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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggtaggttttccatttttgtttttctctcctggttattgaatccttacatcacatgtcacaatagttttgttgaataggctaactgaataccatttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG

Basic information

species Vitis vinifera
transcript Vv08s0040g00670.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 3'ss of exon 20
-------------------gggtaggttttccatttttgtttttct---ctcctggttattgaatccttacatcacatgtcacaatagttttgttgaa------taggct-------aactgaatacca------tttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG
                      | ||||    || ||  ||  |       |     || | |     || ||  ||    | ||  | ||||  |||       ||  |       || |   |  ||      |||||||| |||||||| ||||| ||||| || |||||  | |||||||||||||||||||||| || ||||||| | || || |   |||||||  | ||   ||
gtgcgtttcccttctgtttacttgggttcaatatgttcattgctacagatgcacacatacttaggttgtatatggcaaactaaaaatggtttggagaagctattcagtttgatgttcaattttgtgtcatatttttttcagGTTTGTGCTCCGTCATGTCATGATTGCTCCACATTACGTGCTTGGTGGGAAGAAGATGGAGGAAGAAGAAGCCGTTTCTACCAGACTGTAATTGGTAGTG

upper sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 10
------------------------------gggtaggttttccatttttgtttttctctcctggttattgaatccttacatcacatgtcacaatagttttgttga------ataggc-taactgaataccatttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG
                                |    |||   | | |  |        | |  | ||||||   |  ||       ||| |   | | ||||||      | || | |   |   |    |||||||| |||||||| ||||| |||||||| || ||  | ||||||||||||||||||||||||| ||||||| | || || |  |||||||| || ||   ||
gtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaa-tggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG

upper sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA03G27600.1 (Glycine max), 3'ss of exon 20
gggtaggttttccatttttgtttttctctcctggttattgaatccttacatcacatgtcacaatagttttgttgaataggctaactgaataccattt-cagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG
    |  |  |  || |  |||  ||| |  ||   | | ||| |     |  |   |   |    |||||||  || || | ||| ||  | || | ||||| ||||| || ||||| ||||||||||||||| ||||||||||||||||||||||||||||||||||||   | ||||| |||| |||| | | ||| |
tataatatgctaaatctaagttcatctttattgagaact-aatgcaagtttttctatttggagggcttttgtttgattgggtgacttaaggcaatgtgcagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCAGGTTTTTCAAGAATGTGATGGAGTCCG

upper sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA19G30580.1 (Glycine max), 3'ss of exon 21
gggtaggttttccatttttgtttttctctcctggttattgaatccttacatcacatgtcacaatagttttgttgaataggctaactgaataccattt-cagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG
    |  |  |  || |  ||   |||    ||   | | |||       |  |   |   |    |||||||  || || |||||  |  | || | ||||| ||||| || ||||| ||||||||||||||| ||||||||||||||||||||||||||||||||||||  || ||||| |||| |||| | | ||| |
tataatatgctaaatctgagtccatcttcattgagaact-aatgtaagtttttctatttggagctcttttgtttgattggttaacttgaggcaatgtgcagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG

upper sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT2G40840.1 (Arabidopsis thaliana), 3'ss of exon 20
-------------------gggtaggttttccatttttgtttttctctcctggttatt-----gaatccttacatcacatgtcacaatagttttgttgaataggctaactgaataccatttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG
                      |  || || | |  || |   |  || | | | |||       |   ||  |     ||    | |   |   |     |  ||| |    ||  |||| ||||||||||||| |||||||| ||||| || ||| |||| |||||||||||||| || ||||| |||||||  |  |  || |||   ||| | ||    |
gttagatatttttcctcagacttctgtctttcttacttatagcttcctaccgttcattttctgagaattttgtaatgggtgagtgattcactgcataattcaaactatcgtcttaatattttagGTGTGTGCTCCTTCATGCCACGACTGCTCTACCCTGCGAGCTTGGTGGGAAGAGGACGAAGAGAGAAGACAGCAGTACTTCAAGGAAGTGATTGGTGTAG

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|26264000|gb|CA815063.1|CA815063
EST:     GTGAACCTGGGCTGGAGTTTGGTATTCCTTCTCAATATAGCTATATGACG                         GTGTGTGCTCCATCATGTCATGACTGTTCCACCATGCGTGCTTGGTGGGAA
genomic: GTGAACCTGGGCTGGAGTTTGGTATTCCTTCTCAATATAGCTATATGACGgtaagatcct ... accatttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAA
EST: gi|18458362|gb|BM436640.1|BM436640
EST:     GTGAACCTGGGCTGGAGTTTGGTATTCCTTCTCA-TATAGCTATATGACG                         GTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAA
genomic: GTGAACCTGGGCTGGAGTTTGGTATTCCTTCTCAATATAGCTATATGACGgtaagatcct ... accatttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatcacatgtcacaatagttttgttgaataggctaactgaataccatttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG
                                 ggctaac  putative branch site (score: 2)
                                              ccatttc  putative PPT
                aatagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggtaggttttccatttttgtttttctctcctggttattgaatccttacatcacatgtcacaatagttttgttgaataggctaactgaataccatttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
gggtagg
- - - - - -ccatttt
- - - - - - - - - - - - -ctctcct
- - - - - - - - - - - - - - - - - - - - - - - - - - acatgtc