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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcagttccagtcgtcaaagataaactattggactactcgtcaaaaaaaaaaaaagcaattggactgatggatgtgttgcattttatattgtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT

Basic information

species Vitis vinifera
transcript Vv03s0063g00480.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g00480.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g54780.1 (Oryza sativa), 3'ss of exon 1
----ttcagttccagtcgtcaaagataaactattggactactcgtcaaaaaaaaaaaaagcaattggactgatggatgtgttgcattttatattg-tatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT
    ||   | | |    | || |   |  |  || |  | |  ||||      ||   | |  ||  || ||| ||||    |  | | |  || | || |||||| || ||||||||||| |||||   |||||| ||||| ||||| ||||| || || || || |||||||| |||||||||||  |||| |  |||||||
taactttcttgctaa--attaatgcctacatgctgcataattattcaatttgttaa---gtatatgtccttatgtatgttcctctatatgttctgattttcccagGTAACAGAGAATGGGAAGCAAGAAAAGCATCTTGTTGCGACAGTTGGCAAATTTAGTGTCATTTGGAACTTTCAGCAGGTGAAGGACAGCAACCATGAGT

upper sequence: Vv03s0063g00480.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G363474_T02 (Zea mays), 3'ss of exon 2
-ttcagttccagtcgtcaaagataaactattggactactcgtcaaaaaaaaaaaaagcaattggactgatggatgtgttg-cattttatattgtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT
 |    ||  |      ||| |  |  ||    || || |  ||  |    | |     ||| |  ||     || | |  | |   ||  |   |   |||||||| ||||| ||||| || |||||||||||||| || || ||||| |||| ||||||| | |||||||||| ||||||||| |||||    || ||||
ctctgatttaacaaaaaaaaaaccagttaccc-accacccagcatgagcggacatgtgcatttg-ttggcatttgagctctcgtccaatgattgttgcgcagGTGACGGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCGACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCCTGCAGGTGAAGAACAGCCACCACGAGT

upper sequence: Vv03s0063g00480.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G131638_T01 (Zea mays), 3'ss of exon 3
ttcagttccagtcgtcaaagataaactattggactactcgtcaa--aaaaaaaaaaagcaattggactgatggatgtgttgcattttatattgtatttcc--agGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT
     |   | |   | ||  |  | | |  || ||      |   |  |   |  ||||   | | |  | ||  | |||    | ||    |  || |  ||||||| ||||| ||||| || |||||||||||||| || || ||||| |||| ||||||| | |||||||||  ||||||||| |||||    || ||||
---gctagaaatatcccaaactctattctctgattaacaaaaacccattacccaccagcatgagcattcgttgacat-ttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT

upper sequence: Vv03s0063g00480.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G33490.1 (Glycine max), 3'ss of exon 1
ttcagttccagtcgtcaaagataaactattggactactcgtcaaaaaaaaaaaaagcaattggactga--tggatgtgttgcattt-tatattgtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT
   |  |       |   |||   |  || |   || | ||  |   |   ||    | ||| |   |  || | || |  ||||| | | ||    || ||||| ||||||||||| |||||||| || || || |||||||| ||||||||||| || ||||||||| | || ||||||||||| ||||||  |||||| |
gaaaagtatgcatattttagactgatcatag--ttagtagtttaccgagtcaatta-acttgcagcaacctgcaagtatctcatttgtgtttttgtctttcagGTCACTGAGAATGGTAAACAAGAACGCCACCTTGTTGCAACTGTGGGCAAGTTTAGTGTGATATGGGATTTTCAGCAGGTGAAGAACAGTGCTCATGAAT

upper sequence: Vv03s0063g00480.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G14960.1 (Glycine max), 3'ss of exon 1
ttcagttccagtcgtcaaagataaactattgg--actactcgtcaaaaaaaaaaaaagcaattggactga--tggatgtgt-tgcattttatattgtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT
    |    ||     | |  ||||||  ||   | || | ||  |   |    |   |  ||| |   |  || | || | ||   | | | ||    || ||||| ||||||||||| |||||||| || || || ||||| || ||||||||||| || ||||||||| | || |||| |||||| ||||||   ||||| |
----gaattagaaaatatatgtaaactgatgataattagtagtttaccgagtccattacc-ttgcagcaacctgcaagtatctgacctgtgtttttgtctttcagGTCACTGAGAATGGTAAACAAGAACGCCACCTCGTTGCGACTGTGGGCAAGTTTAGTGTGATATGGGATTTTCAGCGGGTGAAGAACAGTGCACATGAAT

upper sequence: Vv03s0063g00480.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G19240.1 (Arabidopsis thaliana), 3'ss of exon 1
ttcagttccagtcgtcaaagataaactattggactactcgtcaaaaaaaaaaaaagcaattggactgatggatgtgttgcattttatattgtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT
 | |||| || |        | | | ||||    |  || | | |      |      ||   ||  |      |  |   | || | |  | ||| ||||| ||||||| ||| || |||||| | ||  |||| ||||||||||| || ||||| ||||||||| ||||  ||| |||||| ||||||   || || |
gtaagtttcacttc------acacattattactgtcttcctaagattcttgattgtttataaaaccaaatctcattgtctttgttgtgtattgtttgcagGTAACTGAGAGTGGAAAGCAAGAGAGACACATAGTAGCAACAGTGGGGAAATTCAGTGTGATATGGGACTTGGAGCGGGTGAAGAACAGTGCACACGAAT

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|110379909|gb|EC945133.1|EC945133
EST:     CACATATGGCTGGGGTGGATAATAAATTTCACGGTGGCCAATTTTCATGG                         GTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAG
genomic: CACATATGGCTGGGGTGGATAATAAATTTCACGGTGGCCAATTTTCATGGgtaagttgat ... gtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAG
EST: gi|161716247|gb|FC066849.1|FC066849
EST:     CACATATGGCTGGGGTGGATAATAAATTTCACGGTGGCCAATTTTCATGG                         GTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAG
genomic: CACATATGGCTGGGGTGGATAATAAATTTCACGGTGGCCAATTTTCATGGgtaagttgat ... gtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaaaaaagcaattggactgatggatgtgttgcattttatattgtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT
                 gactgat  putative branch site (score: 3)
                                              tatttcc  putative PPT
                                   attttatattgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcagttccagtcgtcaaagataaactattggactactcgtcaaaaaaaaaaaaagcaattggactgatggatgtgttgcattttatattgtatttccagGTGACTGAGAATGGGAAACAAGAGCGGCATCTAGTTGCAACAGTGGGCAAGTTCAGCGTGATATGGAACTTCCAGCAGGTGAAAAACAGTAGTCATGAGT

- - - - - - - - - -gataaac
- - - - - - - - - - - - - - - - - - - - -caaaaaa
- - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgtg