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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattactttgtcaagtatctcttagccaagtgtagtttctcctatgggacattgctcacacagatgtaacttgttttttcccatgcttctcttgcacgccttagtctcttttcatgtttgattgtgtaggccagataattatttcccttttttttttctttgatcctcaattcctgtgttaatcttgaaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAGGCAAGCCCAATGCCAAGCTTCTATCATGAAGGACCACCACCCAAGGCTG

Basic information

species Vitis vinifera
transcript Vv05s0020g04880.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G23090.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatattactttgtcaagtatctcttagccaagtgtagtttctcctatgggacattgctcacacagatgtaacttgttttttcccatgcttctcttgcacgccttagtctcttttcatgtttgattgtgtaggccagataattatttcccttttttttttctttgatcctcaattcctgtgttaatcttgaaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAGGCAAGCCCAATGCCAAGCTTCTATCATGAAGGACCACCACCCAAGGCTG
                                                                          ||  |||||| || |||    |      |  | | | ||   ||||||  |||        | ||| || ||  |||| | ||| |     || | |  | |           |  | |  |  ||||||     || |||||  | |  ||||| ||||| ||||||| |||||| |||| |||||||||||  || ||||||||||| || || || |||| ||
--------------------------------------------------------------------------tgcattttcctatactttgtgtagctagca-atttttttcctatgtttttttg--------acata-ttgttctccttctctttgt-----atgcccggtac-----------tcaacatctaaagGAAGCAACCGAAGCAGCTTTAAGACAATTAAGAAAAAGTTTGAGGTTTAAAGCAAACCCAATGCCAAAATTTTATCATGAAGGGCCTCCCCCAAAGGTTG
















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|351046932|gb|FQ454542.1|FQ454542
EST:     AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG                         GAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
genomic: AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAGgtatattact ... aaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
EST: gi|110374005|gb|EC938470.1|EC938470
EST:     AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG                         GAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
genomic: AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAGgtatattact ... aaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
EST: gi|351029994|gb|FQ430736.1|FQ430736
EST:     AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG                         GAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
genomic: AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAGgtatattact ... aaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
EST: gi|349821897|gb|FQ413068.1|FQ413068
EST:     AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG                         GAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
genomic: AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAGgtatattact ... aaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
EST: gi|110719141|gb|EE096774.1|EE096774
EST:     AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG                         GAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
genomic: AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAGgtatattact ... aaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
EST: gi|351033942|gb|FQ462997.1|FQ462997
EST:     AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG                         GAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
genomic: AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAGgtatattact ... aaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG
EST: gi|30298916|gb|CB975710.1|CB975710
EST:     AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAG                         GAAGAGCGAGAGGCAGCAATTAGGCAATTGAGAAAGAGTTTGATGTTTAAG
genomic: AGCACCAGGCACTGGAGGCTGAGAAAAACCAATGTGAAGCAAGGACCAAGgtatattact ... aaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccttttttttttctttgatcctcaattcctgtgttaatcttgaaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAGGCAAGCCCAATGCCAAGCTTCTATCATGAAGGACCACCACCCAAGGCTG
                                  tgttaat  putative branch site (score: 3)
                                                ctttt  putative PPT
     ttttttttttctttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattactttgtcaagtatctcttagccaagtgtagtttctcctatgggacattgctcacacagatgtaacttgttttttcccatgcttctcttgcacgccttagtctcttttcatgtttgattgtgtaggccagataattatttcccttttttttttctttgatcctcaattcctgtgttaatcttgaaacttttagGAAGAGCGAGAGGCAGCAATTAAGCAATTGAGAAAGAGTTTGATGTTTAAGGCAAGCCCAATGCCAAGCTTCTATCATGAAGGACCACCACCCAAGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT