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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgttgtttctttagatacagataatgtatttttatgttaaattatttctcttttaattaaaggatttatatataatttggatcttatatggattgtgcattatctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTGCAGGATCTGGCAACTCTCACAGGAGGGGAG

Basic information

species Vitis vinifera
transcript Vv05s0051g00340.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaggtgttgtttctttagatacagataatgtatttttatgttaa-attatttctcttttaattaaaggatttatatataatttggatcttatatggattgtgcattatctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTGCAGGATCTGGCAACTCTCACAGGAGGGGAG
                    |    | ||   |   |  |  ||   |    |  ||||||  ||   || ||         || | | ||| ||  || ||   |  || ||  |||||||||||||||| || ||||||||||||||||| |||||||||    |||| || || ||  | || || || || |||
-------------------gtttgaacaacagaagctcttactaccgtctcctgacttttagctat--gactt--------ctttgcttttagattaatagtt--tcctccctgcagGTCTGTGCCATCAAGGCCCCTGGGTTTGGAGAGAATAGGAAGGCCAATTTGCAAGACCTTGCTGCCCTTACTGGTGGAGAG

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaggtgttgtttctttagatacagataatgtattttta-tgttaaattatttctcttttaattaaaggatttatatataatttggatcttatatggattgtgcattatctctaaa----gGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTGCAGGATCTGGCAACTCTCACAGGAGGGGAG
                      |    ||| |   || | ||| | | | ||  ||||| | |       ||  | |  |||    ||       ||| ||  |  | |    |||    ||||||||| ||||| |||||||| ||||| ||||||||||| ||   | |||||||||| ||     | || || ||  ||
---------------------cccatcaatattgcttgactgtgacagtgttgatctttaattatggaagttcttctgcaatagatattgatgtcggaatgctcgattttgtgaaaaatagGTCTGTGCAATCAAGGCACCTGGTTTTGGTGAGAACAGGAAAGCACTCATGCAGGATCTTGCCGTGATTACGGGTGGTCAG
















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|110686767|gb|EE064783.1|EE064783
EST:     GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAG                         GTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG
genomic: GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAGgtaggtgttg ... atctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG
EST: gi|30300026|gb|CB976820.1|CB976820
EST:     GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAG                         GTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAAGCCGCCCTG
genomic: GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAGgtaggtgttg ... atctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG
EST: gi|110691710|gb|EE070124.1|EE070124
EST:     GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAG                         GTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG
genomic: GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAGgtaggtgttg ... atctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG
EST: gi|71873742|gb|DT022797.1|DT022797
EST:     GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAG                         GTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG
genomic: GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAGgtaggtgttg ... atctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG
EST: gi|77586617|gb|DV222437.1|DV222437
EST:     GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAG                         GTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG
genomic: GCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAGgtaggtgttg ... atctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaggatttatatataatttggatcttatatggattgtgcattatctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTGCAGGATCTGGCAACTCTCACAGGAGGGGAG
                                           ttatctct  CT-rich tract
       atttatatataatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtgttgtttctttagatacagataatgtatttttatgttaaattatttctcttttaattaaaggatttatatataatttggatcttatatggattgtgcattatctctaaagGTCTGTGCCATCAAAGCACCTGGGTTTGGAGAGAACAGGAAGGCCGCCCTGCAGGATCTGGCAACTCTCACAGGAGGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG