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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaacctatggccttttctaagataccattttcctccacccttttcttatttatgaatatgccttcgaattgatcattttggtttttgtggatttgacagGCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTGGAAGCTACTTGTAAGGAAGGTGGTGTCAGCCAAAGCCATGTCTTCCTTG

Basic information

species Vitis vinifera
transcript Vv17s0000g09790.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|56409473|gb|CX017725.1|CX017725
EST:     CACTCCTCCATCTGTGACCAAACCGATTTGTGCAGAGTTCCTCTTTGCAG                         GCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
genomic: CACTCCTCCATCTGTGACCAAACCGATTTGTGCAGAGTTCCTCTTTGCAGgtaaaaacag ... gatttgacagGCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
EST: gi|34550620|gb|CF518838.1|CF518838
EST:     CGCTCCTCCATCTGTGACCAAACCGATTTGTGCAGAGTTCCTCTTTGCAG                         GCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
genomic: CACTCCTCCATCTGTGACCAAACCGATTTGTGCAGAGTTCCTCTTTGCAGgtaaaaacag ... gatttgacagGCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
EST: gi|22012019|gb|BQ797053.1|BQ797053
EST:     AAACCGATTTGTGCAGAGTTCCTCTTTGCAG                         GCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
genomic: AAACCGATTTGTGCAGAGTTCCTCTTTGCAGgtaaaaacag ... gatttgacagGCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
EST: gi|161715050|gb|FC062729.1|FC062729
EST:     CACTCCTCCATCTGTGACCAAACCGATTTGTGCAGAGTTCCTCTTTGCAG                         GCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
genomic: CACTCCTCCATCTGTGACCAAACCGATTTGTGCAGAGTTCCTCTTTGCAGgtaaaaacag ... gatttgacagGCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
EST: gi|34550484|gb|CF518702.1|CF518702
EST:     CACTCCTCCATCTGTGACCAAACCGATTTGTGCAGAGTTCCTCTTTGCAG                         GCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG
genomic: CACTCCTCCATCTGTGACCAAACCGATTTGTGCAGAGTTCCTCTTTGCAGgtaaaaacag ... gatttgacagGCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatttatgaatatgccttcgaattgatcattttggtttttgtggatttgacagGCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTGGAAGCTACTTGTAAGGAAGGTGGTGTCAGCCAAAGCCATGTCTTCCTTG
                      aattgat  putative branch site (score: 4)
     ttatgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaacctatggccttttctaagataccattttcctccacccttttcttatttatgaatatgccttcgaattgatcattttggtttttgtggatttgacagGCAATTCAAATTGAAAGCACAACAAGTGAAAAAGGGTGAGGATGCAAGGTGGAAGCTACTTGTAAGGAAGGTGGTGTCAGCCAAAGCCATGTCTTCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
-caaccta
- - - - - - - - - - - -taccatt
- - - - - - - - - - - - - - - -tcctcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccttc