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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCAAAAGGATTACAACCACCACGAAATGGCTCGCATGGTTGCTTGTGCTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattttagcacatatcgtggcttgaagattcatttcaagtagcccaattaattactagtatgtacatgatccttgttgaactgacttgactacct...

Basic information

species Vitis vinifera
transcript Vv11s0016g03880.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT3G24550.1 (Arabidopsis thaliana), 5'ss of exon 7
CTTGCAAAAGGATTACAACCACCACGAAATGGCTCGCATGGTTGCTTGTGCTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaatta----ttttagcacatatcgtggcttgaagattcatttcaagtagcccaattaattacta-gtatgtacatgatccttgttgaactgacttgactacct
  ||   || || ||  ||    | || |||||||||||||||||||| ||||| |||||||| || |||||||| || ||  ||||  | ||||||||||||| |      |||     | |     || |   | ||   |||   |       |  | || || || |    ||| |  ||   |||  |  ||||      
GATGGGTAATGAGTATGACAGAGAGGAGATGGCTCGCATGGTTGCTTGCGCTGCGGCTTGTGTTCGCCATTCAGCTCGCCGCAGACCTCGCATGAGCCAGgtaacttaatccttttctctagagaagagcatattggtttggttctgtttatttggtagaataatatgtttccgtatggtt-ttaaagaaaggttttgata----

upper sequence: Vv11s0016g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT3G24540.1 (Arabidopsis thaliana), 5'ss of exon 7
CTTGCAAAAGGATTACAACCACCACGAAATGGCTCGCATGGTTGCTTGTGCTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattttagcacatatcgtggcttgaagattcatttcaagtagcccaatt--aattactagtatgtacatgatccttgttgaactgacttgactacct
  || | || || ||  |     | || |||||||||||||||||||||||||| |||||||| ||  || |||| || ||  ||||  | |||  |||||||| |   ||||    ||   |   | | | |   |    || |  |    ||  |     |   || |   |  ||  | ||||| |   |  ||     
GCTGAATAATGAGTATGATAGAGAAGAGATGGCTCGCATGGTTGCTTGTGCTGCAGCTTGTGTCCGCTATACAGCTCGCCGAAGACCTCGCATGGACCAGgtaacttaattagtctttaattttcttagcaaaaaaaaaaaaactgtctttgttttaggggttgacatttggtttttcagttttgaaatatgtaaacggt--
















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|37183775|gb|CF603129.1|CF603129
EST:     CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAG                         ATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
genomic: CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattt ... aaaccaacagATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
EST: gi|110376634|gb|EC941696.1|EC941696
EST:     CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAG                         ATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
genomic: CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattt ... aaaccaacagATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
EST: gi|110383107|gb|EC947458.1|EC947458
EST:     CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAG                         ATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
genomic: CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattt ... aaaccaacagATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
EST: gi|110691421|gb|EE069507.1|EE069507
EST:     CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAG                         ATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
genomic: CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattt ... aaaccaacagATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
EST: gi|30320902|gb|CD004164.1|CD004164
EST:     CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAG                         ATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
genomic: CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattt ... aaaccaacagATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
EST: gi|110712846|gb|EE088247.1|EE088247
EST:     CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCA-GAATGAGCCAG                         ATTGTCCGGGCATTGGAAGGA-ATGCATCTCTATCTGATCTTAATGAAGGA
genomic: CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattt ... aaaccaacagATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
EST: gi|110373085|gb|EC937295.1|EC937295
EST:     CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAG                         ATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
genomic: CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattt ... aaaccaacagATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
EST: gi|110372943|gb|EC937140.1|EC937140
EST:     CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAG                         ATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA
genomic: CTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattt ... aaaccaacagATTGTCCGGGCATTGGAAGGAGATGCATCTCTATCTGATCTTAATGAAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCAAAAGGATTACAACCACCACGAAATGGCTCGCATGGTTGCTTGTGCTGCTGCTTGTGTGCGTCATTCAGCCCGGCGTCGACCAAGAATGAGCCAGgtaattattttagcacatatcgtggcttgaagattcatttcaagtagcccaattaattactagtatgtacatgatccttgttgaactgacttgactacct

- - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT