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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtttgtgaatttgtttgagttgccttgtgttccttttttttttccttccttctttactggtatttgaccttacctttgtttgtaaattcaaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGGGATCACAAGGATCTGGTATCTAGGTGGGCTGTCTTACAGGAGACACGTG

Basic information

species Vitis vinifera
transcript Vv06s0004g02280.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 1
----cagtttgtgaatttgtttgagttgccttgtgttcctt--ttttttttccttccttctttactggtatttgaccttacctttgtttgtaaattcaaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGGGATCACAAGGATCTGGTATCTAGGTGGGCTGTCTTACAGGAGACACGTG
    || |||| |  |    || |||||     || |  |   ||||  ||  || | |||||  |  | | ||||  |     | ||      ||    ||||||||||||| ||  || || ||||| || ||| | ||||||||||| || || ||||| |||||  |||| || |||||||||||  |||||||||| ||||
atgtcattttgcgggtcatgttcagttgtgcaatgctgttcagttttgcttttttgcctcttt-ttaatttgtgactgtgttggtctt-----gttttgttttcagAAACAAGTTGTCAAGAAAGATGTGTTCCAGGTTTTTGCTGAGAAGGTTAGAGATCATAAGGAATTGGTTTCAAGGTGGGCTGTTCTACAGGAGACGCGTG

upper sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G20920.1 (Arabidopsis thaliana), 3'ss of exon 1
cagtttgtgaatttgtttgagttgccttgtgttccttttttttttccttcctt--ctttactggt--atttgaccttacctttgtttgtaaattcaaatt-tcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGGGATCACAAGGATCTGGTATCTAGGTGGGCTGTCTTACAGGAGACACGTG
     | ||||||| ||||  ||| | |  || |  ||   |  |  | | ||   |||| || |  || ||  |  |   || ||  |   || |  ||   |||| |||||||  || ||||||  |||||||||||||||||||||||| || || |||||||   | | ||| || ||||||||  |  || |  |||| |
-----tttgaatttttttgttttggccttggtactgttaaatgatgatcctttgcatttagtgattgatatgctcaaatgcttattgttgtctttactttactagAAGCAAGCTGTGAAGAAGGATAGTTTTCAGTTGTTTGCTGAGAAAGTTAGAGACCACAAGGGATTAGAATCCAGATGGGCTGTTATGGAGCAAGCACGAG

upper sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G20920.2 (Arabidopsis thaliana), 3'ss of exon 1
cagtttgtgaatttgtttgagttgccttgtgttccttttttttttccttccttc--tttactggt--atttgaccttacctttgtttgtaaattcaaatt-tcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGGGATCACAAGGATCTGGTATCTAGGTGGGCTGTCTTACAGGAGACACGTG---
        |||||| ||||  ||| | |  || |  ||   |  |  | | ||   |||| || |  || ||  |  |   || ||  |   || |  ||   |||| |||||||  || ||||||  |||||||||||||||||||||||| || || |||||||   | | ||| || ||||||||  |  || |  |||| |   
--------gaatttttttgttttggccttggtactgttaaatgatgatcctttgcatttagtgattgatatgctcaaatgcttattgttgtctttactttactagaagCAAGCTGTGAAGAAGGATAGTTTTCAGTTGTTTGCTGAGAAAGTTAGAGACCACAAGGGATTAGAATCCAGATGGGCTGTTATGGAGCAAGCACGAGTTG

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|37189156|gb|CF608505.1|CF608505
EST:     GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGG                         AAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
genomic: GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGGgtttgctctt ... caaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
EST: gi|110711779|gb|EE088644.1|EE088644
EST:     GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGG                         AAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
genomic: GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGGgtttgctctt ... caaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
EST: gi|110712755|gb|EE088078.1|EE088078
EST:     GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGG                         AAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
genomic: GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGGgtttgctctt ... caaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
EST: gi|161713701|gb|FC062841.1|FC062841
EST:     GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGG                         AAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
genomic: GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGGgtttgctctt ... caaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
EST: gi|110711813|gb|EE088718.1|EE088718
EST:     GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGG                         AAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
genomic: GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGGgtttgctctt ... caaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
EST: gi|33406482|gb|CF212109.1|CF212109
EST:     GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGG                         AAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG
genomic: GATCTTTACAAAATGGCATCAGAGATTCCAACTCCGACACTCCTCCCAGGgtttgctctt ... caaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttccttctttactggtatttgaccttacctttgtttgtaaattcaaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGGGATCACAAGGATCTGGTATCTAGGTGGGCTGTCTTACAGGAGACACGTG
                       accttac  putative branch site (score: 3)
                               tttgtttgtaaattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtttgtgaatttgtttgagttgccttgtgttccttttttttttccttccttctttactggtatttgaccttacctttgtttgtaaattcaaatttcagAAACAAGCTGCAAAAAAGGATGTTTTTCAGTTGTTTGCTGAGAAAGTGAGGGATCACAAGGATCTGGTATCTAGGTGGGCTGTCTTACAGGAGACACGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - tgccttg