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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttgttcaaatgagataaacttaccctttctgctttgtccatatggagcctgctgctgcagtctttggttaactttgttcctggtacttgtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAATGTTGGAAATGAGGATGTGGCCATTAATGGATTTGAAGAAGCCATAAAAT

Basic information

species Vitis vinifera
transcript Vv13s0047g00170.t01
intron # 6
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|30132145|gb|CB917484.1|CB917484
EST:     NGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|351047067|gb|FQ454677.1|FQ454677
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCCAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|28964625|gb|CB343658.1|CB343658
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|29782979|gb|CB348769.2|CB348769
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|352774116|gb|FQ474639.1|FQ474639
EST:     GCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: GCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|351038304|gb|FQ460996.1|FQ460996
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAA-GTTGCTGATGTGAAAAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|110362765|gb|EC926319.1|EC926319
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|110386747|gb|EC951369.1|EC951369
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|71866068|gb|DT015123.1|DT015123
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|351055326|gb|FQ441924.1|FQ441924
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|32457102|gb|CD798276.1|CD798276
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|352764964|gb|FQ473612.1|FQ473612
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|110363678|gb|EC927285.1|EC927285
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAAT
EST: gi|351038515|gb|FQ464381.1|FQ464381
EST:     TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAG                         ATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAAC
genomic: TGGATGTTCGTCGCAATGCAATCAAGGATCGTTCAAATGTTCCATCACAGgttagcaact ... gtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagcctgctgctgcagtctttggttaactttgttcctggtacttgtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAATGTTGGAAATGAGGATGTGGCCATTAATGGATTTGAAGAAGCCATAAAAT
                      ggttaac  putative branch site (score: 3)
 ttaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttgttcaaatgagataaacttaccctttctgctttgtccatatggagcctgctgctgcagtctttggttaactttgttcctggtacttgtgatcatagATTCTAGATGTGGCAGTTTCCCTTGCAAAAGTTGCTGATGTGAACAGGAATGTTGGAAATGAGGATGTGGCCATTAATGGATTTGAAGAAGCCATAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - gataaac
- - - - - - - - - - - - ccctttc
- - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - - - - -cctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagtc