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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCCACTTCCAACTCCAGCAAGTGCTACCTCCACTCCAGCATTGAACTATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtagatttaaatgtgaaaaagggttaaatatttctttatttatgattactcaagaaaaagtgggaacccattggagatggggacgcagccacaa...

Basic information

species Vitis vinifera
transcript Vv10s0003g03510.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03510.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G30070.2 (Arabidopsis thaliana), 5'ss of exon 2
TGCTCCACTTCCAACTCCAGCAAGTGCTACCTCCACTCCAGCATTGAACTATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcg---tagatttaaatgtgaaaaagggttaaatatttctttatt--tatgattactcaagaaaaagtgggaacccattggagatggggacgcagccacaa---------
||| ||  || |  || | |  |   |    ||  || | |||||||||||||| || || ||| ||||||| ||||||||||| ||||| ||||||||||||  |     ||| ||       |  ||   | || ||| |   ||    |||| || |    |   | ||         ||     ||  |    |                
TGCACCGGTTTCTTCTTCGGGTAAGCCGGTTTCTTCTTCGGCATTGAACTATGTAACTCTCGGAACATTCAGCTGGGATCAAGACAATGACAAAGTCAAGgtaaaccattcagagttttcctcaatcaatactcaattatgttaataaccatatgcttgcgtgtggttatgtaatggtgttttcttattgatgcattatttttttgtttatcag
















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|110724230|gb|EE099886.1|EE099886
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|71876428|gb|DT025483.1|DT025483
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|349830432|gb|FQ420692.1|FQ420692
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|37188594|gb|CF607943.1|CF607943
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|32458912|gb|CD800086.1|CD800086
EST:     TCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGT
genomic: TCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCC--TGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGT
EST: gi|33408704|gb|CF214331.1|CF214331
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|30135042|gb|CB920380.1|CB920380
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|110710551|gb|EE087004.1|EE087004
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|110362256|gb|EC925776.1|EC925776
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|110378873|gb|EC944028.1|EC944028
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|110402805|gb|EC963503.1|EC963503
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|22013016|gb|BQ798050.1|BQ798050
EST:     ATGTCACACTTGGATCATTCAG-TGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|77583025|gb|DV220546.1|DV220546
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|110688571|gb|EE067275.1|EE067275
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|33408870|gb|CF214497.1|CF214497
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
EST: gi|110724425|gb|EE100242.1|EE100242
EST:     ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAG                         ATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC
genomic: ATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtag ... ctcccctcagATATATGTGTCCCTGGAAGGTGTTGAGCAGGAGAAAATGGATACACTGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCCACTTCCAACTCCAGCAAGTGCTACCTCCACTCCAGCATTGAACTATGTCACACTTGGATCATTCAGTTGGGATCAAGATAATGAAAAAGTCAAGgtatgcgtagatttaaatgtgaaaaagggttaaatatttctttatttatgattactcaagaaaaagtgggaacccattggagatggggacgcagccacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagatgg