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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtttatttattttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgattacagacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC

Basic information

species Vitis vinifera
transcript Vv18s0001g11700.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os03g42750.2 (Oryza sativa), 3'ss of exon 20
--------------------------gtatttgtttatttattttttgcatga----ttctctaagtagattctt-----cttatgatttcttaattctaaggat--cctgattaca----gacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC
                           || |  | |   | ||||||||||||    || | |   |  ||  ||     || || ||||  |   | ||  | |  |   | ||      | | |||  ||||||| | |||||| | || |||||||| || ||| | || |||||||| ||  ||||||||||||| ||||||||||||||||  || ||||| ||     | 
gttatgtttctttcttgtgttgttcattaatcttctcaatcttttttgcatgaggtcttttttgtttgtatgtttggcacctcatcattttgtggatatacaggtgactaaactattatgtgtctgttggatgcagTCTTTATGACTTGGCTAATGTTGTGCCAACTCTTGCAAAATTCTACCATGAGGCCAGTGAATCATATGAACAAGCTTGCACTCGTCATATCAGTTCACTT

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA14G08570.1 (Glycine max), 3'ss of exon 1
gtatttgtttatttattttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgattaca--gacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC
||| |  | |    |     ||  | |   ||| | ||  ||  | ||   |       |||       |    ||||    |   |||| |  ||||||||||||||| |||||  |||| |||||||| ||||| || ||||| |||||||||||| | |||||||||||||| |  || |||||||||||||| 
gtaatc-tctgccaaaaggctgtttcaaattcttattaagttgattttgcaagaaagatatttgccatttttcaattattttgtttgttttactcagTTTGTATGACCTCGCCAACATTGTGCCCACTTTGGCCAAGTTTTATCATCAGGCCAGTGAAGCCTATGAACAAGCTTGTACACGCCATATTAGCATGATT

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 20
gta-tttgtttatttattttttgcat-gattctc--taagtagattcttcttatgatttcttaattctaaggatcctgattaca--gacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC
||| ||| | |    |     ||  |  ||||||  | | ||  ||    ||   |       |||       |    ||||    ||  |||| |  ||||||||||||||| |||||  |||| || ||||| ||||| || ||||| |||||||||||| | |||||||||||||| |  || |||||||||||||| 
gtaatttctctgccaaaaaggtgtttcaattctcatttattaagttggattttcaagaaagatatttcccatttttcaattattttgatcgttttactcagTTTGTATGACCTCGCCAACATTGTGCCTACTTTGGCCAAGTTTTATCATCAGGCCAGTGAAGCCTATGAACAAGCTTGTACACGCCATATTAGCATGATT

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 20
gta-tttgtttatttattttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgattaca--gacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC
||| ||| | |    |     ||  | |   ||| | ||  ||  | ||   |       |||       |    ||||    |   |||| |  ||||||||||||||| |||||  |||| ||||| || ||||| || ||||| |||||||||||| | |||||||||||||| |  || |||||||||||||| 
gtaatttctctgccaaaaggctgtttcaaattcttattaagttgattttgcaagaaagatatttgccatttttcaattattttgttcgttttactcagTTTGTATGACCTCGCCAACATTGTGCCCACATTGGCCAAGTTTTATCATCAGGCCAGTGAAGCCTATGAACAAGCTTGTACACGCCATATTAGCATGATT

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 20
--------------------------------gtatttgtttattt-attttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgat-tacagacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC
                                |     |  | ||| | || || |||  || | || ||| ||||||  ||      |  |  | |      | |  | |   |    |||    ||||||||||||||| || ||||| ||||||||||| || || || ||||| ||||| |||||| | || || ||||||||||  || ||||||||  |||| 
gtaatgtttacgcatcaccctgccaaatggaggctcgaggctgtttcaattcttccatt-ttttttaggta-attctttatacacagacaaagatatttttcacttattattttgttctttttgctcagTTTGTATGACCTTGCAAATGTCGTTCCCACTTTGGCGAAGTTTTATCATCAGGCTAGTGAAGCCTACGAGCAAGCTTGCACACGCCATATTAGTGTGATT

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 20
gtatttgtttatttattttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgattac-agacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC
    | | |  |||  || ||   |   |||||  || | ||||||||     |||  |||| |    |      | || |     |||| |||||  |||||||||| || |||||||| || ||||||||||| || ||||||||||| |||||| | |||||||||||||| | ||| || ||||||||||| 
---gtaggtccttttcttattctctccctctcttggttg-ttcttctt----cttcccaattgttcatacttccctaaccattttttttcttgcagCCTGTATGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTTTATCACCAGGCAAGTGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 20
gtatttgtttatttattttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgattacagacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC
      ||   |   ||| |  |     |||||   | | ||  |||| | ||| | |||   |    ||  ||            ||  |||||  ||| |||||| || |||||||| || ||||||||||| |||||| ||||||| |  ||| | |||||||||||||| | ||| || ||||||||||| 
------gtaggtccttttctaactc---tctctctcttggtttgtcttcttattccctaaccttgtacattttg------------tttgtgcagCCTGTTTGACCTGGCTAATGTTGTGCCGACTTTAGCCAAGTTCTATGACCAGGCAATGGAAGCATATGAACAAGCTTGTACGCGCCACATTAGCATGATA

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|30305681|gb|CB982475.1|CB982475
EST:     AAATATGCTGATATTTTGCTTTTGGAGAATTTTGCAGCTTTCCAGAATAG                         TTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCA
genomic: AAATATGCTGATATTTTGCTTTTGGAGAATTTTGCAGCTTTCCAGAATAGgtatttgttt ... tttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCA
EST: gi|110385940|gb|EC950502.1|EC950502
EST:     TTCCAGAATAG                         TTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCA
genomic: TTCCAGAATAGgtatttgttt ... tttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcttatgatttcttaattctaaggatcctgattacagacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC
                             tcctgat  putative branch site (score: 3)
      ttatgatttcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtttatttattttttgcatgattctctaagtagattcttcttatgatttcttaattctaaggatcctgattacagacagtttcatgcagTTTGTATGACCTAGCCAATGTTGTTCCCACTTTAGCCAAATTCTATCACCAGGCCAGTGAATCTTATGAACAAGCTTGCATGCGGCATATTAGCATGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT