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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtatggtgctttattctctctctctctctatatatatatgtgtgtgtgtgtgtgtgtgtgtgtgtgttcctgttatgtagcttccatggttactggggagcatctgtattaacatggcacttagcatgtgcattttgtgatgcatttttgcagTGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCTGCATTCATATCGTAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g03970.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03970.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA12G07980.1 (Glycine max), 3'ss of exon 14
gtagtatggtgctttattctctctctctctctatatatatatgtgtgtgtgtgtgtgtgtgtgtgtgtgttcctgttatgtagcttccatggttactggggagcatctgtattaacatggcacttagcatgtgcattttgtgatgcatttttgcagTGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCTGCATTCATATCGTAAG
                                   || || ||| | | | | | | | |||  |  | |  |  | || |  | ||||  |||         | |||||  | |  ||   | ||  |  |   || | | ||  |||||| ||||||||| |  |||||||||||||| |||||| | |||||||||||  | |||||||||||||||
----------------------------------gta-atgtgtctttttttttttctttgtaggactttatcattgatttgacctcca--gtt---------cttctgtcctgatgtgaaccctaatacatagcttgt-tcattaatttttccagTGGGTTGCCTTTGAAAAAGCTTGACAAGAAACTAGAAAGAACACTTTTACATTCATATCGTAAG

upper sequence: Vv06s0004g03970.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA11G15470.1 (Glycine max), 3'ss of exon 15
gtagtatggtgctttattctctctctctctctatatatatatgtgtgtgtgtgtgtgtgtgtgtgtgtgttcctgttatgtagcttccatggttactggggagcatctgtattaacatggcacttagcatgtgcattttgtgatgcatttttgcagTGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCTGCATTCATATCGTAAG
                                     || |||||| | | | ||| |||  |  | | |   ||  || |  | ||||  |||         | |||||  | |  ||   | ||  |  |   |||  | ||  |||||| ||||||||| |  |||||||||||||| |||||| | |||||||||||  | ||||||||||| |||
------------------------------------gta-atgtgtctatttttgtttgtaggactttatcattg--atttgacctcca--gtt---------cttctgtcctgatgtgaaccctaatacata-gtttgttcattaatttttacagTGGGTTGCCTTTGAAAAAGCTTGACAAGAAACTAGAAAGAACACTTTTACATTCATATCGCAAG

upper sequence: Vv06s0004g03970.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT3G46220.3 (Arabidopsis thaliana), 3'ss of exon 14
gtagtatggtgctttattctctctctctctctatatatatatgtgtgtgtgtgtgtgtgtgtgtgtgtgttcctgttatgtagcttccatggttactggggagcatctgtattaacatggcacttagcatgtgcattttgtga--tgcatttttgcagTGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCTGCATTCATATCGTAAG
                                                                  || ||    ||       ||    ||   ||    ||||  | || |    |  |||   |  ||  |    ||| |  || |||| |||||||||||| ||||||| |||||||| || ||| ||||||| |||||||| |||||||||||||||
------------------------------------------------------------------gtattataattcgtatttttttgaggaatctcttaagcaagtctacttttctttcaccgggtttgaactgaatgttaactgtatttgtgcagTGGGTTAGTCTTGAAGAAGCTTGACAAAAAACTGGAAAGGACACTCCTACATTCATATCGTAAG

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|161709009|gb|FC058795.1|FC058795
EST:     CGGGTGGAAATATTCATGACTTCACTGGATGAGATGGCAGAAGACAG                         TGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCT
genomic: CGGGTGGAAATATTCATGACTTCACTGGATGAGATGGCAGAAGACAGgtagtatggt ... atttttgcagTGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCT
EST: gi|30251587|gb|CB969320.1|CB969320
EST:     CGGGTGGAAATATTCATGACTTCACTGGATGAGATGGCAGAAGACAG                         TGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCTGCA
genomic: CGGGTGGAAATATTCATGACTTCACTGGATGAGATGGCAGAAGACAGgtagtatggt ... atttttgcagTGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatctgtattaacatggcacttagcatgtgcattttgtgatgcatttttgcagTGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCTGCATTCATATCGTAAG
        tattaac  putative branch site (score: 1)
                                            cattttt  putative PPT
        tattaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtatggtgctttattctctctctctctctatatatatatgtgtgtgtgtgtgtgtgtgtgtgtgtgttcctgttatgtagcttccatggttactggggagcatctgtattaacatggcacttagcatgtgcattttgtgatgcatttttgcagTGGGTTACTCTTGAAAAAGCTTGATAAGAAATTGGAAAGAACACTCCTGCATTCATATCGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC