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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatttgatccccccctctctcccattttcttccattaccgttaattagattgttttggatcttatgagatttagtgtttcccctttgttaataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGTAAAT

Basic information

species Vitis vinifera
transcript Vv11s0065g00450.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G03080.2 (Glycine max), 3'ss of exon 13
gtgagtgatttgatccccccctctctcccattttcttccattaccgttaattagattgttttggatcttatgagatttagtgtttcccctttgttaataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGTAAAT
|||||  ||    | || | ||  |||  ||||       ||  |   || || | |  |   | | ||     || || |  || ||             ||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||
gtgag-aatgcagtgcctcacta-ctcttatttaacattcttttca--aaatatactaataaaggtttttatgcatgtatttattgcc------------gtagGTACTTCGAACAGGACAGATAGACTTGTCTCAGTTTGGAATTGATCCAAGTAAAT

upper sequence: Vv11s0065g00450.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G36490.2 (Glycine max), 3'ss of exon 12
gtgagtgatttgatccccccctctctcccattttcttccattaccgttaattagattgttttggatcttatgagatttagtgtttcccctttgttaataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGTAAAT
|||||  ||    | || | ||       | | |  |  |  |    |  | | | | |  |  ||   |   | |||  ||| |    ||| ||  ||  |||||||||||||| || |||||||| |||||||| ||||||||||||||||||||||
gtgag-aatgcagtgcctcact-------actcttatttaacatttcttttcaaaatatacttaat---aaaggtttttatgtattta-tttattgcta--tagGTACTTCGAACGGGACAGATAGACTTGTCTCAATTTGGAATTGATCCAAGTAAAT
















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|110702756|gb|EE079004.1|EE079004
EST:     AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT                         GTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
genomic: AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTATgtgagtgatt ... taataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
EST: gi|110395278|gb|EC960936.1|EC960936
EST:     AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT                         GTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
genomic: AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTATgtgagtgatt ... taataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
EST: gi|18459586|gb|BM437864.1|BM437864
EST:     AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT                         GTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
genomic: AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTATgtgagtgatt ... taataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
EST: gi|110391622|gb|EC956610.1|EC956610
EST:     AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT                         GTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
genomic: AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTATgtgagtgatt ... taataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
EST: gi|110377829|gb|EC942921.1|EC942921
EST:     AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTAT                         GTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT
genomic: AGTTGCTGCAGAGCCCACCTTTTCGCCAACAAGTAGATTCATTTACTTATgtgagtgatt ... taataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagattgttttggatcttatgagatttagtgtttcccctttgttaataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGTAAAT
                                          tgttaat  putative branch site (score: 3)
                               tgtttcccctttgtt  CT-rich tract
                                        tttgttaataaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgatttgatccccccctctctcccattttcttccattaccgttaattagattgttttggatcttatgagatttagtgtttcccctttgttaataaatagGTACTTCGAACAGGGCAGATAGATTTGTCTCAGTTTGGAATTGATCCAAGTAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT