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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagcaagttttacttggatctgtcatttcttcccgcctatcacatgagtagctttttaatgagatgctgtattccaatatcttatcttctgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGTGACTGGTACTGCAAAGAAGCAAGTAAAGGAGAAATCATCAGTGTCCAAT

Basic information

species Vitis vinifera
transcript Vv09s0002g01600.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01600.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S371_53V6.1 (Physcomitrella patens), 3'ss of exon 3
gaagcaagttttacttggatctgtcatttcttcccgcctatc-acatgagtagctttttaatgagatgctgtattccaat----atcttatcttctgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGTGACTGGTACTGCAAAGAAGCAAGTAAAGGAGAAATCATCAGTGTCCAAT------
    |    | ||     |      | | |||      | |     || |||| |||| | ||  ||  |    || ||     || ||||  | | |  | ||||||||| |||||||||||||||||||| ||||||||  |||| || || ||||| ||      ||||||||  || ||||| ||  |  | ||    |||      
----ctctctgtagaacaagggaatactcctttttttgtgtttgtgtgtgtaggtttt-attgctatttttctatctaaggaggatattatggtatctcttacagGAAGCGTCTCTTTAATATGATAAATGAACTCCCAACAGTATTCGACGTAGTGACAGG------AAAGAAGCCTGTGAAGGACAAGCCTGCTGTTAATAATTCCTCT
















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|110374261|gb|EC938930.1|EC938930
EST:     GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAG                         GAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
genomic: GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAGgtttttcatt ... tgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
EST: gi|110427146|gb|EC993577.1|EC993577
EST:     GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAG                         GAAGCGGCTCTTTAATATGATAAATGATCTGCCAACCATATTTGAAGTTGT
genomic: GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAGgtttttcatt ... tgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
EST: gi|110707135|gb|EE083281.1|EE083281
EST:     GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAG                         GAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
genomic: GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAGgtttttcatt ... tgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
EST: gi|110685169|gb|EE063284.1|EE063284
EST:     GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAG                         GAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
genomic: GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAGgtttttcatt ... tgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
EST: gi|110385832|gb|EC950388.1|EC950388
EST:     GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAG                         GAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
genomic: GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAGgtttttcatt ... tgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
EST: gi|110703434|gb|EE080277.1|EE080277
EST:     ATTTGGATTTGATAAAGCTGACAG                         GAAGCGGCTCTTTAATATGATAAATGATCTGCCAACCATATTTGAAGTTGT
genomic: ATTTGGATTTGATAAAGCTGACAGgtttttcatt ... tgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT
EST: gi|110402871|gb|EC963673.1|EC963673
EST:     GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAG                         GAAGCGGCTCTTTAATATGATAAATGATCTGCCAACCATATTTGAAGTTGT
genomic: GCTGTTGCCTTCTATTTTGGTGCCAGATTTGGATTTGATAAAGCTGACAGgtttttcatt ... tgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtagctttttaatgagatgctgtattccaatatcttatcttctgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGTGACTGGTACTGCAAAGAAGCAAGTAAAGGAGAAATCATCAGTGTCCAAT
         ttttaat  putative branch site (score: 3)
                                   tcttatcttct  putative PPT
        tttttaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagcaagttttacttggatctgtcatttcttcccgcctatcacatgagtagctttttaatgagatgctgtattccaatatcttatcttctgtggtgcagGAAGCGGCTCTTTAATATGATAAATGATCTCCCAACCATATTTGAAGTTGTGACTGGTACTGCAAAGAAGCAAGTAAAGGAGAAATCATCAGTGTCCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
gaagcaa
- - - - - -tacttgg
- - - - - - - - - - ctgtcat
- - - - - - - - - - - - - - tcttccc
- - - - - - - - - - - - - - - - - - - - tcacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctg