Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtacacataaccctattacagtgaattcttcagttcttttcctaactataaaatctgatggagctgacataatccattgtttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAAACTGAAAAAATTTTGAACAAGCTAATCTCCAAGAATTCCCATGAGATAC

Basic information

species Vitis vinifera
transcript Vv15s0048g02730.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G23700.1 (Glycine max), 3'ss of exon 6
------------------gtctgtacacataaccctattaca-gtgaattcttcagttctt---ttcctaactataaaatctgatgg--agctgacataatccatt--gtttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAAACTGAAAAAATTTTGAACAAGCTAATCTCCAAGAATTCCCATGAGATAC
                  |    || |  |  | ||  | |  || |||| ||   |         || || | | || |    |||  |    || |  |   ||  ||||| || ||||||||||| || |||||||| || || || ||||| || |||| | |||||||||||||||| ||||||||| | |||||||||||||| ||| | ||||
gttgtgcgctgtgctctcgctgatatatgtttctcttgtccgtgtaaattattatatatagaagcacccaatttttaactaaattggctaatcaacttcttttgttttgttttcatctagTTCCTGCCAGTGGTGGAAGGAACCGGGATAGGATCCCTGGAGAGGGAGCAAACTGAAAAAATATTGAACAAGATCATCTCCAAGAATTCTCATAACATAC

upper sequence: Vv15s0048g02730.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G12440.2 (Glycine max), 3'ss of exon 6
------------------gtctgtacacataaccctattacagtgaattcttcagttctt----ttcctaactataaaatctgatgg--agctgacataatccatt--gtttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAAACTGAAAAAATTTTGAACAAGCTAATCTCCAAGAATTCCCATGAGATAC
                       || |  |  | ||  | ||   || |  |||  | |       || || | | || |    |||  |  | || |  |   ||  ||||| || ||||| ||||| ||||||||||| || || || |||||||| |||| | |||||||||| ||||| ||||||||| | |||||||||||||| ||| | ||||
gttgtgtgctgtgctctcactgatatatgtttctcttgtccatgtaaattatcatatatagaagcacccaatttttaactaaattggctaattaacttcctttgttttgttttcatctagTTTCTGCCAGTAGTGGAAGGAACCGGGATAGGATCACTGGAGAGGGAGCAAACTGAGAAAATATTGAACAAGATCATCTCCAAGAATTCTCATAACATAC
















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|110690893|gb|EE068371.1|EE068371
EST:     AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAG                         TTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
genomic: AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAGgtctgtacac ... ttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
EST: gi|26257434|gb|CA808497.1|CA808497
EST:     AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAG                         TTCCTGCCGGTAGTGGAAGGGACTGGAATTGGATCACTAGAGAAGCAGCAA
genomic: AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAGgtctgtacac ... ttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
EST: gi|30252208|gb|CB969759.1|CB969759
EST:     GAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAAGGAAAGTATCGCAAG                         TTCCTGCCGGGAGTGGAAGGGACAGGAATTGGATCACT
genomic: GAAGTTGCCTGGAGAAAAACCTGAAAAACATAAA-GGAAAGTATCGCAAGgtctgtacac ... ttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACT
EST: gi|110409092|gb|EC974748.1|EC974748
EST:     AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAG                         TTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
genomic: AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAGgtctgtacac ... ttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
EST: gi|110715690|gb|EE094027.1|EE094027
EST:     AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAG                         TTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
genomic: AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAGgtctgtacac ... ttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
EST: gi|110367133|gb|EC931058.1|EC931058
EST:     AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAG                         TTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
genomic: AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAGgtctgtacac ... ttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA
EST: gi|26257329|gb|CA808392.1|CA808392
EST:     AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAG                         TTCCTGCCGGTAGTGGAAGGGACTGGAATTGGATCACTAGAGAAGCAGCAA
genomic: AGAAGTTGCCTGGAGAAAAACCTGAAAAACATAAAGGAAAGTATCGCAAGgtctgtacac ... ttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcctaactataaaatctgatggagctgacataatccattgtttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAAACTGAAAAAATTTTGAACAAGCTAATCTCCAAGAATTCCCATGAGATAC
                                            tttttattt  CT-rich tract
                                 ataatccattgttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtacacataaccctattacagtgaattcttcagttcttttcctaactataaaatctgatggagctgacataatccattgtttttatttagTTCCTGCCGGTAGTGGAAGGGACAGGAATTGGATCACTAGAGAAGCAGCAAACTGAAAAAATTTTGAACAAGCTAATCTCCAAGAATTCCCATGAGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT