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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatatcaatataatataaaacaaccaaaacaattttatattgaatttatctcacattttctcatcataaatctccag

Basic information

species Vitis vinifera
transcript Vv01s0011g06290.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06290.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G09880.2 (Glycine max), 5'ss of exon 5
AGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatatcaatataatata--aaacaaccaaaacaatttta----tattgaatttatctcacattttctcat-cataaatctccag----------
 || ||||||||||||||||| || |||||||||||||||||||| ||    |||||  | || |  ||||||||| | |||||||||||||| ||| ||| ||   |   | | |  | |    | || |    |  ||||||    |||  |   || ||  ||    ||  | | ||| | || |           
TGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCGTGCACGGTAATACGGATGAGCTTGTAAAGCAGCTTCTCCCAATTCTTGAGgtaacttttgtatttttctttcctgagcagcagggaatattttaaggttatatatgctagcttccacaaactgttacttaagtttctattgatttccag

upper sequence: Vv01s0011g06290.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G26920.1 (Glycine max), 5'ss of exon 7
AGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatatcaa-------tataatataaaacaaccaa--aacaattt-tatattgaatttat-ctcacattttctcatcataaatctccag-------------------
 || ||||||||||||||||| || |||||||||||||||||||| ||    |||||  | || |  ||||||||| | |||||||||||||| ||| ||| ||   |   ||         | |  | ||    |  |  | || |   ||| || |  |||  ||  |    |  ||  |  | |  ||                     
TGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCTTGCACGGTAATACGGATGAGCTTGTAAAGCAGCTTCTCCCAATTCTTGAGgtaactttgctaaattttttcctcactttaatttcctgagcatcagtgaatattttaaggttacactagctagcttccacaaacagttacctaagtgtctattgattttcag
















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|56688100|gb|CX126003.1|CX126003
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688146|gb|CX126049.1|CX126049
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688532|gb|CX126435.1|CX126435
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|30324780|gb|CD008042.1|CD008042
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|110361763|gb|EC925259.1|EC925259
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|110382161|gb|EC938649.1|EC938649
EST:     ATCACGGGGACACAGTGGAGCTTGTAGAACAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688821|gb|CX126724.1|CX126724
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688240|gb|CX126143.1|CX126143
EST:     ATCACGGGGACACAGTGGAGCTCGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|110405384|gb|EC970925.1|EC970925
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|30330531|gb|CD013793.1|CD013793
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|110378747|gb|EC943895.1|EC943895
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|30128027|gb|CB913366.1|CB913366
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|30127523|gb|CB912862.1|CB912862
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|34542274|gb|CF510506.1|CF510506
EST:     ATCACGGGGACACAGTGGAGCTTGTAGAACAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|110427573|gb|EC994020.1|EC994020
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688741|gb|CX126644.1|CX126644
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|30125391|gb|CB910730.1|CB910730
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688020|gb|CX125923.1|CX125923
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|349811174|gb|FQ406162.1|FQ406162
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAN                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|71867743|gb|DT016798.1|DT016798
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|110701614|gb|EE079386.1|EE079386
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|30126050|gb|CB911389.1|CB911389
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688831|gb|CX126734.1|CX126734
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688837|gb|CX126740.1|CX126740
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688383|gb|CX126286.1|CX126286
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688239|gb|CX126142.1|CX126142
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|110385343|gb|EC949857.1|EC949857
EST:     ATCACGGGGACACAGTGGAGCTTGTAGAACAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|27586836|gb|CB009531.1|CB009531
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
EST: gi|56688885|gb|CX126788.1|CX126788
EST:     ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAG                         GCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC
genomic: ATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatat ... aaatctccagGCAAACAGTGTGGATCTTTACATAAACGGACATGACCATTGCTTGGAACAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGCTTGTAGATCAGCTTCTCCCAATCCTTCAGgcaataatatcaatataatataaaacaaccaaaacaattttatattgaatttatctcacattttctcatcataaatctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT