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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttatttgtaaaactggaatatcgtaagtcatagtttgagaaatgctgcatataaatttaccagttcctttttctctgttctcagaaatcctgctgtttgtgacatttcctaagctatttttgggctaaaatgatatgctgtagctgaaccctattgaactgattgttaattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACAATTGATAATGACATTCCG

Basic information

species Vitis vinifera
transcript Vv11s0016g02850.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 7
gtaattttatttgtaaaactggaatatcgtaagtcatagtttgagaaatgctgcatataaatttaccagttcctttttctctgttctcagaaatcctgctgtttgtgacatttcctaagctatttttgggctaaaatgatatgctgtagctgaaccctattgaactgattgttaattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACAATTGATAATGACATTCCG
                                                                      | |  | |   | |  | |||||     |||   |  |   ||  |    | || ||   |  || |||| |        | ||    |||   |   || | ||||| |||||||||||  || ||||||||||||||||| ||||||||  ||||||| |||||||||||||| ||  ||
---------------------------------------------------------------------gtgcagtgtgcatatcattagaaa-----ctgagggaaaatattgttggagttttgtttttcagaactgattt--------ttaatttgatttttccctttttcaattg-gcagGAAATTCGTAGACGTGGTCTAAAAGTTGCTGTTGCTGGTGTTCCCAAGACAATTGATAATGATATAGCG

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 7
gtaattttatttgtaaaactggaatatcgtaagtcatagtttgagaaatgctgcatataaatttaccagttcctttttctctgttctcagaaatcctgctgtttgtgacatttcc----taagctatttttgggctaaaatgatatgctgtagctgaaccctattgaactgattgttaattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACAATTGATAATGACATTCCG
                 | |  |  |  ||     | |     | || ||||   |||       |   || ||       |||  | | | |||||  |  |     |||| |      |  |  | | |    | ||||  |||  | | | |  |||  ||||   | ||  ||  | |  |||||||| | ||  ||||| ||||| ||| | |||||||| |||||||| ||||| |||||||||||  ||
---------------gtaatttaccactgtgg--tacaaccgtacaagtgctatgtatg------ctgtttgctgaaagaatgtgataatagatcctattcatcaatgcattgcagtagcatacggtatatctatttaaatattattttatcgtt--acctcattgttttcat-attggtgg--cagGAAATCCGAAAACGTGGGCTAAAGGTTTCTGTTGCTGGGATTCCCAAGACAATAGATAATGACATAGCG

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 7
gtaattttatttgtaaaactggaatatcgtaagtcatagtttgagaaatgctgcatataaatttaccagttcctttttctctgttctcagaaatcctgctgtttgtgacatttcctaagctatttttgggctaaaatgatatgctgtagctgaaccctattgaactgattgttaattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACAATTGATAATGACATTCCG
                                                                           | | | | | |  ||  |      | | |   | | |     |   | || |   | | ||   | |  | ||  |   |  ||||      || |        ||||||||| |  || ||||||||| |||| || |||||||| |||||||| || ||||||||||| ||  ||
---------------------------------------------------------------------------tatgtatatgcatagttaaatgtttttatagaaaaataatgcaatgaattgtaatccagaa--gttttttttaattttgctttatttttaaaatcgcc------gcagGAAATCCGGAGACGTGGTCTACAAGTAGCTGTTGCTGGTATTCCCAAGACTATTGATAATGATATAGCG

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 7
gtaattttatttgtaaaactggaatatcgtaagtcatagt-ttgagaaatgctgcatataaatttacca-gttcctttttctctgttctcagaaatcctgctgtttgtgacatttcctaagctatttttgggctaaaatgatatgctgtagctgaaccctattgaactgattgttaattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACAATTGATAATGACATTCCG
|||  | || || ||  | ||    || |||    || || || || |||    |   | |  || |      | |  ||| |||||    || ||  ||   | |||||  ||    ||  |  |||      ||| |  ||  |       | |||||             |||     ||||||||||  ||||||| |||| |||||||||||||  ||||| |||||||| || ||||||||||| |||
gtatatataattttagtattgagg-atagtagactattgtgtttaggaatataac---tgagcttcctgcacacatacttcactgtt----gatatt-tgacatctgtga--ttgtgaaaattgatttca--tcaaagtagtaaac-------gcaccctg-----------attatccacgcagGAAATTAGAAGGCGTCGTCTCAAAGTTGCAGTTGTAGGAATCCCCAAAACCATAGATAATGACATCCCG

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 7
------gtaattttatttgtaa-aactggaatatcgtaagtcatagtttgagaa-atgctgcatataaatttaccagttcctttttctctgttctcagaaatcctgctgtttgtgacatttcctaagctatttttgggctaaaatgatatgctgtagctgaaccctattgaactgattgttaattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACAATTGATAATGACATTCCG
       |||||||| || ||| ||   | ||||   |  ||   ||||  ||| ||     |  |  ||  || | | | |  ||      | |    | |  ||   | |||||  ||    ||  |  |||    | ||| |        | |  || | |||             |||     ||||||||||  ||||||| |||| |||||||||||||  ||||| |||||||| || ||||||||||| |||
gtatatataattttaattttaataatgaggatattagacttctgtgtttaggaatataactgagcttcatgcacaaatacatacttaatcactgttgatatt--tgacatctgtga--ttgtgaaaattgatttca--ccaaagta-------gcaaatgcatcctg-----------attatccacgcagGAAATTAGAAGGCGTCGTCTCAAAGTTGCAGTTGTAGGAATCCCCAAAACCATAGATAATGACATCCCG

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|161717475|gb|FC066878.1|FC066878
EST:     ACATAATTGGAGGTGATGGAACTCAAAAAGGGGCATCTGTGATTTTTGAG                         GAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACA
genomic: ACATAATTGGAGGTGATGGAACTCAAAAAGGGGCATCTGTGATTTTTGAGgtaattttat ... aattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACA
EST: gi|29784840|gb|CB341314.2|CB341314
EST:     TTGGAGGTGATGGAACTCAAAAAGGGGCATCTGTGATTTTTGAG                         GAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACA
genomic: TTGGAGGTGATGGAACTCAAAAAGGGGCATCTGTGATTTTTGAGgtaattttat ... aattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACA
EST: gi|27584897|gb|CB007592.1|CB007592
EST:     ACATAATTGGAGGTGATGGAACTCAAAAAGGGGCATCTGTGATTTTTGAG                         GAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACA
genomic: ACATAATTGGAGGTGATGGAACTCAAAAAGGGGCATCTGTGATTTTTGAGgtaattttat ... aattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggctaaaatgatatgctgtagctgaaccctattgaactgattgttaattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACAATTGATAATGACATTCCG
                                         tgttaat  putative branch site (score: 3)
                                       attgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttatttgtaaaactggaatatcgtaagtcatagtttgagaaatgctgcatataaatttaccagttcctttttctctgttctcagaaatcctgctgtttgtgacatttcctaagctatttttgggctaaaatgatatgctgtagctgaaccctattgaactgattgttaattgtgcagGAAATTCAAAGGCGTGGTCTAAAAGTTGCAGTTGCTGGAATTCCCAAAACAATTGATAATGACATTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA