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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACATTGGAATACCTCCACCTGATGTTTGTGTTGGAACACCTCGTTGGATGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaaatttctcatccattgagtttttaaactatctatctatctatatgtatgtatgtatctgtatatatatatatatatatatatacctgtgtaaaatta...

Basic information

species Vitis vinifera
transcript Vv05s0020g04180.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04180.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G155312_T01 (Zea mays), 5'ss of exon 8
ACACATTGGAATACCTCCACCTGATGTTTGTGTTGGAACACCTCGTTGGATGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaa--atttctcatcca-ttgagtttttaaactatctatctatctatatgtatgtatgtatctgtatatatatatatatatatatatacctgtgtaaaatta
 ||  |||| | ||  ||||||||||||||||||||||||||| |||||||||| || |||||  |   ||| |||||| ||    |    ||||| |||||||  |||| | |   | ||  | ||||    |||  ||   | |   | | |   | |   ||  | |   |   | |   | |     |||    |    
TCAGCTTGGTACACACCCACCTGATGTTTGTGTTGGAACACCTTGTTGGATGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTGgtaagaatttgttagataattatggttttgttttattcatgattttggctctgttattctgcatgcttgttggtgagtttggttgttattttgttctcag---
















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|110358405|gb|EC922592.1|EC922592
EST:     TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTG                         GAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
genomic: TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaaatttct ... ctggctgcagGAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
EST: gi|110419083|gb|EC985277.1|EC985277
EST:     TGGCACCTGAGGTGCTGCAGGCAATGCATAAACGGGAGATATACGGGCTG                         GAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
genomic: TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaaatttct ... ctggctgcagGAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
EST: gi|110363558|gb|EC927155.1|EC927155
EST:     TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTG                         GAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
genomic: TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaaatttct ... ctggctgcagGAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
EST: gi|110701353|gb|EE078829.1|EE078829
EST:     TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTG                         GAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
genomic: TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaaatttct ... ctggctgcagGAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
EST: gi|161718798|gb|FC068610.1|FC068610
EST:     TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTG                         GAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
genomic: TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaaatttct ... ctggctgcagGAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
EST: gi|18458191|gb|BM436469.1|BM436469
EST:     TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTG                         GAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG
genomic: TGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaaatttct ... ctggctgcagGAAGTGGATATTTGGTCATATGGGTGTCTCCTCTTGGAACTATTGACTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACATTGGAATACCTCCACCTGATGTTTGTGTTGGAACACCTCGTTGGATGGCACCTGAGGTGCTGCGGGCAATGCATAAACGGGAGATATATGGGCTGgtaaatttctcatccattgagtttttaaactatctatctatctatatgtatgtatgtatctgtatatatatatatatatatatatacctgtgtaaaatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT