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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatcaatcatattaaacagaatgttgcagtagttcatttaaatctaaaatattttacattgtgatttctcttgctcatgcgtttttatgttatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCTCCATTTTTTCTGGCTTCCTCTGTCTTCTTCGCCATCAAAGATGCAATTG

Basic information

species Vitis vinifera
transcript Vv06s0004g02030.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 9
gatcaatcatattaaacagaatgttgcagtagttcatttaaatctaaaatattttacattgtgatttctcttgctc-atgcgtttttatgttatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCTCCATTTTTTCTGGCTTCCTCTGTCTTCTTCGCCATCAAAGATGCAATTG
  |  | |   | ||| | | |  ||   | |      |  | | ||| |||||||  |  || ||||  ||  |  || |     |   ||   |  ||||||| ||||||||||||||| || ||||| ||||| || ||||| ||||| |||||||| || | |||| | ||||| || || || || ||||| ||  
tttacagcccttgaaatatactaatgtttttgccttggtgta-caaaattattttatctcatgttttcagttattttatcctaaaatgactttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT

upper sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 15
gatcaatcatattaaacagaatgttgcagtagttcatttaaatctaaaatattttacattgtgatttctcttgctcatgcgtttttatgttatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCTCCATTTTTTCTGGCTTCCTCTGTCTTCTTCGCCATCAAAGATGCAATTG------------------
                                                                        | | ||   | | |    ||  ||  ||||   |||||||   ||||||||||||||||| || ||||| ||||||||||||||||| || || ||| |||| || || |||||||| ||||| ||                    
------------------------------------------------------------------------gtttattgttgtgtgcactaattggtagggccatccaaatgttaagGCCATCCATTCATCTAAAGCTGTTGGTGAGCCTCCATTTTTCCTAGCATCCGCTGTGTTATTTGCCATCAAGGATGCTATCATAGCTGCAAGAGCTGAAA

upper sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 14
--gatcaatcatattaaacagaatgttgcagtagttcatttaaatctaaaatattttacattgtgatttctcttgctcatgcgtttttatgttatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCTCCATTTTTTCTGGCTTCCTCTGTCTTCTTCGCCATCAAAGATGCAATTG
   | ||    |   ||  |  || ||    |   |  |  ||||  || ||||   |||   | | ||  | || |  |   | | |  | ||  ||  |||||  |||||||   ||||||||||||||||| || ||||| ||||||||||||||||| || || ||  |||| || || |||||||| ||||| ||  
ctcaccaggtgt-ccaagtatcatatttttattaattctcaaaattaaagatatca-acacgataacttaccctgtttgtttttgtgtgcgctaattggtagGGTCATCCAAATGTTAAGGCCATCCATTCATCTAAAGCTGTTGGTGAGCCTCCATTTTTCCTAGCATCTGCTGTGTTGTTTGCCATCAAGGATGCCATCA

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|22014660|gb|BQ799694.1|BQ799694
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
EST: gi|22014527|gb|BQ799561.1|BQ799561
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
EST: gi|110428986|gb|EC995472.1|EC995472
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
EST: gi|22014504|gb|BQ799538.1|BQ799538
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
EST: gi|22014556|gb|BQ799590.1|BQ799590
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
EST: gi|110368506|gb|EC932487.1|EC932487
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
EST: gi|110422800|gb|EC989131.1|EC989131
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
EST: gi|110699874|gb|EE077267.1|EE077267
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
EST: gi|22014924|gb|BQ799958.1|BQ799958
EST:     TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAG                         GGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT
genomic: TTCCTTCTATCAATGATGTCCCCTTAAAATTTGATGTTTCACTTCTGAAGgtagagaaac ... tatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatattttacattgtgatttctcttgctcatgcgtttttatgttatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCTCCATTTTTTCTGGCTTCCTCTGTCTTCTTCGCCATCAAAGATGCAATTG
 atctaaa  putative branch site (score: 3)
                                    tttttatgttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatcaatcatattaaacagaatgttgcagtagttcatttaaatctaaaatattttacattgtgatttctcttgctcatgcgtttttatgttatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCTCCATTTTTTCTGGCTTCCTCTGTCTTCTTCGCCATCAAAGATGCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- tcaatca
- - - - - - - aacagaa
- - - - - - - - - - - - tgcagta
- - - - - - - - - - - - - - - - - - - - - - -aaaatat