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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcccttttttactcgaatttgttccttggttaatgtgggttcagttggcaaattttatttggtaatgtttactattttcaaactttttaccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG

Basic information

species Vitis vinifera
transcript Vv09s0070g00050.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0070g00050.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G139900_T01 (Zea mays), 3'ss of exon 2
--tgcccttttttact-cgaatttgttccttggttaatgtgggttcagttg-gcaaattttatttggtaatgtttactattttcaaactttttaccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG
  |   |  |||   |  |  ||  ||| |   |   ||||  |||  ||     || |||      | ||  | || || | ||    ||| || || ||||| | || |||||||||||||| || ||||| ||||| || || |||||||||||||| || || |||
tttaatccatttagttgtgtgttgattcttcactagctgtgtattcttttatatgaactttggcct-tgatcgtaacaatctcca---ctttcactccttgcagCTTTGCAAGATTGACTCCGAGGGCAAGGCAAGGAAGGTTGTAGGCTGCTCCTGTGTCGTTGTCAAG
















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|110387824|gb|EC952522.1|EC952522
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|110376453|gb|EC941520.1|EC941520
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCTGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|71865806|gb|DT014861.1|DT014861
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|110429605|gb|EC996101.1|EC996101
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|71865795|gb|DT014850.1|DT014850
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|37188974|gb|CF608323.1|CF608323
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGATTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|37188719|gb|CF608068.1|CF608068
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCTGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|37184989|gb|CF604342.1|CF604342
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCTGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|110400406|gb|EC966968.1|EC966968
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|37188353|gb|CF607702.1|CF607702
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCTGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
EST: gi|110381781|gb|EC935368.1|EC935368
EST:     TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGG                         TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC
genomic: TTAGCTTGATAACTGTTCCTAGTGCTAAGACGCTGGGCGAGTGGGCTGGGgtaagttaaa ... ccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcaaattttatttggtaatgtttactattttcaaactttttaccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG
                                      ctttttacccc  CT-rich tract
     aaattttatttggtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcccttttttactcgaatttgttccttggttaatgtgggttcagttggcaaattttatttggtaatgtttactattttcaaactttttaccccatgcagTTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
tgccctt
- - - - - - - - - - - ttccttg
- - - - - - - - - - - - - - - - - -gtgggtt
- - - - - - - - - - - - - - - - - - - - - cagttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaact