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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgctctctgaaaccattagtcattatcttaataaaccattatgaacttagtaactggtattgttttgcag

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 13
ATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgctctctgaaaccattagtcattatcttaataaaccattatgaactta-gtaactggtattgttttgcag
|| || ||  |||||||||| |||||||||      || |||||||| ||||| || ||||||||||| ||||| ||||| ||||||||||||||  ||| |  |   || | ||       ||||||  |       |    || || | || |    || ||||||||
ATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGAgtaatgtttcatttaaaacctat-----gctatcttgttggctatgtggatacatatgcaattaactttcttttgcag

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 14
ATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgctctctgaaaccattagtcattatcttaataaaccattatgaactta-gtaactggtattgttttgcag
|| || ||  |||||||||| |||||||||      || |||||||| ||||| || ||||||||||| ||||| ||||| ||||||||||||||  ||| |  | | |||||| |      ||| ||  |       |    || || | || |    || ||||||||
ATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGAgtaatgtttcatt-taaaaccaatg----ctatattgttggctatgtggatacatatgcaattaactttattttgcag

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 18
ATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgctctctgaaaccattagtcattatcttaataaaccattatgaactta-gtaactggtattgttttgcag
|| || ||  |||||||||| |||||||||      || |||||||| ||||| || ||||||||||| ||||| ||||| ||||||||||||||  ||| |  |   || | ||       ||||||  |   |   |    || || | || |    || ||||||||
ATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGAgtaatgtttcattaaaaacctat-----gctatcttgttggccatgtggatacatatgcaattaactttcttttgcag

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 12
ATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgctctctgaaaccattagtcattatcttaataaacc------attatgaactta---gtaactgg-tattgttttgcag
|| |||||| |||||||||| ||||||||||    ||| ||||| || ||||| ||  |||||||||| ||||| |||||||||||||||| |||  ||| |  | | || | |  |    |||||||||| |         ||| |  |   |     || | | | || ||||||||
ATCATTTTTCTGGAAACAATATGCAATGATGTAGACATAATTGAGAGGAATATTCGCTTTAAAATTCAGCAAAGTCCTGACTATGCAGAAGTgtaatgtttccttttaaaccaacgacatcttatcttaatgagtatatggaattgtagatacatatacaattagcttttcttttgcag

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 12
ATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggt-tgctctctgaaaccattagtcatt-atcttaataaaccattatgaacttagtaactggtattgttttgcag
|| |||||| |||||||| | ||||||||||||||||||||||||||||| |||||||| ||||| || ||||| ||||||||| ||||||||||   |   | ||||  ||| | || |   |  || |  |  ||     | |||| |||   |  |  |  | |||||
ATCATTTTTCTGGAAACACTATGCAATGATGAGCGCATTATTGAAAGAAACATACGTCTAAAAATCCAGCAAAGTCCTGACTATTCAGAAGAgtactatgctcgctctataactaatattttctcgtcctctttcacgg--gtcaactgagt---ttatgctactctgcag

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|30322291|gb|CD005553.1|CD005553
EST:     GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA                         GCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
genomic: GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgc ... tgttttgcagGCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
EST: gi|30321972|gb|CD005234.1|CD005234
EST:     GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA                         GCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
genomic: GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgc ... tgttttgcagGCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
EST: gi|27580319|gb|CB003014.1|CB003014
EST:     GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA                         GCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
genomic: GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgc ... tgttttgcagGCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
EST: gi|27581545|gb|CB004240.1|CB004240
EST:     GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA                         GCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
genomic: GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgc ... tgttttgcagGCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
EST: gi|27580309|gb|CB003004.1|CB003004
EST:     GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA                         GCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
genomic: GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgc ... tgttttgcagGCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
EST: gi|32250239|gb|CD716058.1|CD716058
EST:     GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA                         GCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
genomic: GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgc ... tgttttgcagGCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
EST: gi|30321898|gb|CD005160.1|CD005160
EST:     GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA                         GCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
genomic: GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgc ... tgttttgcagGCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
EST: gi|30321402|gb|CD004664.1|CD004664
EST:     GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGA                         GCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA
genomic: GAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgc ... tgttttgcagGCCTGACTTTGAAGCTGGATTACAGGACTTCAAAATTCGATTAGCAAATTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTATTTTTTTGGAAACAATCTGCAATGATGAGCGCATTATTGAAAGAAATATACGTCTTAAAATTCAACAAAGCCCTGACTATGCAGAAGAgtatggttgctctctgaaaccattagtcattatcttaataaaccattatgaacttagtaactggtattgttttgcag

- - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - AAGAAA