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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaacatagccttaaggaatagctgatggctgaaacctcttaataagagctttcttcatttatttctcttaatgctgagagcaaccctttctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGATCGACCAGGTGTAGAAATGGAATCGCGAATTGATGCGGAA

Basic information

species Vitis vinifera
transcript Vv16s0050g02630.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 6
-----ccaa--acatagccttaaggaatagctgatggctgaaacctcttaataagagctttcttcatttatttctcttaatgctgagagcaaccctttctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGATCGACCAGGTGTAGAAATGGAATCGCGAATTGATGCGGAA
       |   | |   | || || |||  ||     ||||||  |||  |    |  |||  |    || |   |||  || ||        ||| | |   ||||||||| | ||| |||||||||||| |||| |||||| || |||| ||||| |||||| ||   |||||| | || || |||||||| || 
aattattagttagacgacatttagaaatttctt----ctgaaat-tctggacttaacttttaatttcataatgtgctttgtgttgttttt--tcctctatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG

upper sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 14
----ccaaacatagccttaaggaatagctgatggctgaaacctcttaataagagctttcttcatttatttctcttaatgctgagagcaaccctttctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGATCGACCAGGTGTAGAAATGGAATCGCGAATTGATGCGGAA
        | |||| |   |   | |  |  | |||||||| ||| ||       |||  |    |  |   |||   | ||        ||| | |   ||||||||| | ||| |||||||||||| |||| |||||| || |||| ||||| |||||| ||   |||||| | || || |||||||| || 
aaattattagatagacaacatttacaaatt-tcgctgaaac-tctgaacttatcttttaatttcatgatgagctttgcgttgttttt--tcctctatgcacaagGTATCAAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG
















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|110419126|gb|EC985328.1|EC985328
EST:     CTGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATG                         GTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
genomic: CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATGgtaattttat ... tctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
EST: gi|27580764|gb|CB003459.1|CB003459
EST:     CTGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATG                         GTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
genomic: CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATGgtaattttat ... tctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
EST: gi|110363183|gb|EC926755.1|EC926755
EST:     CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATG                         GTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
genomic: CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATGgtaattttat ... tctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
EST: gi|27579344|gb|CB002039.1|CB002039
EST:     CTGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATG                         GTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
genomic: CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATGgtaattttat ... tctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
EST: gi|110420745|gb|EC987025.1|EC987025
EST:     CTGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATG                         GTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
genomic: CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATGgtaattttat ... tctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
EST: gi|34549961|gb|CF518193.1|CF518193
EST:     CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATG                         GTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
genomic: CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATGgtaattttat ... tctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
EST: gi|110363099|gb|EC926669.1|EC926669
EST:     CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATG                         GTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
genomic: CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATGgtaattttat ... tctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
EST: gi|34550831|gb|CF519047.1|CF519047
EST:     CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATG                         GTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT
genomic: CCGGAGCAAGTAGTGATCTAAACACAGCCACAGAGCTTGCCCAATATATGgtaattttat ... tctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagctttcttcatttatttctcttaatgctgagagcaaccctttctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGATCGACCAGGTGTAGAAATGGAATCGCGAATTGATGCGGAA
                      tcttaat  putative branch site (score: 3)
                                        ccctttctat  putative PPT
             atttatttctcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaacatagccttaaggaatagctgatggctgaaacctcttaataagagctttcttcatttatttctcttaatgctgagagcaaccctttctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGATCGACCAGGTGTAGAAATGGAATCGCGAATTGATGCGGAA

ccaaaca
- - - - - - - -aggaata
- - - - - - - - - - - -ctgatgg
- - - - - - - - - - - - - - - ctgaaac
- - - - - - - - - - - - - - - - - - - - - aataaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaccct