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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcttttttttttttaaattttttgtttttatgtcaattgtcactatacttgatgatatttattcattgaagtcacctatcaaaaaaaaataaaaaataaaattattcattgatttcagtttttaccctttgtttttattatgctagGAGGTAGATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTAAGTGATGATTTTATACAAGGCAATTCTG

Basic information

species Vitis vinifera
transcript Vv16s0013g01510.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G374969_T01 (Zea mays), 3'ss of exon 3
gtaattcttttttttttttaaattttttgtttttatgtcaattgtcactatacttgatgatatttattcattgaagtcacctatcaaaaaaaaataaaaaataaaattattcattgatttcagtttttaccctttgtttttattatgc-tagGAGGTAGATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTAAGTGATGATTTTATACAAGGCAATTCTG------------
                            ||      ||| ||| |     |   |  | |||||    |       |  ||||   ||   |  |     | |||  || |||| |     | |||| | |      |   | ||||  ||||| || ||||| ||   ||||||||||||||||||| ||||| ||||||| |   |    | |  ||   | |            
----------------------------gtaccccagtccattattttgttgacttgttatattagcaccgctgcatggccta---aatttacttcgctgacaaa--taatcatggtacctaattttaatc------tccaaatatgtgtagGAAGTGGATGACCCATGGCAACTTGATATGTCAGAATTATGTCTAAGTGAAGGCCTCTCTCGAAACATGCCAGACAATGGTGCAG

upper sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 3
gtaattcttttttttttttaaattttttgtttttatgtcaattgtcactatacttgatgatatttattcattgaagtcacctatcaaaaaaaaataaaaaataaaattattcattgatttcagtttttaccctttgtttttattatgctagGAGGTAGATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTAAGTGATGATTTTATACAAGGCAATTCTG
                                                                || || ||  || ||| |  |      |    |  |   | |||    |   ||||     ||||||  ||||   |   ||   |||| ||||||||||| || |||||||||||||| ||||||||||| ||||||||||||   |||||  ||  ||
---------------------------------------------------------------gtactccttttagacacttcccctgttgatggtatcacagagattg---agaaattta----tttacc--ttgtccctgaaattgcagGAAGTAGATGAGCCACTACAACTTGATATGTCTGAACTATGTTTGAGTGATGATTTTTCCCAAGGGCATGATG

upper sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 3
gtaattcttttttttttttaaattttttgtttttatgtcaattgtcactatacttgatgatatttattcattgaagtcacctatcaaaaaaaaataaaaaataaaattattcattgatttcagtttttaccctttgtttttattatgctagGAGGTAGATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTAAGTGATGATTTTATACAAGGCAATTCTG
                                                                || || ||  || ||| |  |               ||   || |   |||||    | ||| |   | || |   |   ||   |||| ||||||||||| || |||||||||||||| ||||||||||| ||  ||||||||   |||||  ||  ||
---------------------------------------------------------------gtactccttttagacacttccc---------ctgttgatggtatcacagattgaga--aatttatttaccttatccctgaaatttcagGAAGTAGATGAGCCACTACAACTTGATATGTCTGAACTATGTTTGAGCAATGATTTTTCCCAAGGGCATGATG

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|110700942|gb|EE078040.1|EE078040
EST:     TTTTGCACCTATCTACTGTTCGTGCTCCTTGTTATGCTGCTGTTTTCAAG                         GAAGTAGATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTTAGTGAT
genomic: TTTTGCACCTATCTACTGTTCGTGCTCCTTGTTATGCTGCTGTTTTCAAGgtaattcttt ... attatgctagGAGGTAGATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTAAGTGAT
EST: gi|110700943|gb|EE078041.1|EE078041
EST:     TTTTGCACCTATCTACTGTTCGTGCTCCTTGTTATGCTGCTGTTTTCAAG                         GAG-TANATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTAAGTGAT
genomic: TTTTGCACCTATCTACTGTTCGTGCTCCTTGTTATGCTGCTGTTTTCAAGgtaattcttt ... attatgctagGAGGTAGATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTAAGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaataaaattattcattgatttcagtttttaccctttgtttttattatgctagGAGGTAGATGAGCCTCTGCAACTTGATATGTCAGAACTATGTTTAAGTGATGATTTTATACAAGGCAATTCTG
               cattgat  putative branch site (score: 4)
                           tttttaccctttgttt  putative PPT
     taaaattattcattga  TA-rich tract