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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttgtacttaagttattgttcttttgttttcagcaacatttttgtttttcaacagaagacaatgtgtatcattttgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG

Basic information

species Vitis vinifera
transcript Vv04s0008g05480.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G07190.1 (Glycine max), 3'ss of exon 6
--gtttgttttgtacttaagttattgttcttttgttttcagcaacatttttgtttt--tcaa--cagaagacaatgtgtatcattttgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG
     |  ||  || ||  | |  ||  ||||| | ||   | |   |||  ||||  ||||  || |    ||      | |||||| ||| |||||||| ||||| ||||||||||||| ||| ||||||||| | |||  || |||||||||||| ||  |||||
gtaaataattattattt--gcttctgc-cttttatgttgcacgagggtttcattttgatcaactcatagtttaaaaaaagttattttggtggccagTTCTACACTAAGCTTGAGGAAAAGATTCACGCAAAGGAAGTGGAGGAGAGTAACTTGCAAGCAAAAACCAAG

upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G07100.1 (Glycine max), 3'ss of exon 6
--gtttgttttgtacttaagttattgttcttttgttttcagcaacatttttgtttttcaa---cagaagacaatgtgtatcattttgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG
     |  ||  |||||  | |  ||   |||   || ||  |   ||| | ||    ||   |||     ||    | | |||||| ||| |||||||| ||||| ||||||||||||| |||||| |||||| | |||  || |||| ||||||| ||  |||||
gtaaataattattactt--gcttctgccttttgtgttacatgagggtttcttttggataaactcagttttaaaaaaatgttattttggtggccagTTCTACACTAAGCTTGAGGAAAAGATTCATGCTAAGGAAGTGGAGGAGAGTAACCTGCAAGCAAAAACCAAG
















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|110711956|gb|EE089029.1|EE089029
EST:     CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAG                         TTCTATACTAAACTTGAGGAAAAGACTCATGCNAAGGAAATAGAGCGGACT
genomic: CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAGgtttgttttg ... tgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
EST: gi|110732118|gb|EE107126.1|EE107126
EST:     CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAG                         TTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
genomic: CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAGgtttgttttg ... tgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
EST: gi|37183656|gb|CF603010.1|CF603010
EST:     CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAG                         TTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
genomic: CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAGgtttgttttg ... tgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
EST: gi|110372845|gb|EC937039.1|EC937039
EST:     GAGAAAAGAAGAGAG                         TTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
genomic: GAGAAAAGAAGAGAGgtttgttttg ... tgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
EST: gi|110713754|gb|EE089952.1|EE089952
EST:     CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAG                         TTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
genomic: CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAGgtttgttttg ... tgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACT
EST: gi|294964234|gb|GW838037.1|GW838037
EST:     CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAG                         TTCTATACTAAACTTGAGGAAAAGACTCATGGCAA-GGAAATAGAGCGGAC
genomic: CCTACAATTTCAGCTTTAGGTGTGATGAACGAGCTGAGAAAAGAAGAGAGgtttgttttg ... tgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATG-CAAAGGAAATAGAGCGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagcaacatttttgtttttcaacagaagacaatgtgtatcattttgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG
                                       tcatttt  CT-rich tract
     aacatttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttttgtacttaagttattgttcttttgttttcagcaacatttttgtttttcaacagaagacaatgtgtatcattttgttgggcagTTCTATACTAAACTTGAGGAAAAGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT