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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcgctctttgtagacagggaatctgataattttatcagttttgtaagaatgcacatttgcttgattggatatcttacaacctgcagcaattcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTGCTAAAGGGGCCTGCAGGTTTTGATTACCTTAAAAATGCTTTTGCCAACC

Basic information

species Vitis vinifera
transcript Vv12s0034g02390.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0034g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G20060.1 (Glycine max), 3'ss of exon 8
agcgctctttgtagacagggaatc--tgataattttatcagttttgtaagaatgcacatttgcttgattggatatcttacaacctgcagcaattcct--gacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTGCTAAAGGGGCCTGCAGGTTTTGATTACCTTAAAAATGCTTTTGCCAACC
       || | ||| || |  ||   |   |  || ||    ||||||   |      || |||  ||  |||| ||   || || |  ||||| |  |||||   |||||| | ||||||||||||||||| |||||| | |||||| ||||| | |||||| |||| ||| | || |||||||  ||||| ||||| ||| 
--tttatttagaagatagtgcttcagcgcagacattttctagcttgtaaatgtttgt-cttactttgttttatattttgtgacatg-ataaattcttatgacagATTCTTAAGAAAGAGATAAGCAAAGCACGAATAAGATTAATGGAGTCTTTGGTGAAGGGGTCTGCTGGTCTGGACTACCTTAGGAATGCCTTTGCTAACA

upper sequence: Vv12s0034g02390.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G29160.1 (Glycine max), 3'ss of exon 8
agcgctctttgtagacagggaatctgat--aattttatcagttttgtaagaatgcacatttgcttgattggatatcttacaacctgcagcaattcc-tgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTGCTAAAGGGGCCTGCAGGTTTTGATTACCTTAAAAATGCTTTTGCCAACC
       || | ||| || |  |||| |   |  || ||     |||||   |     ||   ||| ||  |||| ||   || || |  | |    ||||||   |||||| | ||||||||||||||||| |||||| | |||||| ||||| | |||||| |||| ||| | || |||||||  ||||| ||||| ||| 
---ttatttagaagatagtgcttctgcttggacattttctagcctgtaaatgtctgtcttactttgtttttatattttgtgacatgtaaaattcttatgacagATTCTTAAGAAAGAGATAAGCAAAGCACGAATAAGATTAATGGAGTCTTTGGTGAAGGGGTCTGCTGGTCTGGACTACCTTAGGAATGCCTTTGCTAACA
















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|71864151|gb|DT013206.1|DT013206
EST:     ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAG                         GCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
genomic: ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAGgtgtgttttt ... ttcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
EST: gi|71882773|gb|DT031828.1|DT031828
EST:     ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAG                         GCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
genomic: ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAGgtgtgttttt ... ttcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
EST: gi|71883765|gb|DT032820.1|DT032820
EST:     ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAG                         GCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
genomic: ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAGgtgtgttttt ... ttcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
EST: gi|110693590|gb|EE069953.1|EE069953
EST:     ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAG                         GCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
genomic: ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAGgtgtgttttt ... ttcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
EST: gi|71884359|gb|DT033414.1|DT033414
EST:     ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAG                         GCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
genomic: ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAGgtgtgttttt ... ttcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
EST: gi|71887561|gb|DT036616.1|DT036616
EST:     ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAG                         GCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
genomic: ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAGgtgtgttttt ... ttcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
EST: gi|71881157|gb|DT030212.1|DT030212
EST:     ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAG                         GCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG
genomic: ATGTTATTGCAATGATCAAGGGTCTGCGCTTTGTTCTGGAGCAGGTTCAGgtgtgttttt ... ttcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaatgcacatttgcttgattggatatcttacaacctgcagcaattcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTGCTAAAGGGGCCTGCAGGTTTTGATTACCTTAAAAATGCTTTTGCCAACC
                          atcttac  putative branch site (score: 3)
                                             ttcct  putative PPT
                        atatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcgctctttgtagacagggaatctgataattttatcagttttgtaagaatgcacatttgcttgattggatatcttacaacctgcagcaattcctgacagGCACTTAAGCAGGAGATAAGCAAAGCACGTATAAGAATGATGGAGCCTTTGCTAAAGGGGCCTGCAGGTTTTGATTACCTTAAAAATGCTTTTGCCAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - -gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacctgc