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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtaaagcataaaatgttctggacaagtggaatgattttgttccataattttattcagcttatttttctcaacataagcaattttctccacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG

Basic information

species Vitis vinifera
transcript Vv00s0566g00010.t01
intron # 1
splice site 3'
intron type U2

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|110391556|gb|EC956538.1|EC956538
EST:     CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAG                         GGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
genomic: CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAGgtaaaacttt ... cacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
EST: gi|110425102|gb|EC991479.1|EC991479
EST:     CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAG                         GGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
genomic: CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAGgtaaaacttt ... cacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
EST: gi|28966816|gb|CB345849.1|CB345849
EST:     GAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAG                         GGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
genomic: GAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAGgtaaaacttt ... cacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
EST: gi|110718544|gb|EE095497.1|EE095497
EST:     CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAG                         GGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
genomic: CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAGgtaaaacttt ... cacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
EST: gi|29784715|gb|CB345795.2|CB345795
EST:     CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAG                         GGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
genomic: CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAGgtaaaacttt ... cacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
EST: gi|110377599|gb|EC942676.1|EC942676
EST:     CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAG                         GGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
genomic: CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAGgtaaaacttt ... cacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
EST: gi|110417869|gb|EC983965.1|EC983965
EST:     CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAG                         GGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
genomic: CAGCTTCCGGCGAATCCGTGTTGTTTAAGGATCTCTGGGATCAGAAGGAGgtaaaacttt ... cacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataattttattcagcttatttttctcaacataagcaattttctccacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG
                                      ttttctccacttccc  CT-rich tract
                ttatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtaaagcataaaatgttctggacaagtggaatgattttgttccataattttattcagcttatttttctcaacataagcaattttctccacttcccagGGAGTCGCTGTTGTTGCACTTCTGAGACATTTTGGGTGCTTTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - ataaaat
- - - - - - - - -gttctgg
- - - - - - - - - - - - - - - ggaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacataa