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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCTGAAGTGGTTGCTGACCCTCTAGGTGAAATTGCGCAGACATTCCAGAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAGgtatcttttttttctctctgtagtcccatggaaaagatttaagacggtgaaccaattatagtgcacatagcaacaggttttaaatttcagttaatcaatt...

Basic information

species Vitis vinifera
transcript Vv11s0016g04250.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA09G31980.1 (Glycine max), 5'ss of exon 12
ATGCCTGAAGTGGTTGCTGACCCTCTAGGTGAAATTGCGCAGACATTCCAGAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAGgtatc-ttttttttctctctgtagtcccatggaaaaga---tttaagacggtgaaccaattatagtgcacatagcaacaggttttaaatttcagttaatcaatt
|||||||||||||| ||||| |||| ||||||| || |  ||| |||||| || || ||||| |||||||| || ||||||||||| || ||||||||||||||  | ||  | ||   |   ||   |    ||| |   | |||     |  | |||| | | |  |  |      || | || | ||  |  |||      
ATGCCTGAAGTGGTAGCTGATCCTCAAGGTGAAGTTTCCAAGATATTCCAAAATCTAGGAGTATGTGTTGTTCAGCAGTGTGCCAAAATACGCCAACAAGgtattatgttactacttgataatgtttgagaagaaaaagcctctaatcaaatctatcaataacaatata-gtgaagctagttgttcacttgtatctaactg---

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA07G09820.1 (Glycine max), 5'ss of exon 12
ATGCCTGAAGTGGTTGCTGACCCTCTAGGTGAAATTGCGCAGACATTCCAGAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAGgtat-cttttttttctctctgtagtcccatggaaaaga---tttaagacggtgaaccaattatagtgcacatagcaacaggttttaaatttcagttaatcaatt
|||||||||||||| ||||| |||| ||||||| || |  ||| |||||| || || ||||| |||||||| || ||||||||||| || |||||||||||||| |||||  | ||   |   ||   |    ||| |   | ||| |   |  |  ||| | |    || |      |  | ||   ||  |  |||      
ATGCCTGAAGTGGTAGCTGATCCTCAAGGTGAAGTTTCCAAGATATTCCAAAATCTAGGAGTATGTGTTGTTCAGCAGTGTGCCAAAATACGCCAACAAGgtattcttttcctacttgataatgtttgagaagaaaaagcctctaataaaatctattaataacaagatac-tgaagctaattgttctcttgtatctaactg---
















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|32267762|gb|CD716725.1|CD716725
EST:     GAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAG                         TGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAAG
genomic: GAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAGgtatcttttt ... ttctgtccagTGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAAG
EST: gi|110718478|gb|EE095359.1|EE095359
EST:     GAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAG                         TGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAGG
genomic: GAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAGgtatcttttt ... ttctgtccagTGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAAG
EST: gi|30328118|gb|CD011380.1|CD011380
EST:     GAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAG                         TGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAAG
genomic: GAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAGgtatcttttt ... ttctgtccagTGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAAG
EST: gi|32269673|gb|CD718832.1|CD718832
EST:     GAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAG                         TGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAAG
genomic: GAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAGgtatcttttt ... ttctgtccagTGTCAACAGCTGTCACCTATGATAAATTTATCAAAGCAATCAGAGTGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCCTGAAGTGGTTGCTGACCCTCTAGGTGAAATTGCGCAGACATTCCAGAACCTTGGAGTCTGTGTTGTCCAACAGTGTGCCAAGATTCGCCAACAAGgtatcttttttttctctctgtagtcccatggaaaagatttaagacggtgaaccaattatagtgcacatagcaacaggttttaaatttcagttaatcaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaccaa