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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttaccataactgaacaccttgagattctatttatctatttatttactttttatatggattgaagtaaacaattttaattttctctattcaaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAACTTGACACTAATCCAGGCACCCCTAGTTGATGTGGAGATCAGAGGTGTTC

Basic information

species Vitis vinifera
transcript Vv13s0019g04590.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G35320.2 (Glycine max), 3'ss of exon 10
--------------------------------------------------------tcttaccataact----gaacaccttgagattctatttatctatttatttactttttatatggattgaagtaaacaattttaattttctctatt-----caaa----ttccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAACTTGACACTAATCCAGGCACCCCTAGTTGATGTGGAGATCAGAGGTGTTC
                                                         |  |  | ||||    | | |    ||      | |  | | | | | ||| || | |     || |  |||| |  |  || || |  ||       ||||    || |||||||| |||||||||||||| ||  |  || ||||||||||||||||||  ||  || | ||||||||||| || || ||||| ||||| ||||||||||
gtactttaattgttttctctttaattgatatgtaacagaactgatagctgagcataccaaagaagaacttgaaggagaaggggaagaaaaactcttgtgtct-tgtacgttatgttcatttttatttaaagagctaaaacttgcaataccatgaacaaacttttttcagGATCAAATGCGTGCTCTTGATATAGTTCAGAATGATCCAGAACTCTCCAGTTTATCAATGATCCAGGCACCACTCGTAGATGTTGAGATAAGAGGTGTTC

upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G10350.2 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------------------------------------------tcttaccataactgaacaccttgagattctatttatctatttatttacttt-ttatatggattgaagtaaacaattttaattttctctattcaaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAACTTGACACTAATCCAGGCACCCCTAGTTGATGTGGAGATCAGAGGTGTTC
                                                            |    | |  ||  || |||  |    | || |   | | |  ||  ||| || | |||  ||||  |  || | | ||   |    | | ||  | ||||| || ||||| |||||||| ||||||  ||| ||| ||||||||||    |||||||| ||  |||| || || |||||| |||||||||||||||| |
gtatacacacaaacacaaacacaagcttctcatgaactgatagtctctttaaaccaaagaccggtcttgcct--actcctcaaaccacaatgtgcttctgttcttgttttgttctgtggtatgaa-catgca-tctaaaacctgaaaaatgaacatgcagGACCAAATGCGGGCTCTTGATATGATCCGGGAGGATTCAGAACTCTCTGCTTTGACACTGATGGAGGCTCCGCTGGTTGATATGGAGATCAGAGGTGTCC
















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|30328406|gb|CD011668.1|CD011668
EST:     TTCTTCCCCCATCTACCTCAGACTGCAAATTTTGTGCGATGAAGAGGAAG                         GATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
genomic: TTCTTCCCCCATCTACCTCAGACTGCAAATTTTGTGCGATGAAGAGGAAGgtataaatct ... caaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
EST: gi|27578838|gb|CB001533.1|CB001533
EST:     TTCTTCCCCCATCTACCTCAGACTGCAAATTTTGTGCGATGAAGAGGAAG                         GATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
genomic: TTCTTCCCCCATCTACCTCAGACTGCAAATTTTGTGCGATGAAGAGGAAGgtataaatct ... caaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
EST: gi|30328715|gb|CD011977.1|CD011977
EST:     TGCGATGAAGAGGAAG                         GATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
genomic: TGCGATGAAGAGGAAGgtataaatct ... caaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
EST: gi|32267735|gb|CD716698.1|CD716698
EST:     TTCTTCCCCCATCTACCTCAGACTGCAAATTTTGTGCGATGAAGAGGAAG                         GATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
genomic: TTCTTCCCCCATCTACCTCAGACTGCAAATTTTGTGCGATGAAGAGGAAGgtataaatct ... caaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
EST: gi|349822994|gb|FQ399973.1|FQ399973
EST:     TTCTTCCCCCATCTACCTCAGACTGCAAATTTTGTGCGATGAAGAGGAAG                         GATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
genomic: TTCTTCCCCCATCTACCTCAGACTGCAAATTTTGTGCGATGAAGAGGAAGgtataaatct ... caaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
EST: gi|46909628|gb|CN545173.1|CN545173
EST:     CGATGAAGAGGAAG                         GATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC
genomic: CGATGAAGAGGAAGgtataaatct ... caaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttttatatggattgaagtaaacaattttaattttctctattcaaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAACTTGACACTAATCCAGGCACCCCTAGTTGATGTGGAGATCAGAGGTGTTC
                            ttttaat  putative branch site (score: 3)
                                  ttttctctattc  CT-rich tract
                     taaacaattttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttaccataactgaacaccttgagattctatttatctatttatttactttttatatggattgaagtaaacaattttaattttctctattcaaattccagGATCAGATGCGTGCTCTTGACATGATCAAGGATGATCCAGAACTCTCCAACTTGACACTAATCCAGGCACCCCTAGTTGATGTGGAGATCAGAGGTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
-cttacca
- - - - - - - -acacctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaacaa