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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggttttgttcttatacttattttttagtgcatcagtgcttctatgatctgtttagttgtagtgcacttataatgtaaaaaatttgtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTTTGAGCACATTCCATTGAACAA

Basic information

species Vitis vinifera
transcript Vv06s0009g01210.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g59440.3 (Oryza sativa), 3'ss of exon 3
gtaagtggttttgttcttatacttattttttagtgcatcagtgctt--ctatgatctgtttagttgtagtgcacttataatgtaaaaaatttgtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTTTGAGCACATTCCATTGAACAA
                 ||     | ||  | |||| | |||||||  ||   | |  | | |    | ||   | |  || | |     ||||   ||||||||||||||||||||  |  | |||||||||||||| ||| | ||||| ||||||||||||||  | | |||
----------------gtaagtacaattcctggtgc-tgagtgcttggctgcaaacaatcttg----aatgtgataa--attttacccccttgttctttcagTGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCTACATCAGGACCATTTGAGCACATTCCCCTAAGCAA

upper sequence: Vv06s0009g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g59440.2 (Oryza sativa), 3'ss of exon 4
gtaagtggttttgttcttatacttattttttagtgcatcagtgctt--ctatgatctgtttagttgtagtgcacttataatgtaaaaaatttgtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTTTGAGCACATTCCATTGAACAA----------------------------
                 ||     | ||  | |||| | |||||||  ||   | |  | | |    | ||   | |  || | |     ||||   ||||||||||||||||||||  |  | |||||||||||||| ||| | ||||| ||||||||||||||  | | |||                            
----------------gtaagtacaattcctggtgc-tgagtgcttggctgcaaacaatcttg----aatgtgataa--attttacccccttgttctttcagTGATGTTTCAAGCAATGATCTGTGTGGAACAATTCCTACATCAGGACCATTTGAGCACATTCCCCTAAGCAAGTAAGTTTGACTGCCTTTGTGATACTAT

upper sequence: Vv06s0009g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 4
gtaagtggttttgttcttatac-ttattttttagtgcatcagtgcttctatgatctgtttagttgtagtgcactt-ataatgtaaaaaatttgtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTTTGAGCACATTCCATTGAACAA----------------------------
            ||   || |  | | |||  | ||  | ||   ||||||  |||    | | ||  |  | || | ||| ||   |  |||    ||||| ||||||||||||||  | |||||||| || ||||| ||| | ||||| ||||||||||||||  ||| |||                            
------------gtaagtaaatatcaatttcaaatgt-ttagca-ttctattctctccagattagtgctcaatttgacaatctacccaccttgctctttcagCGATGTTTCAAGCAATGATTTATGTGGGACGATTCCCACATCTGGACCATTTGAGCACATTCCTCTGAGCAAGTAAGTTACATTCCTACTTTGCATCTTC

upper sequence: Vv06s0009g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G815009_T02 (Zea mays), 3'ss of exon 4
gtaagtggttttgttcttatac-ttattttttagtgcatcagtgcttctatgatctgtttagttgtagtgcactt-ataatgtaaaaaatttgtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTTTGAGCACATTCCATTGAACAA
            ||   || |  | | |||  | ||  | ||   ||||||  |||    | | ||  |  | || | ||| ||   |  |||    ||||| ||||||||||||||  | |||||||| || ||||| ||| | ||||| ||||||||||||||  ||| |||
------------gtaagtaaatatcaatttcaaatgt-ttagca-ttctattctctccagattagtgctcaatttgacaatctacccaccttgctctttcagCGATGTTTCAAGCAATGATTTATGTGGGACGATTCCCACATCTGGACCATTTGAGCACATTCCTCTGAGCAA

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|351041271|gb|FQ447398.1|FQ447398
EST:     ACTGGTCAAATCCCAAGGGAACTTGTTGGTATATCAAGCCTCAAAATTGT                         TGATGTTTCAAGCAACAACTTATGTGGAACAATTCCCACAACCGGACCCTT
genomic: ACTGGTCAAATCCCAAGGGAACTTGTTGGTATATCAAGCCTCAAAATTGTgtaagtggtt ... gtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTT
EST: gi|110726152|gb|EE101683.1|EE101683
EST:     ACTGGTCAAATCCCAAGGGAACTTGTTGGTATATCAAGCCTCAAAATTGT                         TGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTT
genomic: ACTGGTCAAATCCCAAGGGAACTTGTTGGTATATCAAGCCTCAAAATTGTgtaagtggtt ... gtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTT
EST: gi|352790557|gb|FQ478196.1|FQ478196
EST:     ACTGGTCAAATCCCAAGGGAACTTGTTGGTATATCAAGCCTCAAAATTGT                         TGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTT
genomic: ACTGGTCAAATCCCAAGGGAACTTGTTGGTATATCAAGCCTCAAAATTGTgtaagtggtt ... gtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatgatctgtttagttgtagtgcacttataatgtaaaaaatttgtgtattcagTGATGTTTCAAGCAACAACTTATGTGGAACAATTCCAACAACCGGACCGTTTGAGCACATTCCATTGAACAA
                         acttataatgtaaaaa  TA-rich tract