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

...gaaaaattataattccttatttcatttaatattgccttcatatgtataatgcttctgttcttggtcttacatcatgccaaatgttatccattctacatagATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAGAGATTTGGTTGATCAGGCATACACAAAATTT

Basic information

species Vitis vinifera
transcript Vv18s0001g11700.t01
intron # 18
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 18
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 18
gaaaaattataattccttatttcatttaatattgccttcatatgtataatgcttctgttcttggtcttacatcatgccaaat-----gttatccattctacatagATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAGAGATTTGGTTGATCAGGCATACACAAAATTT
   || ||| |  | |   | |   ||  ||  || |  || | | | |   |||   |||   ||| |    |||  ||||     ||||    || | |||||||||||||| |||||||| || |||||||||||||||||||| || ||||| ||||||||||| || ||||| |||||||||
--gaagttacagctgcaactgtttcttgcta--gcatgtatttatttcaactttcaagtctctttctgat-cgatgttaaatactttgttaattgttttgcatagATTTGCAACCCTTGCAACTCGGATGGAGCAGTACATCCAGGGTCAGTCTAGGGATTTGGTTGACCAAGCATATACAAAATTT

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 18
gaaaaattataattccttatttcatttaatattgccttcatatgtataatgct---tctgttcttggtcttacatcatgccaaatgttatccattctacatagATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAGAGATTTGGTTGATCAGGCATACACAAAATTT
   || ||| |  | |   | |   ||  || |   |   ||| |  | ||     ||| ||  || ||  |  | |       |||||    || | |||||||||||||| |||||||| || |||||||||||||||||||| || ||||| ||||||||||| || ||||| |||||||||
--gaagttacagctgcgactgtttcttgctagtatgtatttatttcaactgtcaagtctctttgtgatcg-atgttaaatactttgttaattgttttgcatagATTTGCAACCCTTGCAACTCGGATGGAGCAGTACATCCAGGGTCAGTCTAGGGATTTGGTTGACCAAGCATATACAAAATTT

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 18
----------------------------------gaaaaattataattcc---ttatttcatttaat---attgcct-tcatatgtataatgcttctgttcttggtcttacatcatgcca-------aatgttatccattctacatagATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAGAGATTTGGTTGATCAGGCATACACAAAATTT
                                    ||  || |  ||||    ||||||    |||   ||||    | | |||   || |   | ||| || || || | | | || |       | | ||||    | | |||||||||||| | ||||| || |||||||| || ||||| || || |||||||||||||||||||||||||||||||||||||||
gtaatcagaaattccaccttgtaaataatttcattcaattttgtggttccgaactatttctcccaattagattgttggttagatgatcaaagaaaccgtttttagtattgcttgaggctatgctaacattattatatcattttcatagATTTGCAGCACTTGCTACTCGTATGGAACAATACATACAAGGGCAATCTAGAGATTTGGTTGATCAGGCATACACAAAATTT

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 18
gaaaaattataattccttatttcatttaatattgccttcatatgtataatgcttctgttcttggtcttacatcatgcca-------aatgttatccattctacatagATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAGAGATTTGGTTGATCAGGCATACACAAAATTT
       |   |||     | |  || |   ||| ||  |  ||    | |   | ||| | |   | |||| | ||         | |||||||   | | |||||||||||| | ||||| || |||||||| |||||||| || || ||||||||| |||||||||||||||| ||||||||||||
------ctcccatttagattgttgttcag-gttgactataggtgatccaagaacccgttatagtattaacatgaggctttcctaatattgttatctcattttcatagATTTGCAGCACTTGCTACTCGTATGGAACAGTACATACAAGGGCAATCTAGAAATTTGGTTGATCAGGCGTACACAAAATTT

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|7593728|gb|AW707979.1|AW707979
EST:     AGAAATGAACGTAACGTTCGGCAGACGGGTGTATTATCATATATTCCCAG                         ATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAG
genomic: AGAAATGAACGTAACGTTCGGCAGACGGGTGTATTATCATATATTCCCAGgtaaactaag ... ttctacatagATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgcttctgttcttggtcttacatcatgccaaatgttatccattctacatagATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAGAGATTTGGTTGATCAGGCATACACAAAATTT
                  gtcttac  putative branch site (score: 3)
                                         tccattct  putative PPT
                                 aaatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaattataattccttatttcatttaatattgccttcatatgtataatgcttctgttcttggtcttacatcatgccaaatgttatccattctacatagATTTGCAACTCTTGCAACCCGTATGGAGCAGTACATCCAGGGACAATCTAGAGATTTGGTTGATCAGGCATACACAAAATTT

gaaaaat
- - - - - - - - - - - - - - - - -gccttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgcc