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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG

Basic information

species Vitis vinifera
transcript Vv03s0038g00970.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 1
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG
                           ||  |    | |   | || ||  ||||||  |   |  |     ||  |  | | |||    | || |  |||||||||| ||||||||||||||||  ||||||||||| || ||||||||||||||||| ||||| || ||||| ||||| || || || || || ||||
---------------------------gtgaatttcaatcgaatttgaa--tttgaactttact--caagtgccatatcactgtttttgttgatgt--agGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 1
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG
           || ||||   | | || |  |    |    ||||   || |        | | |         | |   || |||    | || |  ||| |||||| ||||||||||||||||  ||||||||||| || ||||| ||||||||||| ||||| || ||||| ||||| || || || || || ||||
-------gtgaatttcaa---tcgaatttcaatttgaactttactctcaagtaccgtatcactgtttttattttttatttttatttttgttgatgt--agGTTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAACAGATTCGTTTGAAGATTTTTTCGCCGAATGTTCTCGACATTACGCTCGTGG

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctt---tccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG
  | | | ||  |||  |        |||||||     || |  || || |        ||  |  |      ||   |  ||||   ||   |  ||| |||||||| || ||||||||||| || |  ||||||||||| ||||| |||||||||||  | ||||| || || |||||||| |||||||||||  | || |
--aatgtaatactcttgatgccgatttgtatac-ggtctacttgtttaatcccccctcctatctctctgttgactagtatatcttcactcactttttctgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 1
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccc--cccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG
  |    | |    |            ||| | ||||     | ||||| ||||    ||   | |      |   |  |  |  | ||      ||| |||  ||| || ||||||||||| ||||  ||||||||||| || || |||||||||||  | ||||| || || |||||||| |||||||||||||| || |
--acggctgtttggtggcctcccaacagtaaatcaaacccgcatttaaaccttttttaatctctgctgttggcttgtatatgtattctctctctttctgcagATTGAAACTGATAGGGAAGCAGGAGGGAACAAAGGTGTCTCTGACAAGCAGATTCGACTCAAGATTTTTTCACCAAATGTTCTTGATATCACACTTGTTG

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 1
-ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctt-tccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG
  | ||  |  ||    | |  |    | | |     | || |  |||| |||  |       | ||      | |  | ||  |    |  |  ||| |||||||| || ||||||||||| || |  ||||||||||| ||||| |||||||| ||  | ||||| || || |||||||| |||||||||||||| || |
actcttgatggcaatgtacggataaggtatgtggtctactagt--ttaatactccgccccatctctctattgacttgtatatcttcactctcttttctgcagGCTGAAACTGATAGGGAAGCGGGTGGGAACAAAGGTGTATCAGACAAGCAGATCCGACTTAAGATTTTTTCACCAAATGTTCTTGATATCACACTGGTAG

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|34361920|gb|CF403505.1|CF403505
EST:     TGCCTGGAAAGAAGTTCTTCGATTTCTCGGAGATTCGCCGCGAAATTCAG                         GCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAG
genomic: TGCCTGGAAAGAAGTTCTTCGATTTCTCGGAGATTCGCCGCGAAATTCAGgtgattcatt ... tcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAG
EST: gi|22010867|gb|BQ795901.1|BQ795901
EST:     TGCCTGGAAAGAAGTTCTTCGATTTCTCGGAGATTCGCCGCGAAATTCAG                         GCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAG
genomic: TGCCTGGAAAGAAGTTCTTCGATTTCTCGGAGATTCGCCGCGAAATTCAGgtgattcatt ... tcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaactttgaagatagtttccccccccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG
                                             tcatcttc  CT-rich tract
                               aaaattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG

- - - - - - -ctcaagc
- - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - -ataccaa
- - - - - - - - - - - - - - - - - - - - - -cttaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaattc