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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccttcactctgttagcttttgtcctacctttgatctacatggctcttataccccttttttcttttcttctttgtatctgtaatgtgtttaaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGATGATCCAAACGGCAAGGTTGGTGTGACTGGAAGCGGGAAAGGATTGACAG

Basic information

species Vitis vinifera
transcript Vv12s0035g01830.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01830.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G00560.2 (Glycine max), 3'ss of exon 8
tccttcactctgttagcttttgtcctac-ctttgatctacatggctcttataccccttttttcttttcttctttgtatctgtaatgtgtttaaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGATGATCCAAACGGCAAGGTTGGTGTGACTGGAAGCGGGAAAGGATTGACAG
|  | ||  |   |   ||     | |  |||  ||  |  | |     ||   | |||||    |  |  | || |  |    ||  |||  || | |||||||||||||| || ||  | || || || || || || || ||||||||||||||  | || |||||||||||||| ||||| |||||||| |||||||
ttttgcatacaacttatttgctcacaatgcttaaatagagtttggaacaatgatcttttttgtcctgatattatgcaa-tactttggctttgcatgcacagATTGGTTTCTTCTCTGGAAGAAAACGGGAGAGTATTTTTAAATCTCCTGATGATCCTCAGGGAAAGGTTGGTGTGACGGGAAGTGGGAAAGGTTTGACAG

upper sequence: Vv12s0035g01830.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G40240.1 (Glycine max), 3'ss of exon 7
-tccttcactctgttagcttttgtcctacctttgatctacatggctcttataccccttttttcttttcttctttgtatctgtaatgtgtttaaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGATGATCCAAACGGCAAGGTTGGTGTGACTGGAAGCGGGAAAGGATTGACAG
 |  ||   | |   | |||   | ||  |  || |  |  ||  | |   ||     | || | ||||  | |    |  || | ||  |    |  |||||||||||||| || ||  | || || || || || || || ||||||||||||||  | || |||||||||||||| ||||| |||||||| |||||||
gtgtttttgtatac-aacttagttgcttacaatgcttaaactgagtttgtaacgatgatcttttgttctgatatcatgcaatactttggctttgcttacagATTGGTTTCTTCTCTGGAAGAAAACGGGAGAGTATTTTTAAATCTCCTGATGATCCTCAGGGAAAGGTTGGTGTGACGGGAAGTGGGAAAGGTTTGACAG
















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|32272108|gb|CD721267.1|CD721267
EST:     GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAG                         ATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
genomic: GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAGgtgtgttggg ... aaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
EST: gi|45771787|gb|CN007639.1|CN007639
EST:     GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAG                         ATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
genomic: GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAGgtgtgttggg ... aaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
EST: gi|32271783|gb|CD720942.1|CD720942
EST:     GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAG                         ATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
genomic: GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAGgtgtgttggg ... aaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
EST: gi|30327885|gb|CD011147.1|CD011147
EST:     GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAG                         ATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
genomic: GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAGgtgtgttggg ... aaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
EST: gi|30252727|gb|CB970278.1|CB970278
EST:     GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAG                         ATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
genomic: GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAGgtgtgttggg ... aaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
EST: gi|30323816|gb|CD007078.1|CD007078
EST:     GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAG                         ATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
genomic: GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAGgtgtgttggg ... aaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
EST: gi|30129723|gb|CB915062.1|CB915062
EST:     GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAG                         ATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
genomic: GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAGgtgtgttggg ... aaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
EST: gi|83275932|gb|DV939940.1|DV939940
EST:     GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAG                         ATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT
genomic: GGCAGAATGCTTGGCAGCAGTTCCAGACAACCAAAGGAAGGGCTAAAAAGgtgtgttggg ... aaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttataccccttttttcttttcttctttgtatctgtaatgtgtttaaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGATGATCCAAACGGCAAGGTTGGTGTGACTGGAAGCGGGAAAGGATTGACAG
                                                ttccc  CT-rich tract
                                   taatgtgtttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccttcactctgttagcttttgtcctacctttgatctacatggctcttataccccttttttcttttcttctttgtatctgtaatgtgtttaaattcccagATTGGTTTCTTTTCGGGCCGCAAGCGAGAAAGCATCTTCAAGTCTCCTGATGATCCAAACGGCAAGGTTGGTGTGACTGGAAGCGGGAAAGGATTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
-ccttcac
- - - - -ctgttag
- - - - - - - - - - - -cctacct
- - - - - - - - - - - - - - - - - - tacatgg