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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccagatttcttttcttaattttattaatgctctttcacatcatgataaaacaactttgtttgctttgaggtagttaaatttgcggagagtagat...

Basic information

species Vitis vinifera
transcript Vv09s0002g02500.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 12
GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccagatttcttttcttaattttattaatgctctttcacatcatgataaaacaactttgtttgctttgaggtagttaaatttgcggagagt----agat
|||||||||  | |||||||||||||| || ||||||||||| || || ||||||||||||||||| |||||| |   |  |||||    | ||    ||  |  | ||||   |  |  ||| ||||||  | ||      ||  ||      ||| | |  | |    ||| 
GTACTTGACTGTGCAGTTTGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAGAAGGCAAAGATTTTACGGgtatgttta--tttctcgagtaaaaaacat--actccctttggtaaaactatagaacaacacttttaagcaagaactacacttctttacagtaacttttgagaa

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 12
GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaa-gcccag-atttcttttcttaattttattaatgctctttcacatcatgataaaacaactttgtttgctttgaggtagttaaatttgcggagagtagat-----------------------------
|||||||||  |||||||||| ||||| || ||||| ||||| || || |||||||| |||||||||||||||| || ||  || |  ||| ||   | | ||  ||     | |        |   |||| ||    |     ||  | |||   |||  | |   ||  |                             
GTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAGAAGGCTAAGATTTTGCGGgtaaagctcactatctgcttttttgtgtgtgtttttggatagttattgttgagtcggacaaattatccttggaagaatttgtttgctttctgaaatttattttacaatgtcatcgtgcttggttatctcag

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA08G20900.1 (Glycine max), 5'ss of exon 12
GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccagatttcttttcttaat-----tttattaatgctcttt-----------cacatcatgataaaacaactttgtttgctttgaggtagttaaatttgcggagagtagat---------------
|||||||||  |||||||||| ||||| || ||||| ||||| || || || ||||| |||||||||||||||   |    | |||||| |   |     ||| |  ||  |  ||           || || ||  |   | |  ||||||||||||     |||| | ||  |   |      |               
GTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGGgtagagctcactgtcttttttgtgtgtgtgtttttggatagttattgttgggttggacaaattatccttggaaagttttgtttgctttctaa-agtttatttgacaatgtcatcgtgcttggttatctcag

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT1G51710.2 (Arabidopsis thaliana), 5'ss of exon 9
GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccagatttcttttcttaattttattaatgctctttcacatcatgataaaacaactttgtttgctttgaggtagttaaatttgcggagagtagat
|||||||||  ||||||| || || ||||||||||||||||||   |||||||| ||||||||  |  ||||| |      ||   ||| |   | |||  |       | || ||  | || |  |   |     ||  |  |  | ||| |  ||  | ||       
GTACTTGACTGTTCAGTTCGTGCGGTTTTTCTGGAAAAGGGAGAGTAATCAGAAAGCAAAGATCCTCAGGgtacgtttgctttctatttttgtgtctta--agcaaaagtccagatgctcatcattcttatggtaatgtctccaatttgttgatctt-tgaag-------

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: EFJ12930 (Selaginella moellendorffii), 5'ss of exon 11
GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccagatttcttttcttaattttatt---aatgctctttcacatcatgataaaacaactttgtttgctttgaggtagttaaatttgcggagagtagat
 ||||||||  | |||||||||||||| ||||||||  ||||  |||| ||||| |||||||| ||| |||||||    | |||      ||   || |     ||||  |||| |                                                         
ATACTTGACTGTGCAGTTTGTTCGTTTCTTCTGGAAGCGGGAAACGAAACAGAAAGCAAAGATCTTGAGGgtaagttttggttttaaacatttgcttcaaagaaaatgtccttttaacgtgcag-------------------------------------------------

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: EFJ09332 (Selaginella moellendorffii), 5'ss of exon 11
GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccagatttcttttcttaattttatt---aatgctctttcacatcatgataaaacaactttgtttgctttgaggtagttaaatttgcggagagtagat
    |||||  | |||||||||||||| ||||||||| ||||  |||| ||||| |||||||| ||| |||||||    | |||      ||   || |     ||||| |||| |                                                         
----TTGACTGTGCAGTTTGTTCGTTTCTTCTGGAAACGGGAAACGAAACAGAAAGCAAAGATCTTGAGGgtaagttttggttttagacatttgcttcaaaggaaatgcccttttaacgtgcag-------------------------------------------------

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|30296415|gb|CB973209.1|CB973209
EST:     TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
EST: gi|33404879|gb|CF210506.1|CF210506
EST:     GTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCATTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: GTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
EST: gi|110422111|gb|EC988423.1|EC988423
EST:     TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCATTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
EST: gi|33405442|gb|CF211069.1|CF211069
EST:     TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
EST: gi|22009589|gb|BQ794623.1|BQ794623
EST:     TTCG-TTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCATTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
EST: gi|22012121|gb|BQ797155.1|BQ797155
EST:     TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCATTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
EST: gi|110428084|gb|EC994545.1|EC994545
EST:     TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
EST: gi|22009862|gb|BQ794896.1|BQ794896
EST:     TTCG-TTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCATTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
EST: gi|33404796|gb|CF210423.1|CF210423
EST:     TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGG                         AAAGTGGACTATCCATTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT
genomic: TTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccag ... tgttttgcagAAAGTGGACTATCCACTAGAATTGGATGTTTATGATCTCTGTTCGGATGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTGACCATTCAGTTTGTTCGTTTTTTCTGGAAAAGGGAGTCGAATCAGAAGGCAAAGATTTTGCGGgtaagcccagatttcttttcttaattttattaatgctctttcacatcatgataaaacaactttgtttgctttgaggtagttaaatttgcggagagtagat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagagta