCAATCTGCACTGTAGAAAGCAGCATGTTACAAGCTTTTATTTTTCTATTTAGTATTGGAGTCTATCAATAATATAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - gtatgca
- - - - - - -ccatgct
- - - - - - - - - - - -actgcag
- - - - - - - - - - - - - - - - - - - - - - gccactg