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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcctttagtattgattatttaattcatcatattagctaattgcatttggaaattcttattatgtcttgatctttctgttcttttatttgtgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG

Basic information

species Vitis vinifera
transcript Vv02s0087g00740.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os03g38930.1 (Oryza sativa), 3'ss of exon 5
-------ttcctttagtattgattatttaattcatcatattagcta-attgcatttggaaattcttattatgtcttgatctttctgttcttttatttgtgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG
       |||     || ||    |    | | |   | || | |  ||||   |   |    ||| |     |   ||  |||||  ||  | ||||| | |||||||| ||||||||| ||||||||||  | |||||| | ||||||  ||||||||||||| | || ||  | || || ||||||||||| ||||| ||  |||
agataacttctggaggtgtttgagagcagaattacgctgttcgatgtattgtgctcaaa----cttgtggacacccaat--ttctga-ctactgtttgt-acttttagGTAATGCCTCCATTATGGTGCAGGCTTGATAGGATGTGGTTTGGACATCCTGGAGTTTTGGAAGGAACAATGACCAGACAACCTTTCCTCTGTCCAATGG

upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G011912_T01 (Zea mays), 3'ss of exon 5
ttcctttagtattgattatttaattcatcatattagcta-attgcatttggaaattcttattatgtcttgatctttctgttct---tttatttgtgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG
    | || | |||| |         |  || || |    |||   |||    | | ||  ||  | |||||    || ||||   |  | ||   | |||||||| ||||||||| ||||||||||  | |||||  | ||||||  |||||||||| || | |||||  | || || ||||||||||||||||||||  |||
----tataattttgaatggagggagtaagatttttgaagtattatcttttcgtagtgttcgtacatgttgatgccccttttctgactgcagtttgtacttttagGTAATGCCTCCATTATGGTGCAGGCTTGATAGAATGTGGTTTGGACATCCTGGAATTTTAGAGGGAACAATGACCAGACAACCTTTTCTCTGCCCACTGG

upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G09650.1 (Glycine max), 3'ss of exon 7
ttcctttagtattgattatttaattcatcatattagctaattg-catttggaaattcttattatgtcttgatctttctgttcttttatttgtg-atttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG
 |    |  |   ||||      |||  | |  ||| | |||  || ||   || |  ||| || |  | ||   || ||||||| || |||  || ||||||||||||||||||||||||||||| | ||||||||||||||||| |||||||| ||| | || |||||||| |||||||||||||||||||| |||||||
-tttggtgattaagattgacggtttctcctttgtagttcattttcacttcataaattatataatttgatcataactcagttcttt-atgtgtatatgtttagGTCATGCCTCCACTATGGTGCAGAATTGATAGGTTATGGTTTCCCCATCCTGGTGTTTTGGACGGGTCTATAACTAGACAACCTTTTCTCTGTCCTTTGG

upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 9
ttcctttagtattgattatttaattcatcatattagctaattgcatttgga-aattcttattatgtcttgatctttctgttcttttatttgtg-atttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG
      |  |   ||||      |||  | |  ||| | |||     || | || |  ||| || |  |  |  |||  || |||||| |||  || ||||||| ||||||||||||||||||||| | |||||| |||||||||| |||||||| ||| | || |||||||| |||||||||||||||||||| |||||||
-cttagtgattaagattgacagtttctcctttgtagttcattttcactgcataaattatataattttatcttaattc-atttttttatgtgtatatatttagGTGATGCCTCCACTATGGTGCAGAATTGATAGGCTATGGTTTCCCCATCCTGGTGTTTTAGACGGGTCTATGACTAGACAACCTTTTCTCTGTCCTTTGG

upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G08350.2 (Glycine max), 3'ss of exon 8
-ttcctttagtattgattatttaattcatcatattagcta-attgcatttggaaattcttattatgtcttgatctttctgttcttttatttgtgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG
 |    || || || || ||| |   | |||| ||   |  |||  |  |   |||   |  | | | || |||||   ||   ||  |||||| | ||||||||||||| ||||||||||||||  | |||||| |||||| ||| ||||||||  || | || ||||| || |||||||||||||||||||| |||||||
gtatgcttggtttttatgattgatggcttcattttttttccattttaacttttaataaattctctatttttatcttgaagtagattc-tttgtg-tgtttagGTCATGCCGCCACTATGGTGCAGGATTGATAGGCTATGGTATCCCCATCCTGGTATTTTGGAAGGGTCCATGACTAGACAACCTTTTCTCTGTCCTTTGG

upper sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G20730.1 (Glycine max), 3'ss of exon 9
----ttcctttagtattgattatttaattcatcatat-tagctaattgcatttggaaattcttattatgtcttgatctttctgttcttttatttgtgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG
     | | |   | || |||  |   |||||  | | | |||| ||  | ||   || |  |||    | |  |||||   ||   ||  |||||| | ||||||| ||||||||||||||||||||  | |||||| |||||| | | ||||||||  || | || ||||| || |||||||||||||||||||| |||||||
gggtatgcctggttttttattgatggcttcattttttgttgctattttaacttaataaattctat---atttctatcttgaagtagattc-tttgtg-tgtttagGTTATGCCTCCACTATGGTGCAGGATTGATAGGCTATGGTATGCCCATCCTGGTATTTTGGAAGGGTCCATGACTAGACAACCTTTTCTCTGTCCTTTGG

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|56688584|gb|CX126487.1|CX126487
EST:     GCGCTTGCTATTGCTTCATTATTGAAACGTACACTG                         GTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCT
genomic: GCGCTTGCTATTGCTTCATTATTGAAACGTACACTGgtgagaatga ... tgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCT
EST: gi|56688689|gb|CX126592.1|CX126592
EST:     GCGCTTGCTATTGCTTCATTATTGAAACGTACACTG                         GTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCT
genomic: GCGCTTGCTATTGCTTCATTATTGAAACGTACACTGgtgagaatga ... tgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCT
EST: gi|56688204|gb|CX126107.1|CX126107
EST:     ACAGCGCTTGCTTTTGCTTCATTATTGAAACGTACACTG                         GTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCT
genomic: ACAGCGCTTGCTATTGCTTCATTATTGAAACGTACACTGgtgagaatga ... tgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCT
EST: gi|56688359|gb|CX126262.1|CX126262
EST:     GCGCTTGCTATTGCTTCATTATTGAAACGTACACTG                         GTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCT
genomic: GCGCTTGCTATTGCTTCATTATTGAAACGTACACTGgtgagaatga ... tgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggaaattcttattatgtcttgatctttctgttcttttatttgtgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG
                   tcttgat  putative branch site (score: 4)
                         tctttctgttctttta  CT-rich tract
                                 ttcttttatttgtgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcctttagtattgattatttaattcatcatattagctaattgcatttggaaattcttattatgtcttgatctttctgttcttttatttgtgatttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG

- - - - - - - - - - - - - - - - - - - - - gcatttg