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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgcattgtccttggcccttgctttatctctcattctgtattttattttctaacctaaccaattacccagatctgttttttgggcctgttttgtttgtccaggactgtacctctgtattatgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG

Basic information

species Vitis vinifera
transcript Vv04s0008g04220.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 5
gtgtgtgcattgtccttggcccttgctttatctctcattctgtattttattttctaacctaaccaattacccagatctgttttttgggcctgttttgtttgtccaggactgtacctctgtattatgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG
                                         || | ||| ||  |          |||   || |||  || || |   ||  |||| | |    || ||  || | | ||||   |    |        || |||||    ||||| ||           |  ||||||| ||||||| ||  |  | ||||| ||||| |||||||||||||| ||||| ||||| || ||||||| ||||||  |||| ||  | |||
-----------------------------------------gtgtgttagttattgctt-----gattctgcacatcaattattag---ctaatttggtagcattgg-cttcacttttctattgcttcaaaggggca---gtgttaaccatcttttcttt-----------tgtaacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G094039_T01 (Zea mays), 3'ss of exon 4
gtgtgtgcattgtccttggcccttgctttatctctcattctgtattttattttctaacctaaccaattacccagatctgttttttgggcctgttttgtttgtccaggactgtacctctgtattatgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG
                                                                 |||   || |||  || || |   ||  |||| | |    || ||  || | | ||||   |    |        || |||||    ||||| ||           |  ||||||| ||||||| ||  |  | ||||| ||||| |||||||||||||| ||||| ||||| || ||||||| ||||||  |||| ||  | |||
-------------------------------------------------------------cttgattctgcacatcaattattag---ctaatttggtagcattgg-cttcacttttctattgcttcaaaggggca---gtgttaaccatcttttcttt-----------tgtaacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 5
gtgtgtgcattgtccttggcccttgctttatctctcattctgtattttattttctaacctaaccaattacccagatctgttttttgggcctgttttgtttgtccaggactgtacctctgtattatgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG
                                                                 |||   || |||  || ||   ||   ||| ||   | |||       | ||  ||||||   |           || || ||   || |||||| ||||         ||||||| ||||||| ||  |  | ||||| ||||| |||||||||||||| ||||| ||||| || ||||||| ||||||  |||| ||  | |||
---------------------------------------------------------------tgattctgcatatcaattatt--agctaatttggtagctgcag-------cttcactattattgctccaaaaggccagtgttgacc--atcttcctttctttttg-----taacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 5
gtgtgtgcattgtccttggcccttgctttatctctcattctgtattttattttctaacctaaccaattacccagatctgttttttgggcctgttttgtttgtccaggactgtacctctgtattatgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG
                                         || | ||| ||  |          |||   || |||  || ||   ||   ||| ||   | |||       | ||  ||||||   |           || || ||   || |||||| ||||         ||||||| ||||||| ||  |  | ||||| ||||| |||||||||||||| ||||| ||||| || ||||||| ||||||  |||| ||  | |||
-----------------------------------------gtgtgttagttattgctt-----gattctgcatatcaattatt--agctaatttggtagctgcag-------cttcactattattgctccaaaaggccagtgttgacc--atcttcctttctttttg-----taacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 5
gtgtgtgcattgtccttggcccttgctttatctctcattctgtatttt--attttctaacctaaccaattacccagatctgttttttgggcctgttttgtttgtccaggactgtacctctgtattatgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG
|| |||| ||| | ||||||| |   ||||| ||||||  |  ||| |  | | |||  | ||   | | | |||   || |||  | |||||| ||| ||||||||||  || |    |||||  || ||||||| |  ||  |||||| |  || |  || |||||  |||| ||   ||| |||||||  || || ||||||| |||||||| ||||||||||||||||||||||| || ||||| | | ||||||| |||||||  |||
gtctgtggattattcttggccttcagtttatttctcatgtttcattcttaagtctcttgcttacaaattaaaccatggctttttccttggcctgctttctttgtccagggatgcag---tgtatcttggttgtgtc-tgcttactttaacttctttcttgtt-ctttatcatattca---gATATGCATGAACTACGCCTAATCCACACTGACCTAAAGCCAGAAAATATACTTCTTGTTTCCTCTGAATATGTAAAGCTCCCTAGCTATAAG

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|110378511|gb|EC943648.1|EC943648
EST:     TGGACGTCAGCTTTTGGAATCTGTAGCAT                         ATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATAC
genomic: TGGACGTCAGCTTTTGGAATCTGTAGCATgtgtgtgcat ... tatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgtgtcctttttgttttaacatgattttccttgctttacaatatccaacagATGTGCATGATTTATGCTTAATCCATACTGACCTGAAGCCAGAAAATATACTTCTTGTATCATCTGAGTGTATAAAGCTTCCTAGCTCCAAG
                 ttttaac  putative branch site (score: 2)
           tttttgttttaacatg  TA-rich tract