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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttcttatatattcattttaatttcctgtaaaaaaattttgtttgtgtgttttcacattagatactgattatggtatttcgtttcttcaagATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGCATAGGCTGGGTAGAACTTCTTTTAGGGCCGTAAAATCTAAGCGTGATTA

Basic information

species Vitis vinifera
transcript Vv05s0094g01560.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01560.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 3'ss of exon 4
gtaatttttcttatatattcattttaatttcctgtaaaaaaattttgtttgtgtgttttcacattagatactgattatggtatttcgtttcttcaagATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGCATAGGCTGGGTAGAACTTCTTTTAGGGCCGTAAAATCTAAGCGTGATTA
|||  |  | ||    ||   || | || |  |      |  |     | |  | |       |   | | |  |       || | || | |  ||| || ||||| |||||||  || ||||| || || ||||| |||||||| |||||| ||||||| || ||||||||||| || ||||| |||||||| ||
gtacatgctgttgatgatgttttctcatgttttacttttatgtcacaatcgcatatcagatgttctaacatttgtctaatctttcctttacctgcagACATCTTTGAGGTTGCCACAGAGGATGGTACCGTTTTGGCCATGAAGCTTCATAGGTTGGGTAGGACATCTTTTAGGGCTGTGAAATCCAAGCGTGACTA

upper sequence: Vv05s0094g01560.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G472991_T01 (Zea mays), 3'ss of exon 6
gtaatttttcttatatattcattttaatttcctgtaaaaaaattttgtttgtgtgttttcacattagatactgattatggtatttcgtttcttca-agATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGCATAGGCTGGGTAGAACTTCTTTTAGGGCCGTAAAATCTAAGCGTGATTA
        | |  | | ||||| ||  ||     |       |||    |||| | |  | ||   ||   |  || |  ||| ||  |  |  | |||||||||||| |||||||  || ||||| |||||  | || ||||| || ||||||||||| || || ||||||||||| || |||||||| ||||| ||
-------gtatgttgtgttcatattgtttgttctttg-----tttgtcatgtg-gctagcgcacatgaagttatttctaatatctctatgatatacagATATATTTGAGGTTGCCACAGAGGATGGTACAGTACTCGCCATGAAACTTCATAGGCTGGGAAGGACATCTTTTAGGGCTGTGAAATCTAAACGTGACTA

upper sequence: Vv05s0094g01560.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G038309_T01 (Zea mays), 3'ss of exon 5
gtaatttttcttatatattcattttaatttcctgtaaaaaaattttgtttgtgtgttttcacattagatactgattatggtat-ttcgtttcttcaagATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGCATAGGCTGGGTAGAACTTCTTTTAGGGCCGTAAAATCTAAGCGTGATTA
|||  || | ||  ||| |  || |  |||| | ||  ||  |       ||        ||||||| |  || || |  ||| || ||    |  |||||||||||| || ||||  || ||||| |||||  | || |||||||| |||||| |||| || || |||||||| || || |||||||||||||| ||
gtatgttgtgtt-catagtgcttgttctttcttttagtaacgtggcaagggt--------acattaggt--tgtttctaatatctttgtgatatgcagATATATTTGAGGTAGCCACAGACGATGGTACAGTACTTGCCATGAAGCTTCATAGGTTGGGCAGGACATCTTTTAGAGCTGTGAAATCTAAGCGTGACTA

upper sequence: Vv05s0094g01560.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G33320.1 (Glycine max), 3'ss of exon 4
gtaatttttcttatatattcat--tttaatttcctgtaaaaaaattttgtttgtgtgttttcacattagatactgattatggtatttcgtttcttcaagATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGCATAGGCTGGGTAGAACTTCTTTTAGGGCCGTAAAATCTAAGCGTGATTA
||| |||   | || |  |  |  | |  |  ||| |    ||      ||     ||||||      | || |  |  || | |||    ||| | |||||||||||| ||||||   ||||| || |||||  | || |||||| |||||||||| ||||||   |||||||| || || |||||||||||||| ||
gtattttagttaatgttcttctgatgtggtgccctttgttcaatcacatttcagacgttttct-----gctaattgtgttgctgtttgtgctctgctagATATATTTGAGGTTGCCCGTGAAGACGGAACAGTTCTAGCTATGAAGTTGCATAGGCTTGGTAGAGTCTCTTTTAGAGCTGTCAAATCTAAGCGTGACTA

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|110427485|gb|EC993924.1|EC993924
EST:     TGGAGTATTTGTAGCTGTTGGTCGTCAAATTGGTGTCGGGAAGGAGTCTG                         ATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGC
genomic: TGGAGTATTTGTAGCTGTTGGTCGTCAAATTGGTGTCGGGAAGGAGTCTGgtaatttttc ... tttcttcaagATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtttgtgtgttttcacattagatactgattatggtatttcgtttcttcaagATATATTTGAAGTTGCCAAGGAAGATGGCACAGTCTTGGCAATGAAGCTGCATAGGCTGGGTAGAACTTCTTTTAGGGCCGTAAAATCTAAGCGTGATTA
                          tactgat  putative branch site (score: 2)
                                      tatttcgtttcttc  putative PPT
                    attagata  TA-rich tract