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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgcttaatgttcttcttttggctgttacaatgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT

Basic information

species Vitis vinifera
transcript Vv00s0652g00030.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 46
gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgcttaatgttcttcttttggctgttacaatgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT
                                    | |  | || |  |  |   ||     ||||   |||||   ||| ||  ||   | | ||   |   |   ||  |||   || |   ||   || || ||||| |||||||| ||| |  | ||||| ||||||||  | ||||||||||| |||||||| || || ||||| || ||||||||||| ||||||
------------------------------------gttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagat--acaagta-gatgctttgcatgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGAACTTGTAAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTT

upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 47
gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgcttaatgttcttcttttggctgttacaatgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT
                                            | ||  |     |  |     |  | |||| || |   ||  | || || | || | |  |   |  | |           |  || | ||||| ||||||||||| |||||  | ||||| ||||||||  | ||||||||||| |||||||| ||||| |||||||||||||||||||| ||||||
-------------------------------------------gtctgcctcccttgatagctcttcaacttttttcttgtttttttgaacgtccatcatgtatcatctgtatt-----------ctgtagG-GCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTT

upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 29
gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgcttaatgttcttctt-----ttggctgttaca-atgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT
                                                                  ||  |    |   ||| |  ||||   | |||||     |||| |   | | ||    || |  | |   || ||||| |||||||| || |||||| | ||||| ||||| ||  | ||||||||||| |||||||| ||||| |||||||||||||||||||| ||||||
---------------------------------------------------------------gtctgcctcccttggatagctctttaacaattttcttggattttggtttaaatagatatcctgtataatctgtagGGCTGGTGCTGATGATAAGCCATTAAGAATGGTCAAAACCGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCGATGGTT

upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ11209 (Selaginella moellendorffii), 3'ss of exon 44
gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgctta-atgttcttcttttggctgttacaatgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT
                                                                                 || |  || ||||| ||  |||    |||  ||     |  |  |    | |||| ||||| ||||| || ||  | || ||||| || |||||||| || ||||| || |||||||| ||||| || || |||||||||||||| ||||| 
---------------------------------------------------------------------------------gtagtatacatgtttttagttttctcgttcgaact---tttatcattgca-gAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGAACTAGTAAAGCTTCGTGGAACAGCCATTAAGGGTCACCTTTCCATGGTG

upper sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ15655 (Selaginella moellendorffii), 3'ss of exon 44
gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgctta-atgttcttcttttggctgttacaatgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT
                                                                                 || |  || ||||| ||  |||    |||  ||        | | |    ||||| ||||| ||||| || ||  | || ||||| || |||||||| || ||||| || |||||||| ||||| || || |||||||||||||| ||||| 
---------------------------------------------------------------------------------gtagtatacatgtttttagttttctcgttcgaacttttatgattgc----agAGCCGGAGCCGATGATAAGCCTCTGCGGATGGTGAAGACTGTTCTTCACGAACTAGTAAAGCTTCGTGGAACAGCCATTAAGGGTCACCTTTCCATGGTG

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|161716243|gb|FC066506.1|FC066506
EST:     AGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAG                         AGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGA
genomic: AGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAGgtatcccttg ... ctaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGA
EST: gi|110724440|gb|EE100271.1|EE100271
EST:     AGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAG                         AGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGA
genomic: AGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAGgtatcccttg ... ctaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGA
EST: gi|110731172|gb|EE109088.1|EE109088
EST:     AGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAG                         AGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGA
genomic: AGTATACATGTATACCTGCAAGAATTGGGAATGGAAGAAATCAGAAGAAGgtatcccttg ... ctaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagttgcttaatgttcttcttttggctgttacaatgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT
       gcttaat  putative branch site (score: 4)
         ttaatgtt  TA-rich tract