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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttgtcggtcctcatttggaatgttgtctccttgaattttgaaaaactattcttctccacagtcgacgcacacatacctcgagagctggctattgacacactgagatttttcaatgttgattatgtcatgtccatcagcactgattagacactaccattttgcagGGAGCAGATGATTTGTACAGTCAAGGTTTCAACAGTAAATACTGCTCCAAATCCTCTTGATGGGAAGCAAGTAAAATAATTGTACAGTTGTGTGATGATT

Basic information

species Vitis vinifera
transcript Vv04s0023g02970.t01
intron # 14
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|110716734|gb|EE091976.1|EE091976
EST:     GGATATATTGCAACTGTAACTCTCTTCCAGTCGTGATTAAACATTGAATG                         GGAGCAGATGATTTGTACAGTCAAGGTTTTCA-CAGTAAATACTGCTCCAA
genomic: GGATATATTGCAACTGTAACTCTCTTCCAGTCGTGATTAAACATTGAATGgtatgctttg ... cattttgcagGGAGCAGATGATTTGTACAGTCAAGGTTT-CAACAGTAAATACTGCTCCAA
EST: gi|30330416|gb|CD013678.1|CD013678
EST:     GGATATATTGCAACTGTAACTTTTTTCCAGTCGTGATTAAACATTGAATG                         GGAGCAGATGATTTGTACAGTCAAGGTTTCAACAGTAAATACTGCTCCAAA
genomic: GGATATATTGCAACTGTAACTCTCTTCCAGTCGTGATTAAACATTGAATGgtatgctttg ... cattttgcagGGAGCAGATGATTTGTACAGTCAAGGTTTCAACAGTAAATACTGCTCCAAA
EST: gi|30329939|gb|CD013201.1|CD013201
EST:     GGATATATTGCAACTGTAACTCTCTTCCAGTCGTGATTAAACATTGAATG                         GGAGCAGATGATTTGTACAGTCAAGGTTTCAACAGTAAATACTGCTCCAAA
genomic: GGATATATTGCAACTGTAACTCTCTTCCAGTCGTGATTAAACATTGAATGgtatgctttg ... cattttgcagGGAGCAGATGATTTGTACAGTCAAGGTTTCAACAGTAAATACTGCTCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatgttgattatgtcatgtccatcagcactgattagacactaccattttgcagGGAGCAGATGATTTGTACAGTCAAGGTTTCAACAGTAAATACTGCTCCAAATCCTCTTGATGGGAAGCAAGTAAAATAATTGTACAGTTGTGTGATGATT
                            cactgat  putative branch site (score: 3)
                                            ccatttt  putative PPT
      ttgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttgtcggtcctcatttggaatgttgtctccttgaattttgaaaaactattcttctccacagtcgacgcacacatacctcgagagctggctattgacacactgagatttttcaatgttgattatgtcatgtccatcagcactgattagacactaccattttgcagGGAGCAGATGATTTGTACAGTCAAGGTTTCAACAGTAAATACTGCTCCAAATCCTCTTGATGGGAAGCAAGTAAAATAATTGTACAGTTGTGTGATGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG