Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaatgatttctaagtagtacaaaacttgatcttccttatgcatgccatatcttattataattttttggatgatttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT

Basic information

species Vitis vinifera
transcript Vv11s0016g02120.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g09890.1 (Oryza sativa), 3'ss of exon 4
--gtgtgaatgatt----tctaagtagtacaaaacttgatcttccttatgcatgccatatcttattataattttttggatgatttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT
   |   | | ||        |  ||||||||       |  |    ||| | ||  | | |||  |    || ||   ||  || | |||||| || ||||||||||||||||||||||| ||||| || ||| | ||||| || |||||||| |||||||| || |||||||||
gtataccagtaatcagggctcatatagtacaatggcctttgatatcaatgtaagcatttttttaacacctgttctttattgcctt-tcttagGGCCCCACTGAGAAGGAGCAAATTGATGTGCAAGGGGATATATCGTATGATATCGTGGAGTTCATTACAGATACTTGGCCTGAT

upper sequence: Vv11s0016g02120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G033283_T01 (Zea mays), 3'ss of exon 5
gtgtgaatgatttctaagtagtacaaaacttgatcttccttatgcatgccatatcttattataattttttggatgatttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT
  ||      |           |    | |  | |||    ||    ||  | |   || | | | | |       | |   |||||| || || |||||||||||||| || || ||||| |||||  | ||||| ||||||||||| |||||||| ||||||||||||
--gtaccctgtcgtggttcgtgatgttattgtagcttttgaatttgagcattgttgaatcagactctctcttgctctgttccttagGGCCCTACGGAGAAGGAGCAAATCGACGTACAAGGGGACATCTCATATGATATTGTGGAGTTCATTACAGATACATGGCCTGAT

upper sequence: Vv11s0016g02120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G068352_T01 (Zea mays), 3'ss of exon 4
gtgtgaatgatttctaagtagtacaaaacttgatcttccttatgcatgccatatcttatta---taattttttggatgatttgtt--ttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT
  || |    | ||   || ||     |  | ||  |   | |         | ||| ||     |  |||||   || | ||||  |||||| || || |||||||| || ||||| || ||||| |||||| | ||||| ||||||||||| |||||||| ||||||||||||
--gt-acccctctcgtggtggtctgtgatgttattgtgtctttttgaatttgagcttgttgaaccagatttttctctgctctgttcattagGGCCCGACCGAGAAGGAACAGATTGACGTGCAAGGGGACATATCATATGATATTGTGGAGTTCATTACAGATACATGGCCTGAT

upper sequence: Vv11s0016g02120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G18500.1 (Glycine max), 3'ss of exon 5
------------gtgtgaatgatttctaagtagtacaaaacttgatcttccttatgcat-gccatatcttattataattttttggat-gatttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT
            || |||  | | |      |  ||  |  |  |  |   ||||  || |  |||   | ||||| | || ||| | |||| || | |||| |||| |||||| || ||||||||||| ||||| || ||||| |||||||| |||||||| |||||||| ||||||||||||
attgctatttttgtttgacagctatgatccaaacacccacgtatagttgttttatatatagaaataatgtcttatactattgtgggttgattggtgtcagGGACCAAGTGAGAAAGAACAAATTGATGTTCAAGGGGATATAGCTTATGACATCGTGGAGTTCATTACAGATACATGGCCTGAT

upper sequence: Vv11s0016g02120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G07170.1 (Glycine max), 3'ss of exon 5
--------gtgtgaatgatttctaagt----agtacaaaacttgatcttccttatgcat-gccatatcttattataattttttggat-gatttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT
         || || |||   ||| |     |  ||  |  |  |  |   | ||  || |  |||   | ||||  | || |||||  | | || | |||| || |||||||| || ||||||||||| ||||| || ||||| |||||  |||||||||| |||||||| ||||||||||||
attgctatttgggattgacaactatgatccaaacacgcatttatagttgtttcatatatagatataatgtcttatgctattgtggattaactggtgtcagGGACCTACTGAGAAAGAACAAATTGATGTTCAAGGGGATATAGCTTATGATGTTGTGGAGTTCATTACAGATACATGGCCTGAT

upper sequence: Vv11s0016g02120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S70_238V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------gtgtgaat----gatttctaagtagtacaaaacttgatcttccttatgcatgccatatctt-attataattttttggatgatttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT
           || | |||    |  |||||    | |   |   |||||||    |    | | | | ||| |||     ||||| | |  | | |   |||| ||||||||||| || ||||| ||||| |||||||| ||    ||||||||||||||||| || ||||| || |||    ||
tcacaaattatgttttaatttgtggcttctatcctggatcga--ctgatcttggagaacgctccaagaccttgattgcttgttttttgtttttctttcgcagGGCCCAACTGAGAAAGAACAAATAGATGTTCAAGGAGATATCATGTATGACATTGTGGAGTTCATCACAGACACTTGGAAGAAT

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|349813672|gb|FQ413906.1|FQ413906
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|110686305|gb|EE063793.1|EE063793
EST:     CGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|27581864|gb|CB004559.1|CB004559
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|110715741|gb|EE094134.1|EE094134
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|351021773|gb|FQ437158.1|FQ437158
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|22009051|gb|BQ794085.1|BQ794085
EST:     AGAAGCTTGGGAAAAAGTTCGCTACATGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: AGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|349814495|gb|FQ399135.1|FQ399135
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|22008909|gb|BQ793943.1|BQ793943
EST:     AGAAGCTTGGGAAAAAGTTCGCTACATGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: AGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|349813673|gb|FQ413907.1|FQ413907
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|294966348|gb|GW837599.1|GW837599
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTC
EST: gi|110694056|gb|EE070826.1|EE070826
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|110699500|gb|EE076555.1|EE076555
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|110698221|gb|EE075521.1|EE075521
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|351055019|gb|FQ440358.1|FQ440358
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC
EST: gi|349808342|gb|FQ405486.1|FQ405486
EST:     CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAG                         GGTCCAACTGAGAAGGAGCGAATTGATGTCCAAGGAGACATAGCCTATGAC
genomic: CTTCAAAGAAGCTTGGGAAAAAGTTCGCTACAGGAGCATCTGTTGTCAAGgtgtgaatga ... tttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcttccttatgcatgccatatcttattataattttttggatgatttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT
 acttgat  putative branch site (score: 5)
                                             tttgtttt  putative PPT
                   atatcttattataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgaatgatttctaagtagtacaaaacttgatcttccttatgcatgccatatcttattataattttttggatgatttgttttagGGTCCAACTGAGAAGGAGCAAATTGATGTCCAAGGAGACATAGCCTATGACATTGTGGAGTTTATTACAGAAACATGGCCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG