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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA

Basic information

species Vitis vinifera
transcript Vv03s0017g00680.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
gtgagtcaacttttccatcaatctggatgtttcttaacatgcat-ctgtctcatagat-ctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
                 | | |   | |   | ||   || |||    |  | |  |  |||| |||   | |  || ||    || |   |||||||||| ||||| |||||||| |||||||| |||||||| ||||| || |||||||| || |||||||| || ||||||||  ||||||||||||||||
----------------gtgagtgcag-taacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctt-taaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G167872_T02 (Zea mays), 3'ss of exon 2
----gt-gagtcaacttttccatcaatctg--gatg--tttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
    || |||| || |||| ||     | |  ||||   |||||    |    || |||  ||  | ||| | |||||  ||| | |||      |  ||||||| |||||||| |||||||| || ||||| || ||||| |||||||| ||||||||||| || |||||||||||||||||  | ||||||||||||||
gtcagtagagtaaaattttgcactgtgccgctgatggccttcttgttctaacact-tcttttatgtttttgtcattttgatttgagtatc-----tgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATTGGATTGGGCCAAGGATGGATTTCATTCCTGGTGTCGATGGTCCTAGTGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
gtgagtcaacttttccatcaatctggatgtttcttaacatgca-tctgtctcatagatct--ttctaattttttttttattatt-attatttac-agCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
|| ||| || |      | | | | |    |   || |      |||  ||  | | | |  || | ||| |  |||| ||||| |  ||  || ||||||||||||||| |||||||| || ||||| || ||||| ||||| || |||||||| || || ||||| |||||||||||  ||||||||||||||||
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 4
gtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
||||||     |||   |   | | | ||||  ||    |   | |   |  |  || ||  ||||| |   |    | | ||||||  ||||||| ||||| || |||||| | |||||||| |||||||||||||||||||||||||| ||| ||||||||||||||||||||||||||||||| |||||
gtgagttttgatttgtttttgtttaggtgttgttt----ttttttttctttttcaattttgttaattctcactgatgtgtgattattggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTGAGGCCTTTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGCATTGATGGTCCAAGTGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
gtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
||||||  | || |   |         |||||      |||  | | |||   | || ||  ||||| ||  |    | | || ||   ||||||| ||||| || |||||| | |||||||| ||||| ||||| |||||||||||||| ||| ||||||||||||||||||| ||||||||||| |||||
gtgagttgatttgtattttt-------tgttttggtgtatgtttttttctttca-attttgataattcttactagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 4
gtgagtcaacttt--tccatcaatctggatgtttcttaacatgcatctgtctcat-agatctttctaattttttttttattat--tattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
|||||   | |||  |   |  |  |   | || | ||   ||  ||  | |  | |  ||||     || | |   |   ||   ||| ||  ||||||| ||||| || |||||| | || ||||| ||||||||||||||||| |||||||| ||  |||||||||||||||| ||||||||||| || |||||
gtgagctgattttgtttggtttaattttttattgcgtacactgtttccattttttcatgtcttgacctttgtctcactgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGGCCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGCCCAAGTGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 2
gtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
|||||     |||    |     |  || |||  |  |||  |    |  |||   |    ||   | |   |    |   ||| ||  ||||||| ||||| || |||||| | || ||||| |||||||| |||||||| |||||||| ||  |||||||||||||||| |||||||||||||| |||||
gtgagctgctttt---gtttggtttaattttttattgcatatactgtttccatgtcttgacctttgtctcactgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGACCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGTCCAAGTGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtcaacttttccatcaatctggatgtttcttaacatgcatct-gtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
  |  |  | |||||   ||     ||  ||| ||     |  ||| | | || | |  ||||| |  |   |||| |      |  || ||||||| ||||| |||||||| || |||||||||||||| || || || ||||||||||| ||||| ||||||||||| |||||||||||||||||||| ||
--gtatgtagttttcttacacgaaagaaatttttt-----gtttctagacacaaaaaagtttctcacgtcacttttttc-----tggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
    || | | ||||  |  |    ||||||  | || |   |    |  ||   | |||    | || ||| || | |          ||||||| ||||| |||||||| || ||||||||||| ||  | ||||||||||||||||| ||||| ||||||||||| || ||||||||||||||||| ||
----gtaagcatttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaacttc---acttgtttcttgtga----------cagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA

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|110732834|gb|EE108465.1|EE108465
EST:     GAGGTGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGCTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTANAGTTCACCATTGTGAGGCCTTTTTACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|71857207|gb|DT006262.1|DT006262
EST:     GAGGTGGTCCTATGCTTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|71859790|gb|DT008845.1|DT008845
EST:     GAGGTGGTCCTATGCTTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|110686702|gb|EE064638.1|EE064638
EST:     GAGGTGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTANAGTTCACCATTGTGAGGCCTTTTAACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|110359156|gb|EC920189.1|EC920189
EST:     GAGGTGGTCCTATGCTTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|30253074|gb|CB970625.1|CB970625
EST:     GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|110696696|gb|EE073040.1|EE073040
EST:     GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|30320980|gb|CD004242.1|CD004242
EST:     GAGGTGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGCTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|110685502|gb|EE062276.1|EE062276
EST:     GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTTACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
EST: gi|77585098|gb|DV221638.1|DV221638
EST:     GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTT
EST: gi|71855470|gb|DT004525.1|DT004525
EST:     GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATG                         CTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT
genomic: GAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaac ... ttatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA
                      ttctaat  putative branch site (score: 2)
              atagatctttctaatt  TA-rich tract