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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatattttttctattttatgtgtctcactgataggatggtgtataattgattcatcaaaatgggatatctaattttttgcttttctgttatactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA

Basic information

species Vitis vinifera
transcript Vv05s0051g00830.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 10
tcatattttttctattttatgtgtctcactgataggatggtgta-taattgattcat-caaaatgggatatctaatt-ttttgcttttctgttatactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA
   |||||  | |        || |      ||    | ||  | |     |  ||| || | |    |    ||||  | ||||    ||  ||     |||||||| |||||  | ||  ||||||| ||||| || || || ||||| |||||||||||| |||||||||| || ||||||||||| || ||||||||||
---tatttccttttacgctcttgacaagggaatgcattagttcactgggacaaccatgcatagtcttgttctgaattactctgctggcatgcaatcacaacagGGGAAGGTAGTAGTGATACGAGGAGAAGGACCGAAAGGTGGACCAGGGATGCCTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGA

upper sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------tcatattttttctat------tttatgtgtctcactgataggatggtgtataatt---gattca---tcaaaatgggatatctaatt-ttttgcttttctgtta-tactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA
                                                          || |  ||||| | |        | |   |||| |||||||     | |||  ||   ||   |   |   | |   ||  | |||  ||||  |  |||| |  |     ||||| || |||||  | ||  ||||||| ||||| || || |||||||| ||||| |||||||||||||||||||||||||||||||| || |||||||| |
gtaatatgtgcagtgcaagtattttctgcatttgctactgccgctattgaatgccatttcttcctttttttgtagattgccttttcttctctctgatagtggaatatattgtttcagagcaagttttgcattcttatgacaaatcattttattgctctgatggtttcaacagGGAAAGGTAGTAGTGATCCGAGGAGAAGGACCAAAAGGCGGGCCAGGGATGCCCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAA

upper sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 10
------------------------------------------------------------------------------tcat-attttttctattttatgtgtctcactgataggatggtgtataattg-attcatcaaaatgggatatctaattttttgcttttctgttatactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA
                                                                               ||  |||   | | | || | | |   | ||  |  ||  ||| | |  | || |||    |||  | ||| | ||| ||||| |  || | |     ||||| || |||||  | ||  ||||||| ||||| || || |||||||| |||||||||||||||||||||||||| ||||||||||| || ||||| || |
gtaatatgtgcgatgcaagtattttctgcatgtgccactgtcgctattgcttgccatttcttcctttttatttggagagcacgattgcctttttcttctctctgcgagtgg-aacatattgtttcagagcatgcattcgtatgacaaatc-attttattgctctgatggttt--caacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAA

upper sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
tcatattttttctattttatgtgtctcact-gataggatggtg--tataattgat--tcatcaaaatgggatatctaattttttgcttttctgttatactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA
    | |||| || |  ||| ||| |   | || |      |    | | | | |  |    ||||||| | || | |||| ||   | | | | ||  |||||||||||||| ||| | || || ||||||||||||||||| || || ||||||||||| ||||| || |||||||| ||||||||||| ||||||||||| |
---caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaa-atatgatttcttttgtattt-tcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA

upper sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
tcatattttttctattttatgtgtctcactgataggatggtgtataattgattcatcaaaatgggatatctaattttttgcttttctgttatac----tttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA
                 ||  |  ||  |||||| ||        | || ||       |   || ||| ||  ||||  ||  |    | ||     |||||||| |  || ||| |||| ||||||||||| || || || || ||||| |||||||| |||||||| || ||||| ||||||||||| || |||||||| |
----------------gtaatttcctttctgatatga--------agttcatct-caggagctggttatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA

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|37189217|gb|CF608566.1|CF608566
EST:     GTGAGGAAGCTATGATTGCAGCTATAGCAGAGAATCCTATGAGCTTTAAG                         GGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGCCCAGGAATG
genomic: GTGAGGAAGCTATGATTGCAGCTATAGCAGAGAATCCTATGAGCTTTAAGgtatgtgtac ... atactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATG
EST: gi|30320752|gb|CD004014.1|CD004014
EST:     GTGAGGAAGCTATGATTGCAGCTATAGCAGAGAATCCTATGAGCTTTAAG                         GGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGCCCAGGAATG
genomic: GTGAGGAAGCTATGATTGCAGCTATAGCAGAGAATCCTATGAGCTTTAAGgtatgtgtac ... atactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATG
EST: gi|110732410|gb|EE107670.1|EE107670
EST:     GTGAGGAAGCTATGATTGCAGCTATAGCAGAGAATCCTATGAGCTTTAAG                         GGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGCCCAGGAATG
genomic: GTGAGGAAGCTATGATTGCAGCTATAGCAGAGAATCCTATGAGCTTTAAGgtatgtgtac ... atactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgattcatcaaaatgggatatctaattttttgcttttctgttatactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA
                      atctaat  putative branch site (score: 3)
                                              tactttc  putative PPT
                    atatctaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatattttttctattttatgtgtctcactgataggatggtgtataattgattcatcaaaatgggatatctaattttttgcttttctgttatactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - ctcactg
- - - - - - - - - - - - - - - - - -gatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaaat