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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcacatttgattctctcctatgttttagcagttcatttcgtcttacatttttctctctttctcggcttttcttgttgctacagAATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAG

Basic information

species Vitis vinifera
transcript Vv12s0059g02280.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G10670.1 (Glycine max), 3'ss of exon 4
gtactcacatttgattctctcctat-gttttagcagt--tcatttcgtcttacatttttctctctttctcggcttttcttg-------ttgctacagAATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAG
||||  | || |  ||  | ||||| | || |   ||   | | | |    | |    |       | |     | | |||       ||  |  |||  || ||||||||| ||||||||||||||||||| |||||||| || || || |||||  ||||||||||  | || | | ||
gtacatatatgtttttggcacctatagcttaaattgtaggcgtgtggatgcagaggaatgggggaatgttaaagtgttttgcgctaaatttttgtagACGGCAATTCCAGTGTTGATTGGAACCAAGTTTGATGATTTCATTCAGCTCCCTATTGATTTGCAATGGACCATCGCCAATGAG

upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G46250.1 (Glycine max), 3'ss of exon 2
gtactcacatttgattctct----cctat-gttttagcagtt--catttcgtcttacatttttctctctttctcggcttttcttg-----ttgctacagAATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAG
||||  | ||||  || | |    || || | || |   ||   ||| | |    | |    |     | |    |  |||  ||     ||  |  |||   | ||||||||| ||||||||||||||||||| |||||||| || ||    |||||  ||||||||||  | || | | ||
gtacgtatatttatttttttggcaccaatagcttaaattgtaggcatgtggatgcaaaggaatgagaatgttatagtgttttgtgctcaatttttgtagACGACAATTCCAGTGTTGATTGGAACCAAGTTTGATGATTTCATTCAGCTCTGTATTGATTTGCAATGGACCATAGCCAATGAG

upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G46120.1 (Glycine max), 3'ss of exon 4
gtactcacatttgattctct--cctat-gttttagcagtt--catttcgtcttacatttttctctctttctcggcttttcttg-----ttgctacagAATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAG
||||  | ||||  || |    || || | || |   ||   ||| | |    | |    |     | |    |  |||  ||     ||  |  |||  || || |||||| ||||||||||||||||||| |||||||| || || || |||||  ||||||||||  | || | | ||
gtacatatatttatttttggaaccaatagcttaaattgtaggcatgtggatgcagaggaatgagaatgttatagtgttttgtgctcaatttttgtagACGGCAATCCCAGTGTTGATTGGAACCAAGTTTGATGATTTCATTCAGCTCCCTATTGATTTGCAATGGACCATAGCCAATGAG

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|26265133|gb|CA816196.1|CA816196
EST:     TGTCATCAGTTGGTATCACCAAGCAAGGAAATGGAATCAG                         AATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTT
genomic: TGTCATCAGTTGGTATCACCAAGCAAGGAAATGGAATCAGgtactcacat ... gttgctacagAATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTT
EST: gi|110383289|gb|EC947654.1|EC947654
EST:     TGTCATCAGTTGGTATCACCAAGCAAGGAAATGGAATCAG                         AATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTT
genomic: TGTCATCAGTTGGTATCACCAAGCAAGGAAATGGAATCAGgtactcacat ... gttgctacagAATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTT
EST: gi|34544942|gb|CF513174.1|CF513174
EST:     TGTCATCAGTTGGTATCACCAAGCAAGGAAATGGAATCAG                         AATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTT
genomic: TGTCATCAGTTGGTATCACCAAGCAAGGAAATGGAATCAGgtactcacat ... gttgctacagAATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttcatttcgtcttacatttttctctctttctcggcttttcttgttgctacagAATGCCATTCCAGTGCTGATTGGAACCAAGTTTGACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAG
           gtcttac  putative branch site (score: 3)
            tcttacatttttctct  CT-rich tract
              ttacattttt  TA-rich tract