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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacaagacggatgctccaaaccctaaatagttgagatgaagccatgatattaatgataatgttcaacaatgatgtgtttttttttatttgcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGACCCCCAGATTCCTGACCGTGTAAATTTGCCAGACTTTGCTGGACCTGAG

Basic information

species Vitis vinifera
transcript Vv05s0102g01110.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0102g01110.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 15
-gaacaagacggatgctccaaaccctaaatagttgagatgaagccatgatattaatgataatgttcaacaatgat--gtgtttttttttatttgcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGACCCCCAGATTCCTGACCGTGTAAATTTGCCAGACTTTGCTGGACCTGAG
   | || |      |   ||   || | || ||       ||  ||  | ||   | | || |||      |||  |  ||| | |||| || | |   |||||||||||| ||||| || ||||| |||||  |||||||||  ||||| |||||  |||||||||| | ||||||||| ||||  | ||||| |||||| 
ttgataa-ataatgacagaaattactgactattttgtcaacagatatagt-ttgcagttcattttctttctcgataggcatttatatttagttccat-cgcagGAGCAACACAAATCATGAACATGATCAACCTCCTCATCTTCGTTTGAGAGACCCAAAGATTCCTGAACTTGTAAATTTACCAGTGTATGCTGCACCTGAA
















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|30251567|gb|CB969300.1|CB969300
EST:     CCAGAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
EST: gi|18459158|gb|BM437436.1|BM437436
EST:     CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
EST: gi|30251648|gb|CB969381.1|CB969381
EST:     CCAGAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
EST: gi|30251671|gb|CB969404.1|CB969404
EST:     CCAGAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATTTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
EST: gi|110364442|gb|EC924185.1|EC924185
EST:     CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
EST: gi|30320658|gb|CD003920.1|CD003920
EST:     CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
EST: gi|30321185|gb|CD004447.1|CD004447
EST:     CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
EST: gi|30251591|gb|CB969324.1|CB969324
EST:     CCAGAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
EST: gi|30251604|gb|CB969337.1|CB969337
EST:     CCAGAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAG                         GAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA
genomic: CCAAAGCCAGATGGGATTGTATCTTTTGATGTGCCAACATCTCTATACAGgtttttttca ... gcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatattaatgataatgttcaacaatgatgtgtttttttttatttgcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGACCCCCAGATTCCTGACCGTGTAAATTTGCCAGACTTTGCTGGACCTGAG
   tattaat  putative branch site (score: 2)
                                tttttttttatttgct  putative PPT
                       aatgatgtgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacaagacggatgctccaaaccctaaatagttgagatgaagccatgatattaatgataatgttcaacaatgatgtgtttttttttatttgcttattcagGAGCAACACGAATCACGATCATGACCAACCATCTCATCTTCACTTGAGGGACCCCCAGATTCCTGACCGTGTAAATTTGCCAGACTTTGCTGGACCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
-aacaaga
- - - - -ggatgct
- - - - - - - - ccaaacc
- - - - - - - - - - - - - - - - - - - - - ccatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - aatgataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaacaa