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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgcataaattctgagtaatgaaagtatcacattgttgttatttttatccttacaagtatacttggcttatcttaaggtattttttgcccattctctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT

Basic information

species Vitis vinifera
transcript Vv15s0046g01890.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 13
aatgcataaattctgagtaatgaaagtatcacattgttgtta----tttttatcct-tacaagtatact--tggcttatcttaaggtattttttgcccattctctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT
       |||   |    |   | ||| || || | |  | |    ||   || |  |||||  || ||  |   |  | |      | |  |  | |||  |||||| | ||||||||||||||||||||| ||||||| || ||||| |||||||| || || 
-------aaaacttacccaccaacagtgtctcaatttgatcaagatttggaatacaatacaataattctgctaattcttttagtaaaactgatccctcatgttctagGATGTTTGAGGAATGCTTCCAACGGCGATGGTATAGGACTGCTGCTTGCTACATTCTG

upper sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 13
aatgcataaattctgagta-atgaaagtatcacattgttgttatttttat---ccttacaagtatacttggcttatcttaaggtattttttgcccattctc-tagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT
     |    ||||||  | ||   | || | |   ||  | | ||| |      || ||| || | |   | |   || || |||       |  |  |  |||| | ||||||||||||||||||| ||| |||||||| ||||| |||||||| ||||| 
----aaattgttctgacaatatcttaataacccgcagtattaaatttgacaaagatttcaaataaaataatcatgcttttag-tatgaccaaactttcatgatagGATGTTTGAGGAATGCTTCCAACAGAGGTGGTACAGGACTGCTGCTTGCTACATACTG

upper sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 13
--aatgcataaat-tctgagtaatgaaagtatcacattgttgttatttttatccttacaagtatacttggcttatcttaaggtattttttgcccattctctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT
  ||     || | | |    ||| |   ||  | |  ||   |||||  ||       | |  |  |    ||  |     | |  | || ||||  |  ||| | ||||||||||||||||||| ||| |||||||| ||||| |||||||| ||||| 
tgaacttgaaattgtttagacaataactttacta-accgtcagtatttaaatttgacagatttcaaataatatacttatgcttttagtatgaccatgat--agGATGTTTGAGGAATGCTTCCAACAGAGGTGGTACAGGACTGCTGCTTGCTACATACTG

upper sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA09G39270.2 (Glycine max), 3'ss of exon 14
-----------aatgcataaattctgagtaatg-aaagtatcacattgttgttatttttatccttacaagtatacttggcttatcttaaggtattttttgcccattctctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT
             | | |     || | || || ||| ||| |   | || | | |     | ||| | | ||| ||      | ||  ||  |||| |        | ||| || |||||||||||||| ||||| ||||||||  | |||||||||||||||||||||
atctgaattttgcttccttttggctaattagtgcaaattataatgcttttttcactgcatactttagatgaataattt-----ttttggggggttttcta-------tatagATTGTTTGAGGAATGCTTTCAACGTAGATGGTATCGCACTGCAGCTTGCTATATACTT

upper sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 14
-----aatgca--taaattctgagtaatgaaagta--tcacattgttgttatttttatccttacaagtatacttggcttatcttaaggtattttttgcccattctctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT
     |||     |   || ||  || | |  | |  | | | || | || ||  |     |   || ||   |   || | ||  ||  ||| |         | ||| || |||||||||||||| ||||| ||||||||  | ||||||||||| |||||||||
atttgaattttgttcccttttggctagttagtgcaagttataatgctttttttactgcatattttag-atgtgtaattttttttggggggtttcta--------tatagATTGTTTGAGGAATGCTTTCAACGTAGATGGTATCGCACTGCAGCTTGTTATATACTT

upper sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT5G28350.2 (Arabidopsis thaliana), 3'ss of exon 14
-------------------------------------------------------------------------------------aatgcataaattctgagtaatgaaagtatcacattgttgt----tatttttatccttacaagtatacttggcttatcttaaggtattttttgcccat--tctctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT
                                                                                     | |    |  | || ||  |  ||| |    || | ||||    | ||||| |      || | || |  |     |  ||| |  | ||  |   |    ||||||||||||||||| |||||||| || ||||||||  ||||||||||||||||||| |||
gtatgttttcctgtctctatgtttggcttttgtttcttgtaacgttcatgaaactaggttagtttactgtactagacacgtgagcagttagcagttgctaagatagcaaacttcaccaatcttgtctgctctttttgttgagtaaactgtattctgtgctacgaaagttgatattctcttttgggttctagGTTATTTGAGGACTGCTTCCAGCGAAGATGGTATCGAACTGCAGCTTGCTATATCCTT

upper sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G61480.1 (Arabidopsis thaliana), 3'ss of exon 14
-------------------------------------------------------------------------------------aatgcataaattctgagtaatgaaagtatcacattgttgttatttttatccttacaagtatact-tggcttatcttaaggtattttttgcccattc------tctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT
                                                                                     | |       | || ||  |  ||| |    || | |||     | | |   |   |||| ||| |    | |  || |  | ||  |   |  |       ||||| || |||||||| |||||||| || ||||||||  ||||||||||||||||||| |||
gtatgtttctctatctctgtgtttggcttttgtttcttgtaacgtgtatgaaactagttttgtttactgtactagacacgtgagcagttagccgttgctaagatagcaaacttcaccaatcttgcctgctctttttgt-tgagtaaactgtattctgtgctacgaaacttgatattctcttttgggttctagATTGTTTGAGGACTGCTTCCAGCGAAGATGGTATCGAACTGCAGCTTGCTATATCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatccttacaagtatacttggcttatcttaaggtattttttgcccattctctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT
   tccttac  putative branch site (score: 2)
                                    ttttttgcccattctc  putative PPT
                            ttaaggtatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgcataaattctgagtaatgaaagtatcacattgttgttatttttatccttacaagtatacttggcttatcttaaggtattttttgcccattctctagGTTATTTGAGGAATGCTTCCAACGGAGATGGTACAGAACTGCAGCTTGCTATATACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
aatgcat
- - - - - - - - - aatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgcc