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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag

Basic information

species Vitis vinifera
transcript Vv03s0017g00680.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaact--tttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag
 | || ||||||||||  |||||||||||||||||| |||||| ||| ||| ||||||| ||||| ||||| |||||  | ||||||||| | |||| ||||||||  | |   ||   | | ||  |   || | | | |  | | |||  |   |  |||| | |  |||                      
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcagtaacttttgttattcatgtcattacctga-acac-tttgtaaccgtgtgctttttgagctttaaccag----------------

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgca-tctgtctcatagatct--ttctaattttttttttattatt-attatttacag-
 |||| ||||||||||  || ||||| ||||||||| |||| | ||| || |||||||||||||| || ||||||||| | ||||||||| |  | | |||| ||| || |      | | | | |    |   || |      |||  ||  | | | |  || | ||| |  |||| ||||| |  ||  ||   
GTTCTTAAAGAAGATGAGTCGCCCTGTATTTTTGGTCCAATCGTGAAACAAAGATGGTCCTATGCATGCGCAAAGCAACTTATTGAGAGGCTTGTATTTGgttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G30490.2 (Glycine max), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttt--tccatcaatctggatgtttcttaacatgcatctgtctcat-agatctttctaattttttttttattat--tattatttacag
 | || || || ||||  || || || ||||||||||||||||| |||||||||||||||||||||||||| ||||| || ||||||||| |  |||||||||||   | |||  |   |  |  |   | || | ||   ||  ||  | |  | |  ||||     || | |   |   ||   ||| ||  |||
GTACTTAAGGAGGATGAGTCTCCTTGTATTTTTGGTTCAATTGAAAAGCAGAGATGGTCCTATGCCTGTGCTAAGCAGTTGATTGAGAGGCTTGTTTATGgtgagctgattttgtttggtttaattttttattgcgtacactgtttccattttttcatgtcttgacctttgtctcactgagatgacattgttggcag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 2
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag
 | || || || ||||  || || || ||||||||||||||||| |||||||||||||||||||| ||||| ||||| || ||||||||| |  |||||||||||     |||    |     |  || |||  |  |||  |    |  |||   |    ||   | |   |    |   ||| ||  |||
GTACTTAAGGAGGATGAATCTCCTTGTATTTTTGGTTCAATTGAAAAGCAGAGATGGTCCTATGCATGTGCTAAGCAGTTGATTGAGAGGCTTGTTTATGgtgagctgctttt---gtttggtttaattttttattgcatatactgtttccatgtcttgacctttgtctcactgagatgacattgttggcag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag
 |||| |||||||| |  || || |||||||||||||| ||||| || ||||| ||||| ||||||||||| || || || ||||||||| |||||||||||||||     |||   |   | | | ||||  ||    |   | |   |  |  || ||  ||||| |   |    | | ||||||  |||
GTTCTTAAAGAAGACGAGTCTCCTTGCATTTTTGGTTCTATTGAAAAACAGAGGTGGTCTTATGCCTGTGCGAAACAGTTGATTGAGAGGCTGATTTATGgtgagttttgatttgtttttgtttaggtgttgttt----ttttttttctttttcaattttgttaattctcactgatgtgtgattattggcag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag
 |||| |||||||| |  || || |||||||||||||| || ||||||||||| ||||| ||||| |||||||| || || ||||||||| |||||| ||||||||  | || |   |         |||||      |||  | | |||   | || ||  ||||| ||  |    | | || ||   |||
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttt-------tgttttggtgtatgtttttttctttca-attttgataattcttactagtgtgtgatcatcggcag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatct-gtctcatagatctttctaattttttttttattattattatttacag
 | ||||||||||||   ||||| ||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||| | ||||||||  |  |||| |||  ||  | |||||   ||     ||  ||| ||     |  ||| | | || | |  ||||| |  |   |||| |      |  || |||
GTACTCAAAGAAGATATATCCCCTTGCATCTTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgt--agttttcttacacgaaagaaatttttt-----gtttctagacacaaaaaagtttctcacgtcacttttttc-----tggttgcag

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag
 |||| |||||||||   ||||| ||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||| | ||||||||  |  |||| ||| ||    | ||||  |  |    ||||||  | || |   |    |  ||   | |||    | || ||| || | |             
GTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaag----catttctgtttaagatgatgttggtaaaaacaaaaggtttacacttaacttc---acttgtttcttgtgacag----------

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: EFJ18978 (Selaginella moellendorffii), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatctg-tctcata-gatctttctaattttttttttattattattatttacag
 | || || || || |  || || |||||||||||  | |||||||||||| ||||||| ||||| |||||||||||  | || ||| |  | || |||||| ||  || |||    |  |    ||   |   | |  ||  | || | | |||  ||||||| |                            
GTGCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCGAGCGTGTCATCTATGgtaagcaaagtttctgtttga--aagaaactaagtcatgtggttgtggtgttatataatctttccag---------------------------

upper sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: EFJ07025 (Selaginella moellendorffii), 5'ss of exon 4
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctgga-tgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag
 | || || || || |  || || |||||||||||  | |||||||||||| ||||||| ||||| |||||||||||  | || ||| |  | || |||||| ||  || |||    |  |     | |   |  |    |     ||| | ||| ||||||| |                            
GTCCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCGAGCGTGTCATCTATGgtaagcaaagtttctgtttgaaagaaactaagttatgtggttgtggtgttttata-atctttccag---------------------------

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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG