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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggagtcatctctgcaattctcatttgctttctactatagaccttcttgactcaaagactaattcagggttttttcctttttcttttttctcaatcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCATGAGTGTGCTGGCATCATAGAAGAAGTTGGGAGTGAAGTGAAGAATCTTG

Basic information

species Vitis vinifera
transcript Vv16s0100g00290.t01
intron # 10
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|110686578|gb|EE064378.1|EE064378
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110688657|gb|EE067457.1|EE067457
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110713731|gb|EE089908.1|EE089908
EST:     TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|161713022|gb|FC062444.1|FC062444
EST:     TTAGGATCATAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTTATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110702046|gb|EE080314.1|EE080314
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|37187764|gb|CF607117.1|CF607117
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110710421|gb|EE086742.1|EE086742
EST:     TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110711468|gb|EE087981.1|EE087981
EST:     TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|161719033|gb|FC067653.1|FC067653
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110702995|gb|EE079453.1|EE079453
EST:     TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110430276|gb|EC996819.1|EC996819
EST:     TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110422161|gb|EC988475.1|EC988475
EST:     GTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: GTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110710333|gb|EE086577.1|EE086577
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110699843|gb|EE077221.1|EE077221
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110685996|gb|EE063203.1|EE063203
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110687807|gb|EE065639.1|EE065639
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|110420392|gb|EC986664.1|EC986664
EST:     TTACGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|71890669|gb|DT039724.1|DT039724
EST:     TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTTATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT
EST: gi|161716957|gb|FC068142.1|FC068142
EST:     TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAG                         ACAATGAGGTGCGCAAATTTTATTGTGAAGAAGCCAATGGTGATAGGGCAT
genomic: TTAGGATCAAAGCTGTAGGGATATGTGGAAGTGATGTTCATCACTTCAAGgtggagtcat ... atcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactcaaagactaattcagggttttttcctttttcttttttctcaatcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCATGAGTGTGCTGGCATCATAGAAGAAGTTGGGAGTGAAGTGAAGAATCTTG
        gactaat  putative branch site (score: 2)
                     ttttttcctttttctt  putative PPT
                             tttttcttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggagtcatctctgcaattctcatttgctttctactatagaccttcttgactcaaagactaattcagggttttttcctttttcttttttctcaatcttatcagACAATGAGGTGCGCAAATTTCATTGTGAAGAAGCCAATGGTGATAGGGCATGAGTGTGCTGGCATCATAGAAGAAGTTGGGAGTGAAGTGAAGAATCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA