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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtaatatctttatttatatttattcatttggtttttcatatggccatttatagcttttactatgaaactatgctacagaatatctttatttatatttattcatttggtttttcaaatggccctttgtatagctttcactatcaaactataatacaattactttcatttaacatatcatggaatctttcagGGTTGTAACAGTCTCACCAACTGACACAGTTCTAACAGCAGCAAAGAAGATGCTTGAACTTAAATTAAGTTGTGCAGTCGTAGCAGTTGAAAACAGACCA

Basic information

species Vitis vinifera
transcript Vv17s0000g01200.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 5
gtaggtaatatctttatttatatttattcatttggtttttcatatggccatttatagcttttactatgaaactatgctacagaatatctttatttatatttattcatttggtttttcaaatggccctttgtatagctttcactatcaaactataatacaatt-actttcatttaacatatcatggaatctttcagGGTTGTAACAGTCTCACCAACTGACACAGTTCTAACAGCAGCAAAGAAGATGCTTGAACTTAAATTAAGTTGTGCAGTCGTAGCAGTTGAAAACAGACCA
                                                                             ||   ||||||  |   | | |  | |  || || ||||| |        ||  |    ||| | |  ||   | |   |||| | ||||     | |||        ||  | | || || || || ||  ||||||||||||||||  | || ||| |||| |||||||||||| ||||| ||||||  || || |||||| |||||||||  || 
----------------------------------------------------------------------------gtaggtaatatccattcctttttcaagtt-ttaggcttttccagca-----tttcaggaatttaagtgcca--ttgttgaacaactgacttattgctgaca--------aacttcttagAGTGGTGACTGTTGCACCAACTGACACAGTGTTGACGGCATCAAAAAAGATGCTTGAAGTTAAAGTAAGTTCAGCGGTTGTAGCAATTGAAAACAAGCCT

upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G01470.1 (Glycine max), 3'ss of exon 4
gtaggtaatatctttatttatatttattcatttggtttttcatatggccatttatagcttttactatgaaactatgctacagaatatctttatttatatttatt---catttggtttttcaaatggccctttgtatagctttcactatcaaactataatacaattactttcatttaacatatcatggaatctttcagGGTTGTAACAGTCTCACCAACTGACACAGTTCTAACAGCAGCAAAGAAGATGCTTGAACTTAAATTAAGTTGTGCAGTCGTAGCAGTTGAAAACAGACCA
                                                                             ||   |||| |||  ||| | ||   |   ||   | | | ||| ||     ||  | |   ||    | |  |  | | ||||    |  || ||| | || ||  ||| |  || ||||||||||||||| |||||||| ||| ||||| | ||  || ||||||||||||||||||||     |||||  || || ||  | ||||   ||| ||  
----------------------------------------------------------------------------gtaggtaataccttcttttgttttagctgaacaaaagttgtctcagat-----ttaatttgttttcgtgtttggagttgttatac---caagttaattcagcagatagtggcactttccagGGTTGTAACAGTTTCACCAACAGACTCAGTTTTGACGACAACAAAGAAGATGCTTGAACTTCGTGCAAGTTCAGCTGTTGTGACGGTTGGTGACAAACTT

upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G38140.1 (Glycine max), 3'ss of exon 5
gtaggtaatatctttatttatatttattcatttggtttttcatatggccatttatagcttttactatgaaactatgctacagaatatctttatttatatttattcatttggtttttcaaatggccctttgtatagctttcactatcaaactataatacaattactttcatttaacatatcatggaatctttcagGGTTGTAACAGTCTCACCAACTGACACAGTTCTAACAGCAGCAAAGAAGATGCTTGAACTTAAATTAAGTTGTGCAGTCGTAGCAGTTGAAAACAGACCA
                                                                             ||   |||| |||  ||| | ||   | |       || |   |     ||  | |   |  |    | ||  ||| |||   | |  || ||| | || ||  ||| |  || ||||||||||||||| |||||||| ||| | ||| | ||  || ||||||||||||||||||||     |||||  || || ||  |  ||||  ||| ||| 
----------------------------------------------------------------------------gtaggtaataccttcttttgttttggctgaacaaaagttgcc--tcaaatttaatttgtttgcctgcttgaagttattata---tcaagttaattcagcagatagtggcactttccagGGTTGTAACAGTTTCACCAACAGACTCGGTTTTGACTACAACAAAGAAGATGCTTGAACTTCGTGCAAGTTCAGCTGTTGTGACGATTGATGACAAACCT

upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G63490.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaggtaatatctttatttatatttattcatttggtttttcatatggccatttatagcttttactatgaaactatgctacagaatatctttatttatatttattcatttggtttttcaa-atggccctttgtatagctttcactatcaaactataatacaattactttcatttaacatatcatgg--aatctttcagGGTTGTAACAGTCTCACCAACTGACACAGTTCTAACAGCAGCAAAGAAGATGCTTGAACTTAAATTAAGTTGTGCAGTCGTAGCAGTTGAAAACAGACCA
                                                                                                ||  || ||  ||  ||||  ||       |||| || |   || | |       |    | |  ||   ||  |||||| || ||  |    |  ||||||||| | | |||||||||||||||||||||  | || | ||||||||||||| ||||| |  ||| ||| |||||||||||   | | ||  |||  |  
-----------------------------------------------------------------------------------------------gtaggtaatctcttatttttctaatgaaattctttttacaatcttgattgagtgtttcctgt-ctcttttgttgttttaacttaacaccgctgtttgttcagGGTTTTGAAAGTCTCACCAACTGACACAGTGTTGACTGTAGCAAAGAAGATGGTTGAATTCCAATCAAGCTGTGCAGTCGTGATAATCGAGGACAAGCTT

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|26264368|gb|CA815431.1|CA815431
EST:     GAGAGGATGTTTAGGCCTGCTTTGTCCACGATCATCCCCGAGAATTCAAG                         GGTTGTAACAGTCTCACCAACTGACACAGTTCTAACAGCAGCAAAGAAGAT
genomic: GAGAGGATGTTTAGGCCTGCTTTGTCCACGATCATCCCCGAGAATTCAAAgtaggtaata ... aatctttcagGGTTGTAACAGTCTCACCAACTGACACAGTTCTAACAGCAGCAAAGAAGAT
EST: gi|71858444|gb|DT007499.1|DT007499
EST:     GATCATCCCCGAGAATTCAAAGTA                       
genomic: GATCATCCCCGAGAATTC-AA--Agtaggtaata ... aatctttc
EST: gi|71858444|gb|DT007499.1|DT007499
EST:     GATCATCCCCGAGAATTCAAAGTA                       
genomic: GATCATCCCCGAGAATTC-AA--Agtaggtaata ... aatctttc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactatcaaactataatacaattactttcatttaacatatcatggaatctttcagGGTTGTAACAGTCTCACCAACTGACACAGTTCTAACAGCAGCAAAGAAGATGCTTGAACTTAAATTAAGTTGTGCAGTCGTAGCAGTTGAAAACAGACCA
                             atttaac  putative branch site (score: 3)
                                               tctttc  putative PPT
           tataatacaattactt  TA-rich tract