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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaacttgggaggtgttggatcatgctctcacgaatgttgcattatttctttttagcttttaggaagcctgtctcataactgttgctttgcaatgacagGAGGAATACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTGGTCATGATTACCATGTGGGCTGCATCAGGAAATGGTTGTCACTGAAGAATTTCT

Basic information

species Vitis vinifera
transcript Vv13s0019g04100.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04100.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G37150.3 (Arabidopsis thaliana), 3'ss of exon 6
----------------tagaacttgggaggtgttggatcatgctctcacgaatgttgcattatttcttt-ttagcttttaggaagcctgtctcataactgttgc-----tttgcaat--gacagGAGGAATACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTGGTCATGATTACCATGTGGGCTGCATCAGGAAATGGTTGTCACTGAAGAATTTCT
                |     ||           | | |   |     |  ||   |||||| | | | | |  ||  | | || ||  || |    || ||      || | ||    | ||||||| |||||    || |||||  |||||  | | |||   ||||||||||| ||||||| | | ||||||| ||||||||||||  ||||||| |  |
gtaagatttagttttttttttttttttcacaacctggtaagatttagttgtctgaaacattatgtgtctataaagttagaagtaggctaacttaagggtgatgtggtaattggtaaacaaatagGAGGAGTACAAGGAAAAAGAAGAGTTAGGGGAAGTTAAGGGGTGTGGTCATGACTACCATGGGAGGTGCATCAAGAAATGGTTGTCTATGAAGAACTCTT
















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|111125052|gb|EE253642.1|EE253642
EST:     ACCATTCATCAGATCAAAACCAGGAGGAAGCAATGTGCACAATATGCCTT                         GAGGAATACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTGGTCAT
genomic: ACCATTCATCAGATCAAAACCAGGAGGAAGCAATGTGCACAATATGCCTTgtaagaactg ... gcaatgacagGAGGAATACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTGGTCAT
EST: gi|30127866|gb|CB913205.1|CB913205
EST:     ACCATTCATCAGATCAAAACCAGGAGGAAGCAATGTGCACAATATGCCTT                         GAGGAATACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTGGTCAT
genomic: ACCATTCATCAGATCAAAACCAGGAGGAAGCAATGTGCACAATATGCCTTgtaagaactg ... gcaatgacagGAGGAATACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTGGTCAT
EST: gi|110696472|gb|EE072620.1|EE072620
EST:     ACCATTCATCAGATCAAAACCAGGAGGAAGCAATGTGCACAATATGCCTT                         GANGGAAATACAAA-GCA-GGAAGAAGTAGGNAGAATGAAGAACTGTG
genomic: ACCATTCATCAGATCAAAACCAGGAGGAAGCAATGTGCACAATATGCCTTgtaagaactg ... gcaatgacagGA-GGAA-TACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctttttagcttttaggaagcctgtctcataactgttgctttgcaatgacagGAGGAATACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTGGTCATGATTACCATGTGGGCTGCATCAGGAAATGGTTGTCACTGAAGAATTTCT
                             tcataac  putative branch site (score: 2)
     ttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaacttgggaggtgttggatcatgctctcacgaatgttgcattatttctttttagcttttaggaagcctgtctcataactgttgctttgcaatgacagGAGGAATACAAAAGCAAGGAAGAAGTAGGGAGAATGAAGAACTGTGGTCATGATTACCATGTGGGCTGCATCAGGAAATGGTTGTCACTGAAGAATTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - -gtgttgg
- - - - - - - - - - - - - ctctcac
- - - - - - - - - - - - - - - - - - tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct