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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacaatctcaccttctctggtttattttccgttaggctttttaccaaaagagactatattttgaagacaattgttgttgatatgctattgttttgttgtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATGAGGCAAACAGATGGGTTAGCGGGATTCACCAAGCGCTCGGAGAGTGAAT

Basic information

species Vitis vinifera
transcript Vv05s0020g02130.t01
intron # 3
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|352777281|gb|FQ473915.1|FQ473915
EST:     ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAG                         TCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
genomic: ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAGgttacaatct ... gtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
EST: gi|352773800|gb|FQ472582.1|FQ472582
EST:     ATGTCTTCAATGCCCCTCAAGACACGATACTATGGGATGTTGGTCATCAG                         TCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
genomic: ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAGgttacaatct ... gtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
EST: gi|352781778|gb|FQ469076.1|FQ469076
EST:     ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAG                         TCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
genomic: ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAGgttacaatct ... gtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
EST: gi|161713384|gb|FC063376.1|FC063376
EST:     ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAG                         TCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
genomic: ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAGgttacaatct ... gtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
EST: gi|352774221|gb|FQ474744.1|FQ474744
EST:     ATGTCTTCAATGCACCTCAAGACAGGATACTATGGGATGTTGGTCATCAG                         TCTTACCCACACAAAATTTTTAACTGGGAGAAGAGATC
genomic: ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAGgttacaatct ... gtttctgaagTCTTACCCACACAAAATTCT-AACTGGGAGAAGAGATC
EST: gi|294967320|gb|GW836674.1|GW836674
EST:     ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGACATCAG                         TCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
genomic: ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAGgttacaatct ... gtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
EST: gi|352768724|gb|FQ467936.1|FQ467936
EST:     ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAG                         TCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG
genomic: ATGTCTTCAATGCCCCTCAAGACAGGATACTATGGGATGTTGGTCATCAGgttacaatct ... gtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatattttgaagacaattgttgttgatatgctattgttttgttgtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATGAGGCAAACAGATGGGTTAGCGGGATTCACCAAGCGCTCGGAGAGTGAAT
                      tgttgat  putative branch site (score: 4)
                                           ttgtttct  putative PPT
                                 tattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacaatctcaccttctctggtttattttccgttaggctttttaccaaaagagactatattttgaagacaattgttgttgatatgctattgttttgttgtttctgaagTCTTACCCACACAAAATTCTAACTGGGAGAAGAGATCAAATGCATACCATGAGGCAAACAGATGGGTTAGCGGGATTCACCAAGCGCTCGGAGAGTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG