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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttattggtacttgtgatttgattcatttgaaggggcaatccatgttgttttgtgcctaaatattctgtgagttaaaaacttgcggatggatttaaatggtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGCTACCGTTCTTTTCCTATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT

Basic information

species Vitis vinifera
transcript Vv08s0040g02640.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
gtaagtatttattggtacttgtgatttgattcatttgaaggggcaatccatgttgttttgtgcctaaatattctgtgagttaaaaacttgcggatggatttaaatggtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGCTACCGTTCTTTTCCTATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT
                    || | |  ||     | |||  |        | | |  | | | |   | ||   |||  | |     ||    || |||   ||| | |   ||||| |||||||||||||| |||||| |||| || ||||| || || || ||||||||||| ||||||||||| ||||| || ||  ||| ||||||| | |
--------------------gtaagtgaatatgcgtcaagaag--------gctatactttacttg--tttttgatga--tcaggttatgatattgaatt--gatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT

upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 5
gtaagtatttattggtacttgtgatttgattcatttgaaggggcaatccatgttgttttgtgcctaaatattctgtgagttaaaaa-cttgcggatggatttaaatggtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGCTACCGTTCTTTTCCTATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT
|||||||||||||| || |||| |||| ||| | |   |||   |||   | ||   |  ||| |||||||||||||||||||||| |||||||||||||||||||||||| | ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||| |||||||||||||||
gtaagtatttattgatatttgtaatttaattaaatgacagg---aatgtctattcaatcatgcttaaatattctgtgagttaaaaaacttgcggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTATCGTTCTTTTCCTATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT

upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 3
gtaagtatttattggtacttgtgatttgattcatttgaaggggcaatccatgttgttttgtgcctaaatattctgtgagtt-aaaaacttgcggatggatttaaatggtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGCTACCGTTCTTTTCCTATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT
|||||||||||||| || |||| |||||||| | | |||||                 ||||| |   |||  || ||||| ||||||||| ||||||||||||||||||| | ||||| ||||||||||||||||||||||||||||||||||||||||||||||  || ||||||||  | |||||||||||||||||| |||||||||||||||
gtaagtatttattgatatttgtaatttgattaaat-gaaggaa---------------tgtgcat---tatcatgcgagttgaaaaacttgtggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAATTATCGTTCTTTATCAATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT

upper sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 7
gtaagtatttattggtacttgtgatttgattcatttgaaggggcaatccatgttgttttgtgcctaaatattctgtgagttaaaa--acttgcggatggatttaaatggtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGCTACCGTTCTTTTCCTATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT
    |||  |  || ||| | | ||||||    ||||| |||  ||| ||  ||  ||   ||| |||| || ||||||||||||  ||||||| |||| |||||||||||| | ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||
----gtaagtgctgttaccttt-atttgacaagtttgaggggaaaatgca-atttcttcacgcccaaatgttatgtgagttaaaagaacttgcgcatgggtttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTACCGTTCATTTCCCATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT

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|352774223|gb|FQ474746.1|FQ474746
EST:     TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT                         GTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGC
genomic: TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATTgtaagtattt ... gtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGC
EST: gi|352789724|gb|FQ476322.1|FQ476322
EST:     TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT                         GTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGC
genomic: TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATTgtaagtattt ... gtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGC
EST: gi|71860081|gb|DT009136.1|DT009136
EST:     TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT                         GTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGC
genomic: TTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATTgtaagtattt ... gtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctaaatattctgtgagttaaaaacttgcggatggatttaaatggtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGCTACCGTTCTTTTCCTATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT
 gcctaaa  putative branch site (score: 3)
                  ttaaaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttattggtacttgtgatttgattcatttgaaggggcaatccatgttgttttgtgcctaaatattctgtgagttaaaaacttgcggatggatttaaatggtttgagcagGTCTTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAGCTACCGTTCTTTTCCTATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT