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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattctttaatgctttctcccaattgttttttgaaatttggcctcacttgcagctaaagcaagcctcattatttatcttttatggacatatgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAACAGAGCAATTGGGTTGTATGGAGCAAGTTTTCTTCAAAGCCATATAAAAG

Basic information

species Vitis vinifera
transcript Vv11s0016g00830.t01
intron # 5
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|110719863|gb|EE095357.1|EE095357
EST:     TAATATTAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAG                         GCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
genomic: TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAGgtagcttatt ... tgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
EST: gi|30252087|gb|CB968726.1|CB968726
EST:     TAATATCAAATGCTGCCGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAG                         GCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
genomic: TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAGgtagcttatt ... tgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
EST: gi|71856942|gb|DT005997.1|DT005997
EST:     TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAG                         GCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTG
genomic: TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAGgtagcttatt ... tgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTG
EST: gi|71864847|gb|DT013902.1|DT013902
EST:     TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAG                         GCTTTTCTAGAGGCTGCTGAAGACATGCTTAGG
genomic: TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAGgtagcttatt ... tgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGG
EST: gi|71864848|gb|DT013903.1|DT013903
EST:     TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAG                         GCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
genomic: TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAGgtagcttatt ... tgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
EST: gi|161721519|gb|FC070079.1|FC070079
EST:     TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAG                         GCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
genomic: TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAGgtagcttatt ... tgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
EST: gi|110707370|gb|EE083712.1|EE083712
EST:     TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAA                         GCTTTTCTAGAGGCTGCTGAAGACATGCTTANGGAGGATGTTGCTGCAAAC
genomic: TAATATCAAATGCTGCTGCCACTGCTTTTGAAGCCATGAGTGTTTTTCAGgtagcttatt ... tgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
EST: gi|110366059|gb|EC929706.1|EC929706
EST:     GAAGCCATGAGTGTTTTTCAG                         GCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC
genomic: GAAGCCATGAGTGTTTTTCAGgtagcttatt ... tgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttgcagctaaagcaagcctcattatttatcttttatggacatatgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAACAGAGCAATTGGGTTGTATGGAGCAAGTTTTCTTCAAAGCCATATAAAAG
      agctaaa  putative branch site (score: 3)
                    tcattatttatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattctttaatgctttctcccaattgttttttgaaatttggcctcacttgcagctaaagcaagcctcattatttatcttttatggacatatgatctatagGCTTTTCTAGAGGCTGCTGAAGACATGCTTAGGGAGGATGTTGCTGCAAACAGAGCAATTGGGTTGTATGGAGCAAGTTTTCTTCAAAGCCATATAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - ttctccc
- - - - - - - - - - - - - - - - - - - - - - cacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcatt