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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgaaattaaatactgttttattgctcagtagcatgttttttttaataggtcatgctcgatagcatgttatatgacactccaattttgttgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGTGAGGCTCAAGCTCATGCAACCGTGAAGGATTTTGATTTCAG

Basic information

species Vitis vinifera
transcript Vv01s0011g04970.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g04970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G34340.1 (Glycine max), 3'ss of exon 3
--aatgaaattaaatactgttttattgctcagtagcatgttttttttaataggtcatgctcgatagcatgttatatgacactccaattttgttgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGTGAGGCTCAAGCTCATGCAACCGTGAAGGATTTTGATTTCAG
    |      ||  |||   | |    | |   | |     || ||    | | | |     | | ||| | ||||| | |  ||||||| |||||||||||| |||||| ||||||| |||||||||||||||||||||| | ||||||  ||| || | |||||| |  |  ||||||| ||  |||||||
ttcttctggcaaataactaaataagcattaaaatgtagaaaattctttgctgataaagg--agtggaatgctttatgatattgtaattttggtgcagtacagGATGGCAATCTAAGGGTTTTCAAGTGGCCTAGCATGGAAATTATTCTCAACGAGACTAATGCTCATTCTTCTTTGAAGGACTTACATTTCAG
















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|110713595|gb|EE089653.1|EE089653
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAAGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110711442|gb|EE087923.1|EE087923
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110712942|gb|EE088427.1|EE088427
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110698023|gb|EE075561.1|EE075561
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|26261968|gb|CA813031.1|CA813031
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGNCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110713391|gb|EE089281.1|EE089281
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110377427|gb|EC942492.1|EC942492
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110360943|gb|EC924388.1|EC924388
EST:     AATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: AATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110404868|gb|EC970393.1|EC970393
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|161721290|gb|FC069698.1|FC069698
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|33402025|gb|CF207652.1|CF207652
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGATCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110709550|gb|EE085108.1|EE085108
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAA                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110711776|gb|EE088641.1|EE088641
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
EST: gi|110380366|gb|EC945626.1|EC945626
EST:     TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAG                         GACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT
genomic: TAGCACTGACATTCAATAATGATGGTTCAATGCTTGCTGTTGGTGGCGAGgtagagacta ... tgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataggtcatgctcgatagcatgttatatgacactccaattttgttgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGTGAGGCTCAAGCTCATGCAACCGTGAAGGATTTTGATTTCAG
 ttttaat  putative branch site (score: 3)
                                       ttttgtt  putative PPT
                    atgttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgaaattaaatactgttttattgctcagtagcatgttttttttaataggtcatgctcgatagcatgttatatgacactccaattttgttgcagtacagGACGGCAATTTAAGGGTGTTCAAGTGGCCTAGCATGGAAAATGTTCTCAGTGAGGCTCAAGCTCATGCAACCGTGAAGGATTTTGATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - aaattaa
- - - - - - - - - - - - - - - - gcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - catgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactcca