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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacactccacacacaagtgatccaggtgattttacttttgagggatttttgggttgacctgcttccttgggcttgttttcag

Basic information

species Vitis vinifera
transcript Vv09s0070g00050.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0070g00050.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G139900_T01 (Zea mays), 5'ss of exon 3
TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgta---tgacactcca-------cacacaagtgatccaggtgattttacttttgagggatttttgggttgacctgcttccttgggcttgttttcag
 | || |||||||||||||| || ||||| ||||| || || |||||||||||||| || || ||||||   |  || |||        |  |||| | |   |  |   ||||| || | |  | |     |        ||   |        ||  |||
CTTTGCAAGATTGACTCCGAGGGCAAGGCAAGGAAGGTTGTAGGCTGCTCCTGTGTCGTTGTCAAGgtagcatatcaatcccttactttcctacaaattaattattttggtttaccttagggcaagtaacatgacatttcactgtttcatttcaattaccag
















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:     CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
EST: gi|110376453|gb|EC941520.1|EC941520
EST:     CTGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
EST: gi|71865806|gb|DT014861.1|DT014861
EST:     CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
EST: gi|110429605|gb|EC996101.1|EC996101
EST:     CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
EST: gi|71865795|gb|DT014850.1|DT014850
EST:     CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
EST: gi|37188974|gb|CF608323.1|CF608323
EST:     CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGA
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGA
EST: gi|37188719|gb|CF608068.1|CF608068
EST:     CTGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTT
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTT
EST: gi|37184989|gb|CF604342.1|CF604342
EST:     CTGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
EST: gi|110400406|gb|EC966968.1|EC966968
EST:     CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
EST: gi|37188353|gb|CF607702.1|CF607702
EST:     CTGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCA
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCA
EST: gi|110381781|gb|EC935368.1|EC935368
EST:     CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAG                         GACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG
genomic: CCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacact ... ttgttttcagGACTTTGGGGAGGAAACTGAAGCTATGAATGTTGTCCAGCAGCAGGTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGTAAGATTGACTCCGAAGGGAAGGCCAGGAAAGTGGTGGGCTGCTCCTGTGTTGTCGTTAAGgtatgacactccacacacaagtgatccaggtgattttacttttgagggatttttgggttgacctgcttccttgggcttgttttcag

- - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - -  GCTGCT