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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgcccttttaatagtggattagtggtcttatttatttggttgttttcggcttcatatgtattcacaatgctgacattttactctaatgagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGGAGGTTTTAGGCCATGCTGCAAAGGTGGTGCTTACCAAGGATACAACCAC

Basic information

species Vitis vinifera
transcript Vv06s0004g00240.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 6
-----------------tattgcccttttaatagtggattagtggtcttatttatttggttgttttcggcttcatatgtattcacaatgctgacattttactctaatgagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGGAGGTTTTAGGCCATGCTGCAAAGGTGGTGCTTACCAAGGATACAACCAC
                 | |    | ||| ||  ||||   ||     |  || |||   | | ||    ||   |  | || | ||       |||||     |||  | ||  ||| |||||||| ||||| ||||| || || ||  | |||||||||| ||| |||||| | ||  ||||  | ||||||||||| |||||||||||||||||
gtctttaaatataaaaatttcatgcctttgattttggaagtgtatatatgcttttttttctatctttttgtttccagatgttgataagatatgtatttt--ctcaattggtttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAGAGGTTCTCGGATATGCCTCCAAGGTGGTGCTCACCAAGGATACAACCAC
















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|351017572|gb|FQ435925.1|FQ435925
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAAACAAAGCTGAGAAAG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAA-G
EST: gi|351022937|gb|FQ428846.1|FQ428846
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|110701933|gb|EE080073.1|EE080073
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|110686609|gb|EE064441.1|EE064441
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|351036299|gb|FQ458674.1|FQ458674
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACGTTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|34550178|gb|CF518396.1|CF518396
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAAGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|110713396|gb|EE089279.1|EE089279
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAANG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|349807747|gb|FQ402138.1|FQ402138
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|351034062|gb|FQ447979.1|FQ447979
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|30256318|gb|CB972161.1|CB972161
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAAGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|349815356|gb|FQ400511.1|FQ400511
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
EST: gi|34549838|gb|CF518070.1|CF518070
EST:     TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAG                         GAACTGTAATTAGAGATGAAGTGGGGCTCACCCTAGACAAAGCTGAGAAGG
genomic: TGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatag ... gagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcggcttcatatgtattcacaatgctgacattttactctaatgagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGGAGGTTTTAGGCCATGCTGCAAAGGTGGTGCTTACCAAGGATACAACCAC
           atatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgcccttttaatagtggattagtggtcttatttatttggttgttttcggcttcatatgtattcacaatgctgacattttactctaatgagcttgtagGAACTGTAATTAGAGATGAGGTGGGGCTCACCCTAGACAAAGCTGAGAAGGAGGTTTTAGGCCATGCTGCAAAGGTGGTGCTTACCAAGGATACAACCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- -tgccctt
- - - - - - - - - - - - - - - - - - - -tggttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgct