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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaggaaaagaaaatatattaatatatgatcacctaatgggagttgaaaactgctatgtccattgttgcaattgacatatcaaactttcattgtgcagACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAG

Basic information

species Vitis vinifera
transcript Vv05s0020g04620.t01
intron # 4
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|349808681|gb|FQ405825.1|FQ405825
EST:     TAGCAGAAAGAATGAAGGCTTTGCAAGAACTTGTCCCTAGCTCCAACAAG                         ACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTA
genomic: TAGCAGAAAGAATGAAGGCTTTGCAAGAACTTGTCCCTAGCTCCAACAAGgtgattggca ... cattgtgcagACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTA
EST: gi|110701293|gb|EE078706.1|EE078706
EST:     TAGCAGAAAGAATGAAGGCTTTGCAAGAACTTGTCCCTAGCTCCAACAAG                         ACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTA
genomic: TAGCAGAAAGAATGAAGGCTTTGCAAGAACTTGTCCCTAGCTCCAACAAGgtgattggca ... cattgtgcagACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTA
EST: gi|110718182|gb|EE094719.1|EE094719
EST:     TAGCAGAAAGAATGAAGGCTTTGCAAGAACTTGTCCCTAGC-CCAACAAG                         ACGGATAGGGCTGCA-TGCCTGATGAAATTGTG
genomic: TAGCAGAAAGAATGAAGGCTTTGCAAGAACTTGTCCCTAGCTCCAACAAGgtgattggca ... cattgtgcagACGGATAGGGCTGCAATGCTTGATGAAATTGTG
EST: gi|110387925|gb|EC952633.1|EC952633
EST:     TAGCAGAAAGAATGAAGGCTTTGCAAGAACTTGTCCCTAGCTCCAACAAG                         ACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTA
genomic: TAGCAGAAAGAATGAAGGCTTTGCAAGAACTTGTCCCTAGCTCCAACAAGgtgattggca ... cattgtgcagACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaaactgctatgtccattgttgcaattgacatatcaaactttcattgtgcagACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAG
                          aattgac  putative branch site (score: 3)
                                         ctttcatt  putative PPT
                                 atatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaggaaaagaaaatatattaatatatgatcacctaatgggagttgaaaactgctatgtccattgttgcaattgacatatcaaactttcattgtgcagACGGATAGGGCTGCAATGCTTGATGAAATTGTGGACTATGTGAAGTTCCTAAGGCTCCAAGTCAAG

- aaaggaa
- - - - -aagaaaa
- - - - - - - - - - - - - - - - cacctaa
- - - - - - - - - - - - - - - - - - - - - - -ttgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaact