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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccataatgtttccaattaccgatacttcacttaatatttagttcaaagtcccatagttatattttcatttttctaatcttgtttggtgatctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG

Basic information

species Vitis vinifera
transcript Vv08s0040g01630.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|351031601|gb|FQ459858.1|FQ459858
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351019552|gb|FQ439369.1|FQ439369
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351045913|gb|FQ441296.1|FQ441296
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351054135|gb|FQ450217.1|FQ450217
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351037841|gb|FQ464282.1|FQ464282
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351015919|gb|FQ431874.1|FQ431874
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351048601|gb|FQ448875.1|FQ448875
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351037852|gb|FQ464293.1|FQ464293
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351023294|gb|FQ432677.1|FQ432677
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|349828488|gb|FQ417230.1|FQ417230
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|122688630|gb|EC920009.1|EC920009
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351049390|gb|FQ449991.1|FQ449991
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351042935|gb|FQ451229.1|FQ451229
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|349826497|gb|FQ418588.1|FQ418588
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351037891|gb|FQ465129.1|FQ465129
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351055498|gb|FQ442294.1|FQ442294
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351026072|gb|FQ428084.1|FQ428084
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351047717|gb|FQ455114.1|FQ455114
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|122689997|gb|EC938839.1|EC938839
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351035274|gb|FQ459541.1|FQ459541
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
EST: gi|351052410|gb|FQ452443.1|FQ452443
EST:     AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCT                         TGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
genomic: AGAAACAGGAAATCTTCTTATGCATACTGAAGCCGAGCAGAAACTTGGCTgtaagtttaa ... atctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagtcccatagttatattttcatttttctaatcttgtttggtgatctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG
                           ttctaat  putative branch site (score: 2)
         atagttatattttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccataatgtttccaattaccgatacttcacttaatatttagttcaaagtcccatagttatattttcatttttctaatcttgtttggtgatctatgcagTGAATGCTTCAGATTTTGGTCTGGATATTGAAGACTATTTAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - tgtttcc
- - - - - - - - - - - - -acttcac
- - - - - - - - - - - - - - - - - - - - - - - - agtccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg