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'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA

Basic information

species Vitis vinifera
transcript Vv06s0009g00960.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 12
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
    | | | |     |  |      ||      ||||    |       || ||||  ||    |||   | | |||  ||||  |       ||||||        ||||| || || || |||||||||||||||| ||||||  |||  ||||| ||| |||||||||| |||||||| ||||| || |||||||||||||  || |
---gtatatacacacatgaacactggaagccccaagtcggcct-------tttacttctattagtttt---attaatgtcttttttt------tctgtta--------cagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
----------------gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
                 |||   ||  || |||  |  |||    ||| |    |  |||      ||  | | ||| || | |  |  ||||  | ||   |  ||  | | |  |||   ||||| |||| || | ||| ||||| || ||||||||||| |||||||| || |||||||| ||||| |||||||| || ||||| ||||| || |||||||| |
gtcgtttttactattaataactgttcattaagtgcaattcactgatttag----tggttgcagcaatttccct-catcttgtatttatgtcatcatcttatttgtttctcttttggatgg--aacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 8
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
    ||| ||||      ||  | ||| |   |||    |  | ||   || ||  ||  |||| |   |    | |  ||||     ||||          | | ||||| |||| || | ||||||||| || || ||| | || |||||||| || |||||||||||||| |||||||| || || || ||||| ||||| |||||||
---gtgtgttctacctgataattgatattgaatgatatgagatattgaactacatatgtttgttttcctgtttccgtaattttaatctctttt-------gggctgaacagTTGCCTCAAATAAATCCTGGTTTCAACAACGCTCCATTTAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTACATCCGTGAGAGTGATAAGGACA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 2
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcact-tgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
                      | | | | |||  | | | |  | ||||   ||  | | ||     | | | | |   ||  || || ||   || |  |||   ||||| |||| || | ||| ||||| || |||||||| || |||||||| || |||||||| ||||| |||||||| || ||||||||||| |||||||| || |
---------------------gtaacattctttatgacaaatgttcattcaatacaatacttgcggacttgtattaac-tttcctcttatttcttctttgtatgg--aacagTTGCCTCAAATAAACCCTGGTTTCAATAACACGCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 12
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
||||  || | |  |    |  ||||    |   |  |  ||  ||       ||||| ||    |||| |  |  |||||      ||| |   | ||  |    ||||| |||| || | ||| ||||| || |||||||| || || ||||| || |||||||||||||| |||||||| || ||||||||||| | ||||||||| |
gtaaaattctttataac--aattcattcaatacaatacagttacttgagg---acttgtataaattttccacttattgctta-----actcttattctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACACCATTCAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTATATACGTGAGAATGACAAGGATA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 6
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
            | ||||    |  |  ||||| | || |      |||||      |  |      || |  |    |  |   |||  || |   ||     | ||||| | ||||| | ||| ||||| || || ||| | || |||||||| |||||||||||||| || || ||||| || ||||| |||||||||| |||||| |
-----------gtaagttctatttgtttttttttattcaaggataaattctgtgaa-gtctacctcatctacttatcaccatcgtctatgtttctcttttggattaaacagTTACCCCAAATAAACCCTGGTTTCAACAACGCTCCATTTAAATTCACGAAGTATTCAAACGCGTATATGCTTGTTTATATTCGTGAAAGTGCCAAGGAGA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 12
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctt-tttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
                         |||||     |  | ||||  |||      | ||||||  ||  ||||   | ||| |    || ||  ||  ||     ||||||| | || ||||||||||||||||| || ||||| || |||||||| || || ||||||||||| || |||||||||||||||||||||  |||||||||||
------------------------gtaatt-----gcttttttgcaattggctg-tggcatgtattt--gaacatttacttgtcggttatttaaccacttgtattttaacagTTACCACAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 12
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttc-ctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
                  ||  |  |  ||||||    |   |||     || |     || ||     ||||   ||||| ||   || ||  ||  ||     ||||||| | || ||||||||||||||||| || ||||| || |||||||| || || ||||||||||| || |||||||||||||||||||||  |||||||||||
-----------------gtaattgtt--tttttgcaattggctgtggcatttgatccctatattt----gaacatttgcttgttggttatttaaccacttgtattttaacagTTACCGCAGACAAATCCTGGATTTAACAACACTCCTTTTAAATTCACCAAATATTCAAATGCTTATATGCTGGTGTATATACGTGAAGCTGACAAGGACA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 4
gtaatgttttcttgagtttagctcataatt--tttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
                         |||||  |||    | |||    || |  || ||   | | |||| |||    | |||||    |||    ||  |  | |  ||||| | || ||||||||||||||||| || ||||| || ||||| || || ||||| |||||||| || ||||| ||||||||||||||||||||||||||||
------------------------gtaattgttttattgccattgaccatgc--cattt---tttccttttgaatatgt-cttttgatgactgaatcttgtgttta--aacagTTACCACAGACAAATCCTGGATTCAACAACACTCCATTTAAGTTCACCAAGTACTCAAATGCTTATATGCTTGTGTATATACGTGAAAGTGACAAGGACA

upper sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
                                                         ||||||  ||   ||||     |||     ||||    ||||  |   | |||| |||| ||||| ||||| ||||| || ||| | || || |||||||||||||| || |||||||||||||| || |||||  | || || || |||||||
-----------------------------------------------------gtaagcatgtcatt--aaact---agtttcggtgactta--ttgtt--tttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA

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|110388155|gb|EC952874.1|EC952874
EST:     AAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAG                         CTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAG
genomic: AAGAAGACGTGAAGAGGGCTTTGGAGGAGCAATATGGTGGTGAAGAAGAGgtaatgtttt ... tgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA
                                       tgttaat  putative branch site (score: 3)
                                         ttaatgattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttttcttgagtttagctcataatttttgagtctatttgttattcttcacttgcatgttctttcgaactcatgctttttcctactttgcctgttaatgattaacagCTGCCCCAGACAAATCCTGGATTGAATAACACCCCCTTTAAATTTACGAAGTATTCAAATGCATACATGCTGGTGTATATACGTGAAAGTGACAAGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG