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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattcacttcttttatgcctttgccaaggataaatcttataggttaataatttcatattatgttggttttcctcctaaacaaatttttccatattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCTGGATGGGACACACTCTTGAGAGTTGG

Basic information

species Vitis vinifera
transcript Vv06s0004g02050.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|30129730|gb|CB915069.1|CB915069
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACTAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|110702580|gb|EE081092.1|EE081092
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACTAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|30136412|gb|CB921750.1|CB921750
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACTAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|30126105|gb|CB911444.1|CB911444
EST:     TGGTGCATGAACTCTATCANACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACTAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|30130177|gb|CB915516.1|CB915516
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACTAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|110361075|gb|EC924528.1|EC924528
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|33405995|gb|CF211622.1|CF211622
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|87583901|gb|DY473272.1|DY473272
EST:     CGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|110362552|gb|EC926095.1|EC926095
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|110363917|gb|EC927549.1|EC927549
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|33406095|gb|CF211722.1|CF211722
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|110363719|gb|EC927329.1|EC927329
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT
EST: gi|30329378|gb|CD012640.1|CD012640
EST:     TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACCACTTTTGAAAAG                         TTGTCAGTGACTGTTTCATGCCTCTGTACTAGCAATGGAGAAAAGTTCCCT
genomic: TGGTGCATGAACTCTATCAAACAGGAATGGCAGAGACTACTTTTAAAAAGgtcaacttct ... catattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataatttcatattatgttggttttcctcctaaacaaatttttccatattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCTGGATGGGACACACTCTTGAGAGTTGG
                            tcctaaa  putative branch site (score: 2)
                                       tttttccat  putative PPT
     atttcatattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcacttcttttatgcctttgccaaggataaatcttataggttaataatttcatattatgttggttttcctcctaaacaaatttttccatattgcagTTGTCAGTGACTGTTTCATGCCTCTGTACAAGCAATGGAGAAAAGTTCCCTGGATGGGACACACTCTTGAGAGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
-tattcac
- - - - - - - tatgcct
- - - - - - - - - - -ttgccaa
- - - - - - - - - - - - - - ggataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa