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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgactttcctgccttcataggtttttgaatataatggaaaccatttacttgcatagatctgatacctctcggattgagcatttgaacttttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG

Basic information

species Vitis vinifera
transcript Vv09s0002g05800.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 8
------ctgactttcctgccttcatag-gtttttgaatataatggaaaccatttacttgcatagatctgatacctctcggattgagcatttgaacttttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
         |  | | |   | || ||   | | |||  | || |   | ||   ||||    ||||    | || |   ||| |   | |      |  | | |||||||| ||||||||||| || ||||||||| |  | ||||| ||||| || |||||||| || || || |||||||| || || || ||||||||||| |
ttcaaaacaatgtgcatatatacacagcactatagaacgtcatagctcctatac-cttgt---gatcatgcaacttt---attcactttctctttcatcatcttcagGCGGTCTGCACAGAAGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCATGTAACACAAGAGGACTTTGAGATGGCAGTGGCGAAGGTGATGAAGAAAG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 8
-ctgactttcctgccttcataggtttttgaatataatggaaaccattta---cttgcatagatctgatacctctcggattgagcatttgaacttttgtt-tgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
  |   |       ||||||  | |      | |  ||     | |||    ||||  | |||  ||     |     || | |||||    ||| | | | ||||| || || ||||| || || ||||||||| |  | ||||| ||||| ||||| |||||||| || ||||||||||| || ||||| ||||||||||| |
gtttgttaaatccacttcatctgatgaactgtttgctgcctctcgtttcaatcttgtgttgattcgaagtaac----gtttaacattttttttttggctgttcagGCCGTCTGTACAGAGGCTGGAATGTTTGCTCTCCGTGAGAGAAGGGTGCACGTTACACAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
ctgactttcctgccttcataggtttttgaatataatggaaaccat--ttacttgcatagatctgatacctctcggattgagcatttgaacttttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
 |    | | |     ||    ||| |||   | || |   | ||   |   ||  |   | | | || | |    || |   |||     || |||  ||||| || |||||||| || || ||||||||| |  | ||||| ||||| ||||| || ||||| || ||||||||||| || ||||| ||||||||||| |
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggtt--cagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 8
ctgactttcctgccttcataggtttttgaatat-aatggaaaccatttacttgcatagatctgatacctctcggattgagcatttgaacttt---tgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
   |||        | || ||   ||||  | | ||||  |||    |   |   ||  | |  ||   |  |     | |  |  || |||     ||||||||| || ||||| ||||| || |||||||| ||||||||| ||||||| ||||| || ||||| ||||| ||||||||||| ||||| |||||||| ||||
--tactaatgcaaatgcagagcaatttgtttgtcaatgttaacttaatgtgttattaagtattttatagcctgacc--aacgctcaaattttgtgcctttgcagGCTGTTTGCACCGAAGCTGGAATGTTTGCATTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCTGTGGCCAAGGTGATGAAAAAGG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 8
-------ctgactttcctgccttcataggtttttgaatataatggaaaccatttac---ttgcatagatctgatacctctcggattgagcatttgaacttttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
       | ||      ||  |    | ||| || | | ||||| ||   |||||    ||  ||||       | | |||  |||      |||  | || || ||||||| || ||||| ||||| || |||||||||||||||||| ||||||| ||||| || ||||| ||||| |||||||| || || || |||||||| ||||
gcaaatgcagagcaatttgtttgtcaatgttgttaact-taatgcaa--tatttaagtattttatagcctgaccaacgctcaaatt------ttgtgcctt-gtatgcagGCTGTTTGCACTGAAGCTGGAATGTTTGCTTTGAGGGAGCGGAGGGTACACGTGACTCAGGAGGATTTTGAGATGGCCGTGGCGAAGGTGATGAAAAAGG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ28638 (Selaginella moellendorffii), 3'ss of exon 7
ctgactttcctgccttcataggtttttgaatataatggaaaccatttacttgcatagatctgatacctctcggattgagcatttgaacttttgtt-tgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
                           |  | | |||    |  |||| ||     | ||    ||  |   |  ||    |||    ||||| | | |||||||| ||||| || || || ||||||||| || | |||||| | ||||| || || |||||||||||||| ||||| || |||||||||||||||||||
---------------------------gtttgtgatgctcgcgctttagtt-----ggtccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGATTTCGACATGGCGGTGGCCAAAGTGATGAAGAAGG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
ctgactttcctgccttcataggtttttgaatataatggaaaccatttacttgcatagatctgatacctctcggattgagcatttgaacttttgtt-tgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
                           |  | | |||    |  |||| ||     | ||    ||  |   |  ||    |||    ||||| | | |||||||| ||||| || || || ||||||||| || | |||||| | ||||| || || |||||||| ||||| ||| | || |||||||||||||||||||
---------------------------gtttgtgatgctcgcgctttagtt-----ggtccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ20576 (Selaginella moellendorffii), 3'ss of exon 7
ctgactttcctgccttcataggtttttgaatataatggaaaccatttacttgcatagatctgatacctctcggattgagcatttgaacttttgtt-tgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
                           |  | | |||    |  |||| ||     | ||    ||  |   |  ||    |||    ||||| | | |||||||| ||||| || || || ||||||||| || | |||||| | ||||| || || |||||||| ||||| ||||| || |||||||||||||||||||
---------------------------gtttgtgatgctcgcgctttagtt-----ggtccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGGCGGTGGCCAAAGTGATGAAGAAGG

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|45368074|gb|CK906433.1|CK906433
EST:     TGAAGAAGATTGCAGAGAAGATGAATGGTGCATTTGGTGCAGAGCTCAAG                         GCGGTATGCACAGAAGCAGGGATGTTTTCTTTGAGGGAGAGGAGGGTTCAC
genomic: TGAAGAAGATTGCAGAGAAGATGAATGGTGCATCTGGTGCAGAGCTCAAGgtctgtttcc ... ttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCAC
EST: gi|110733070|gb|EE108911.1|EE108911
EST:     TGAAGAAGATTGCAGAGAAGATGAATGGTGCATCTGGTGCAGAGCTCAAG                         GCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCAC
genomic: TGAAGAAGATTGCAGAGAAGATGAATGGTGCATCTGGTGCAGAGCTCAAGgtctgtttcc ... ttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCAC
EST: gi|30305623|gb|CB982417.1|CB982417
EST:     TGAAGAAGATTGCAGAGAAGATGAATGGTGCATCTGGTGCAGAGCTCAAG                         GCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCAC
genomic: TGAAGAAGATTGCAGAGAAGATGAATGGTGCATCTGGTGCAGAGCTCAAGgtctgtttcc ... ttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttgcatagatctgatacctctcggattgagcatttgaacttttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
            atctgat  putative branch site (score: 4)
                                          cttttgttt  putative PPT
                                           ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgactttcctgccttcataggtttttgaatataatggaaaccatttacttgcatagatctgatacctctcggattgagcatttgaacttttgtttgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - -tcctgcc
- - - - - - - - - - - - - - - - - - - aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - - tgcatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatttg