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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttcttcaatcctttgtgtgggaaaccatttttaagccttatttttagtcaatagaacttctaaatcatattgaatgcaaccatgtgagacctctgctattttcattttgcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG

Basic information

species Vitis vinifera
transcript Vv05s0020g04880.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G34780.4 (Glycine max), 3'ss of exon 5
gtagttcttcaatcctttgtgtgggaaaccatttttaagccttatttttagtcaatagaacttctaaatcata--ttgaatgcaaccatgtgagacctctgctattttcattttgcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG
                    ||   ||    | | | ||  |   |||   |  ||||   |||  |||| ||  |  |||  |    ||   |  | || | ||                 |||||||||| || || ||||||||||| || ||| |||| |||||||| || ||| ||||||| |||||||||
--------------------gtaacaacttgtatattagt-tagctttgtttggatagcttttcctaatcctacctcaaattgattggtgcatggtcccttccat-----------------agTTTTATTCAAAATTAGAGGAAAAGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG

upper sequence: Vv05s0020g04880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G32860.1 (Glycine max), 3'ss of exon 4
gtagttcttcaatcctttgtgtgggaaaccatttttaagccttatttttagtcaatagaacttctaaatcata--ttgaatgcaaccatgtgagacctctgctattttcattttgcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG
                    ||   ||    | | | ||  |   |||   |  |||||  |||  |||| ||  |  |||  |    ||   |  | || |                  |||||||||| | || || ||||||||||| || ||| |||| |||||||| || ||| ||||||| |||||||||
--------------------gtaacaacttgtatattagt-tagctttgtttggatagattttcctaatcctacctcaaattgattggtgcatggtcccttcc-----------------ttagTTTTATACAAAATTAGAGGAAAAGCAGCAAGCAATGGAAGCTGAGAAGAATCAAAGTGAAGCTAGGACCAAG
















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|351046932|gb|FQ454542.1|FQ454542
EST:     CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAG                         TTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
genomic: CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAGgtagttcttc ... gcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
EST: gi|110374005|gb|EC938470.1|EC938470
EST:     CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAG                         TTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
genomic: CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAGgtagttcttc ... gcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
EST: gi|351029994|gb|FQ430736.1|FQ430736
EST:     CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAG                         TTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
genomic: CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAGgtagttcttc ... gcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
EST: gi|349821897|gb|FQ413068.1|FQ413068
EST:     CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAG                         TTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
genomic: CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAGgtagttcttc ... gcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
EST: gi|110719141|gb|EE096774.1|EE096774
EST:     CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAG                         TTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
genomic: CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAGgtagttcttc ... gcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
EST: gi|351033942|gb|FQ462997.1|FQ462997
EST:     CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAG                         TTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
genomic: CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAGgtagttcttc ... gcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
EST: gi|30298916|gb|CB975710.1|CB975710
EST:     CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAG                         TTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC
genomic: CATCAGCTCCTGTATTTAGATGCACTGCTCGTGCAGAAAAACGGAAGGAGgtagttcttc ... gcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatattgaatgcaaccatgtgagacctctgctattttcattttgcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG
                                 tattttcattttgcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttcttcaatcctttgtgtgggaaaccatttttaagccttatttttagtcaatagaacttctaaatcatattgaatgcaaccatgtgagacctctgctattttcattttgcaattttagTTTTATTCGAAGTTGGAGGAAAAGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG