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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgctaagtaaaaactagttcagtggcataaaatcatctgaaataatcttggtttattgattttttctattcactacttcgtgtcttatatctgcagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCGAATGGTCAAGACACAGGCAACTGTGTATCTCTGTTACGGGTAAAT

Basic information

species Vitis vinifera
transcript Vv12s0059g02310.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G46000.1 (Glycine max), 3'ss of exon 9
cttttgctaagtaaaaac-tagttcagtggcataaaatcatctgaaataatcttggtttattgattttttctattcactacttcgtgtcttatatctgcagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCGAATGGTCAAGACACAGGCAACTGTGTATCTCTGTTACGGGTAAAT
   |    |||   |  | |   |  ||||  || |   || |  |||| |  |   || |   ||| |  | || ||   |||      |  |    |||||||||||||| || |||||||| ||||| |||||||||||||| || || || ||   |||||| || ||||||||||||||  |||| ||||||
aagtgataaagcgcaggcatgcgtttgtgggttatatctat-tagaatatttgtatattgtatgtttgtcattttaacattttcaacctcttaaataacagTGGGATATTCTTTCCAATGGTGGAGTTGTCCAAGAAATGGCACACATTGCAAACGGAAGAGACACTGGAAACTGTGTATCTCTACTACGAGTAAAT

upper sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G32050.1 (Glycine max), 3'ss of exon 10
cttttgctaagtaaaaactagttcagtggcataaaatcatctgaaataatcttggtttattgattttttctat-tcactacttcgtgtcttatatctgcagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCGAATGGTCAAGACACAGGCAACTGTGTATCTCTGTTACGGGTAAAT
 ||    |   |    | || |    |  | | |  |||||| || |||  ||||||| ||  | |  |  || | |||  |||    |||        ||||||||||||| || || ||||| |||||||||||||||||||| || || ||||| | |||||| || || ||||| |||||  | ||||| |||
tttcatgtgtttgtcgattaatgttatctcttcatctcatcttaattaaa-ttggtttgtttttgtgattcatctaactttttcaaccctttggaaaatagTGGGATATTCTTTCCAACGGTGGAGTTGTTCAAGAAATGGCACACATTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT

upper sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G10710.1 (Glycine max), 3'ss of exon 10
cttttgctaagtaaaaactagttcagtgg-cataaaatcatctgaaataatcttggtttattgattttttcta--ttcactacttc--gtgtcttatatctgcagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCGAATGGTCAAGACACAGGCAACTGTGTATCTCTGTTACGGGTAAAT
    || |  || |   ||| |    ||  | | |  ||   | | ||    || || ||||| || ||| |   || |  | ||       |||| | |  |||||||| ||||| || ||||| || ||||| |||||||||||||| || || || ||   ||||||||| ||||||||||||||  | || ||||||
----tg-tgggtcagtcctaatatcttgatctttatttctatttagatttaatttgtatattgtttctttgtcattttaacattttcaaccccttaaaacgacagTGGGACATTCTTTCCAATGGAGGAGTTGTCCAAGAAATGGCACACATTGCAAACGGAAGAGACACAGGAAACTGTGTATCTCTACTTCGAGTAAAT

upper sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G38430.1 (Glycine max), 3'ss of exon 10
cttttgctaagtaaaaactagttcagtggcataaaatcatctgaaataatcttggtttattgattttttctattcactacttcgtgtcttatatctg-cagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCGAATGGTCAAGACACAGGCAACTGTGTATCTCTGTTACGGGTAAAT
 | ||  |   | ||   ||  ||     | | |  | |  | || |  | |   |||  |||||  |   | |   |    ||   | | |      |||||||||||||| || || ||||| ||||| |||||||||||||| || || ||||| | |||||| || || ||||| || ||  | || || |||
gtgtttgtctttgaatgttatctcttcatc-tcatcttaattaaatttgtttgttttttatgattcatctaactttttcaaccggaccctttggaaaacagTGGGATATTCTTTCCAACGGTGGAGTTGTCCAAGAAATGGCACACATTGCCAATGGCCGAGACACTGGAAATTGTGTCTCCCTACTTCGTGTGAAT

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|351024273|gb|FQ423696.1|FQ423696
EST:     CGCCAAAGAGAGTATTTGATTTTCTCCGTGATGAGAATTCTCGCAGCGAG                         TGGGATATTCTCTCAAATGGTGAGGTTGTTCAAGA
genomic: CGCCAAAGAGAGTATTTGATTTTCTCCGTGATGAGAATTCTCGCAGCGAGgtatgattgt ... atatctgcagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGA
EST: gi|110418253|gb|EC984389.1|EC984389
EST:     CGCCAAAGAGAGTATTTGATTTTCTCCGTGATGAGAATTCTCGCAGCGAG                         TGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCG
genomic: CGCCAAAGAGAGTATTTGATTTTCTCCGTGATGAGAATTCTCGCAGCGAGgtatgattgt ... atatctgcagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatcttggtttattgattttttctattcactacttcgtgtcttatatctgcagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCGAATGGTCAAGACACAGGCAACTGTGTATCTCTGTTACGGGTAAAT
            tattgat  putative branch site (score: 3)
          tttattgattttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgctaagtaaaaactagttcagtggcataaaatcatctgaaataatcttggtttattgattttttctattcactacttcgtgtcttatatctgcagTGGGATATTCTCTCAAATGGTGGGGTTGTTCAAGAAATGGCACATATAGCGAATGGTCAAGACACAGGCAACTGTGTATCTCTGTTACGGGTAAAT

cttttgc
- - - - - gtaaaaa
- - - - - - - - - - - - - - - - aaaatca
- - - - - - - - - - - - - - - - - - - - - gaaataa