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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCCAACCCATCTGTTGATCCTATTCTGGAAACACGAGAATCGGTTCTAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaatttgacacaatttttgcggatagggtaagcattagacatgttttgcatgaatgggtccatttggatagccctcttcaaccattctcacatcgcttgggataccttcttggcgtttctctagcattcttgacccacatatcaaacacctatttctgcag

Basic information

species Vitis vinifera
transcript Vv00s0516g00030.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0516g00030.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G05530.1 (Arabidopsis thaliana), 5'ss of exon 3
TGCTGCCAACCCATCTGTTGATCCTATTCTGGAAACACGAGAATCGGTTCTAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaatttgacaca----atttttgcggatagggtaagcattagacatgttttgcatgaatgggtccatttggatagccctcttcaaccattctcacatcgcttgggataccttcttggcgtttctctagcattcttgacccacatatcaaacacctatttctgcag
||||||||| ||||||   || || ||  ||   |    |||| | ||||| |||||||| ||||||||||| |||||||| ||||||||  | || ||||||    ||    |      |  |||  |  |     |  |  ||||    ||||   | |  |  |  |||||  |   |||||      ||| |  ||                                                                     
TGCTGCCAATCCATCTACAGACCCAATCTTGTCTAGCAAAGAAGCTGTTCTTGACAAGCTTTGGGAAATCAATGTCAAATCCTCTATACTTCTCCTGCAGgtaaagcttccgtaagtgttagctttttgtttccatgacccgatagatcaattttttctta--gatttgatttgact---cctctatgtttattttatcag--------------------------------------------------------------------
















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|294965201|gb|GW837032.1|GW837032
EST:     TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAG                         GAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTTGTCCTAATTTCCTC
genomic: TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaattt ... atttctgcagGAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTT-GTCCTAATTTCCTC
EST: gi|349823977|gb|FQ417364.1|FQ417364
EST:     TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAG                         GAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
genomic: TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaattt ... atttctgcagGAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
EST: gi|26262355|gb|CA813418.1|CA813418
EST:     TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAG                         GAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
genomic: TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaattt ... atttctgcagGAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
EST: gi|110730981|gb|EE108681.1|EE108681
EST:     TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAG                         GAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
genomic: TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaattt ... atttctgcagGAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
EST: gi|26262314|gb|CA813377.1|CA813377
EST:     TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAG                         GAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
genomic: TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaattt ... atttctgcagGAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
EST: gi|351022557|gb|FQ447079.1|FQ447079
EST:     TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAG                         GAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT
genomic: TAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaattt ... atttctgcagGAGGCAGCTCCTCACTTGAGAAAGGGTTCGTCGGTTGTCCTAATTTCCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGCCAACCCATCTGTTGATCCTATTCTGGAAACACGAGAATCGGTTCTAGACAAGCTATGGGAAATCAACGTCAAATCTTCTATACTCATTCTACAGgtatgaatttgacacaatttttgcggatagggtaagcattagacatgttttgcatgaatgggtccatttggatagccctcttcaaccattctcacatcgcttgggataccttcttggcgtttctctagcattcttgacccacatatcaaacacctatttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT