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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatttgattctacatcttagtttacctctttccaaaatgttgacaaaatgatgcccatcattaaaaattttctctggccactcggttttgctgattgtagGAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAGATTCATCGCATTCACACAAGTTGATTCATCTGAGATACCGCTTTTCAGAATCA

Basic information

species Vitis vinifera
transcript Vv16s0098g01880.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01880.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G41440.2 (Glycine max), 3'ss of exon 3
-----gtaagaatttgattctacatcttagtttacctctttccaaaatgttgacaaaatgatgcccatcattaaaaattttctctggccactcggttttgctgattgtagGAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAGATTCATCGCATTCACACAAGTTGATTCATCTGAGATACCGCTTTTCAGAATCA
       ||||| |  | ||| |     || |||     ||      ||       |||| |    ||| ||   |||    | |          |||| | ||||  |||||||||||||||| || | ||| || ||||||||||||||||||| ||  || || |||||  |||||||||| ||||| ||||| ||||| ||||| |
cagtgacaagaact-aactcttctaaaaagcttaatatgttatgtgctggccctggaatggtttttatctttgccaataacatgta---------tttttcggatttcagGAGGAGATGGATAGAAAAACTGGATATTGGTGGTCACTGGACAGTAAATATATTGCTTTCACTGAAGTTGATTCTTCTGAAATACCACTTTTTAGAATTA

upper sequence: Vv16s0098g01880.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G13410.1 (Glycine max), 3'ss of exon 4
------gtaagaatttgattctacatcttagtttacctctttccaaaatgttgacaaaatgatgcccatcattaaaaattttctctggccactcggttttgctgattgtagGAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAGATTCATCGCATTCACACAAGTTGATTCATCTGAGATACCGCTTTTCAGAATCA
       ||||||    | ||| | |   || |||  |  ||      ||       |||| |    ||| |||  |||    | |          |||| | ||||  |||||||||||||||| || | ||| || ||||||||||||||||||| ||  || || |||||  ||||||| || ||||| ||||| ||||| ||||| |
acattgataagaacc-aactctcc-taaaagcttaatttgttatgtgctggccctggaatggtttttatctttaccaataacatgta---------tttttcggatttcagGAGGAGATGGATAGAAAAACTGGATATTGGTGGTCACTGGACAGTAAATATATTGCTTTCACTGAAGTTGACTCTTCTGAAATACCACTTTTTAGAATTA
















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|161718650|gb|FC068226.1|FC068226
EST:     ACACATGGGCTTGCTGAATATATAGCCCAG                         GAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAGATTC
genomic: ACACATGGGCTTGCTGAATATATAGCCCAGgtaagaattt ... ctgattgtagGAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAGATTC
EST: gi|161711730|gb|FC059978.1|FC059978
EST:     ACACATGGGCTTGCTGAATATATAGCCCAG                         GAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAG
genomic: ACACATGGGCTTGCTGAATATATAGCCCAGgtaagaattt ... ctgattgtagGAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAG
EST: gi|161713891|gb|FC062864.1|FC062864
EST:     ACACATGGGCTTGCTGAATATATAGCCCAG                         GAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAGATTC
genomic: ACACATGGGCTTGCTGAATATATAGCCCAGgtaagaattt ... ctgattgtagGAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAGATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgatgcccatcattaaaaattttctctggccactcggttttgctgattgtagGAGGAGATGGATAGGAAGAATGGGTACTGGTGGTCACTGGACAGTAGATTCATCGCATTCACACAAGTTGATTCATCTGAGATACCGCTTTTCAGAATCA
                                           tgctgat  putative branch site (score: 3)
                                        ttttgct  CT-rich tract
           atcattaaaaattttc  TA-rich tract