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

gtttgttctttacctcaagatgagctaattgaagccaaaatcctttgttggaaggttgttccacattattattattatttcttttcattttttagGTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAG

Basic information

species Vitis vinifera
transcript Vv14s0036g01460.t01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g01460.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os10g31970.1 (Oryza sativa), 3'ss of exon 23
gtttgttctttacctcaagatgagctaattgaagccaaaatcctttgttggaaggttgttccacattattattattatttcttttcattttttagGTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAG
               |||||     |   |  |     | |  |  |||| |   |  |   |   | |  ||| |     | |    |||  ||||||||||| || ||||| |||| |||||||||  | |||||||||| ||| |||||||| ||||| ||||| || |||
--------------gcaagaacttgttgcttgatttttactagtaagttgaacaatcatgtgattatttgtttactcaccgtatgttctttccagGTATGGCCAGACCAAGCCTGTGTATGCTTACCGCCTAATGGCTCATGCAACAATGGAAGAGAAAATATATAAACGGCAG

upper sequence: Vv14s0036g01460.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: GLYMA20G37100.1 (Glycine max), 3'ss of exon 28
-gtttgttctttacctcaagatgagctaattgaagccaaaatcctttgttggaaggttgttccacattattattattat-----ttcttttcat-tttttagGTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAG
     | |   |   | |   |     | ||  |    |  |  |||||   ||  |||    ||| | | |||   ||     |  ||||||| ||| ||||||||| || |  ||||| ||||||||||| |||||| ||||||||||||||||||| || || || |||||||| |||
aaaaggatacatgttttatatttgctcatttacaaattatttaatttgtaacaa--ttgacaaacaatgtgattgaaatcaaaataattttcatgtttatagGTATGGGCAGAAAAAGCCTGTGTTTGCTTATCGATTGCTGGCTCATGGAACTATGGAGGAGAAGATATATAAGCGCCAG

upper sequence: Vv14s0036g01460.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: AT1G08600.1 (Arabidopsis thaliana), 3'ss of exon 25
gtttgttctttacctcaagatgagctaattgaagccaaaatcctttgttggaaggttgttccacattattattattatttcttttcattttttagGTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAG
|| | ||||  ||      || |   ||||   | ||| ||    |     | ||| | |      ||||||   |     | ||  ||    |||||||||||||  ||||| || ||||| ||| |||||||||| | ||| ||||| ||||||||||| ||||| ||||||
gtattttctagactatggaattaa--aattt--gtcaatatagcattacaaacggtggct------tattatacgtggacttattggttgc--agGTATGGCCAAAAGAAGCCCGTATTTGCGTACAGATTGATGGCACGTGGGACTATTGAAGAAAAAATATATAAACGTCAG

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|161710320|gb|FC059834.1|FC059834
EST:     GGATCATGGAATCCAACATATGATCTTCAGGCTATATATCGGGCTTGGAG                         GTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAAC
genomic: GGATCATGGAATCCAACATATGATCTTCAGGCTATATATCGGGCTTGGAGgtttgttctt ... cattttttagGTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAAC
EST: gi|161713628|gb|FC062542.1|FC062542
EST:     GGATCATGGAATCCAACATATGATCTTCAGGCTATATATCGGGCTTGGAG                         GTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAAC
genomic: GGATCATGGAATCCAACATATGATCTTCAGGCTATATATCGGGCTTGGAGgtttgttctt ... cattttttagGTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttgttggaaggttgttccacattattattattatttcttttcattttttagGTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAG
                               ttattatttcttttca  CT-rich tract
                  ttccacattattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttctttacctcaagatgagctaattgaagccaaaatcctttgttggaaggttgttccacattattattattatttcttttcattttttagGTATGGCCAAACTAAGCCAGTGTTTGCTTACCGATTGATGGCTCATGGAACTATGGAAGAAAAAATTTATAAGCGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA