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

gtagaagcatttttattctcttgctagataggcttaattattgttttcccttgatactggttttaggcacattggataatctaataagtattgattatctattctttgctttctgttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAGCCACCAAAAAGAGAGCGGAAGCGGAA

Basic information

species Vitis vinifera
transcript Vv05s0020g01780.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 12
gtagaagcatttttattctcttgctagataggcttaattattgttttcccttgatactggttttaggcacattggataatctaataagtattgattatctattctttgctttctgttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAGCCACCAAAAAGAGAGCGGAAGCGGAA
    |  ||||   |   ||     |  | |  || || | |  |||   ||||     || |   || |||     ||| ||||            |||  ||  || || ||     || ||||||| |||||| |||| ||||||||| |||| ||||| ||||||||||||||||| | ||||||  ||||| | ||
--gtagtcattcaaacattcaattcatgt-gctttgatgagttattttttttga----agtgtcttgctcatcac-caatttaat------------tctcctccatgattgct-----tgaagGATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAA

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 15
gtagaagcatttttattctcttgctagataggcttaattattgttttcccttgatactggttttaggcacattggataatctaataagtattga------ttatctat-tctttgctttctgttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAGCCACCAAAAAGAGAGCGGAAGCGGAA
|||     |  | |  ||| ||||||  || |    ||  || || |  ||  ||  ||   | |  | |  ||      ||  |  || || |       | | ||| | |||  ||||| |  ||| ||||||||||||| ||||| ||||| |||||||| |||||||| ||| | |||||||||| |||||| |||||||| ||
gtaagttgacgtattatct-ttgctaactatggactat-gtttttattgctcaattttg-catcaacccccctgccctgcctcttgtgtttttaaccaacctctgtatgtgttttttttctttaaatgaagGATGAGAACAAATTTGATTTCAAAAAAATTGTGAGTGAAAATTGGGTCGAGCCACCAAGAAGAGAACGGAAGCGCAA

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 15
gtaga-agcatttttattctcttgctagataggcttaattattgttttcccttgatactggttttaggca--cattggataatctaataagtattgattatctattctttgctttctgttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAGCCACCAAAAAGAGAGCGGAAGCGGAA
||| | |  |    |  | |  |  | |  |   ||   ||||| |||   |  |  ||  | |    |   |  | | ||      ||| |     |    |||   || |  | | |  ||  ||||||| | ||  |||||  | || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||||| ||
gtaaacatgacacattgttttatctttggcaactttttgtattgctttgtatcaaccctactctcctcctttcccttgttatctatttaactgacattggcatatcaatttccctttttaaataaagGATGAAAGCAGATTTGATATAAAAAAAATTGTGAGTGAGAACTGGATTGAACCACCCAAAAGGGAGCGGAAGCGCAA

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 15
-----gtagaagcatt-tttattctcttgc--tagataggcttaattattgttttcccttgatactggttttaggcacattggataatctaat-aagtattgattatctattctttgctttctgttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAGCCACCAAAAAGAGAGCGGAAGCGGAA
     |  ||  |||     ||| | ||    | |  |   ||   ||||| |||   |  |       |       |  ||  | ||||| | || |     |    ||||  ||    | | |  ||  ||||||| ||||  |||||  | || |||||||| || || ||||||||||| ||||||||||| |||||||| || ||
gtaaagatgacacatgacacattgttttatctttggcaactttttgtattgctttgtatcaacctactctcccctttccctgtcttatctatttaactgacattggcatattaattaacctttttaaataaagGATGAAAACAGATTTGATATAAAAAAAATTGTGAGCGAGAACTGGATTGAACCACCAAAAAGGGAGCGGAAACGCAA

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 15
gtagaagcatttttattctcttgctagataggcttaattattgttttcccttgatactggttttaggcacattggataatctaataagtattgattatctattctttgctttctgttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAGCCACCAAAAAGAGAGCGGAAGCGGAA
      | ||| ||      ||  | ||  |  | ||  |  | |||  |   ||||||   ||| || |    | |  || ||||    ||  | || | || |||  |||   |||  ||||||||||| |||| | || || || || ||||| |||||||| |||| ||| ||||||||||||||| | ||||| ||
------gtattcttggataattaattgaatgattgaaggaaaggtttaacgc-atactgtggttatgctctgcagtttttcgaatatcgtttcctgatttcttttttaattttgtttg--gtagGATGAGAGCAAGGTGGATTTTAAAAAGATTGTGAGTGAAAATTGGAATGATCCACCAAAAAGAGAGAGAAAGCGCAA

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|28967912|gb|CB346945.1|CB346945
EST:     CTGCTGAGTTGTATGATTTTGATGATGAAAAG                         GATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAG
genomic: CTGCTGAGTTGTATGATTTTGATGATGAAAAGgtagaagcat ... gttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattggataatctaataagtattgattatctattctttgctttctgttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAGCCACCAAAAAGAGAGCGGAAGCGGAA
                                ttctttgctttctgtt  CT-rich tract
      ataatctaataagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaagcatttttattctcttgctagataggcttaattattgttttcccttgatactggttttaggcacattggataatctaataagtattgattatctattctttgctttctgttgatgtagGATGAGAACAAGTTTGACTTCAAGAAAATTGTCAGTGAAAACTGGATTGAGCCACCAAAAAGAGAGCGGAAGCGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA