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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG

Basic information

species Vitis vinifera
transcript Vv13s0019g02360.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
                              |   ||   |  | |  | ||||| |  | |||||  |  |||   ||   | || |   ||        |||||   ||||||||||||| || || ||||| || |||||||| || ||||| ||||| |||||||| ||||  ||||| || ||||||||||| || |||||||
-----------------------------gtgtgtatgcaattctatattttcaaagcgttgatactaccaatt--tggctaaacccgtaat----acactgtgc---agCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 12
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
                          |   ||  ||||   |||    ||||  |  || | |  | || |||   |  ||  |  ||| | |     | |||||   |||||||||||||||| || |||||||| |||||||| |||||||| || ||||| || || || |   |||| || ||||||||||| || |||||||
-------------------------gtgagtatgtaaagtgatt----cttt--gggtgataaatttaagaatt--taatctaaaccagaagt---actctgtgc---agCTTGATGATGTGATTGATCTTGTAATACCAAGAGGTAGCAATAAGCTCGTTTCCCAGATCAAAGCAGCAACCAAGATTCCTGTTCTTGGTCATGCTG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G375504_T03 (Zea mays), 3'ss of exon 11
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
                                  |||    | |   |   | | |||  ||||   |  |||     |    |  |   | |  |  | ||| || |||||||||||||| || || ||||| || ||||||||||||||||| || ||||| ||||| || |  ||||| || || ||||| || || ||||| |
---------------------------------gtaagtgtaat-atatcatgaaaataatgattctaccaatatgcatgataagcctaaactcataatatgttctacagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCGCAAATCAAAGCATCAACTAAGATACCTGTCCTCGGTCATGCGG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
gtgagctgatgtgctgagaatgatcattga-tagttaaaaacatt-tgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
             |  | | || | ||| | ||      | | |  |  | | | | |||| ||||   |  | |     |    |  |   | |  |  |     || |||||| ||||||| || || ||||| || ||||||||||||||||| || ||||| ||||| |||   ||||| || || |||||||| || |||||||
------------acgaaaattgctgatttactaaaggtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G41850.1 (Glycine max), 3'ss of exon 9
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
                    ||| | |    |||  |    | ||  | ||||| ||   || |    |   |     ||  |||       |||   |||    | ||||| |||||||| ||||| || || || |||||||||||||| |||||||||||||| || |||  ||| || |||||||||||| | || |||||||
-------------------gtgaac-taatcagtggagcttaatttcagtttcataaccctgttc---accttaagcattggcacc------tttctatttaaatttcagCTGGATGATGTAATCGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAGATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCATGCTG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 9
gtgagctgatgtgctgagaa-tgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
               | ||| | |||| ||    ||||   || ||  |   | ||  || | |  | ||  || |  |    |  | | || ||   |||       ||||| ||||| || || || || || || |||||||||||||| ||||||||||||||||| |||  ||| || |||||||||||| | || || ||||
---------------gtgaactaatcagtggagcttaatttcaatttca---taagcctgttcactttaagcattg--gccacctttaaatacttaaattt-------cagCTGGATGACGTAATTGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAAATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCACGCTG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggt-gatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
                 | | |   || ||||  ||  ||        |      | || |     |     |   ||  |   || ||  ||||   |||| || | ||||||||||| || || || ||||| ||||||||||||||||| || |||||||||||||||||  | || || ||||| || || || ||||||||||
-----------------gtaagcagatagatacatatgaatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttt-tggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G39800.4 (Arabidopsis thaliana), 3'ss of exon 12
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
              | ||||      ||   || ||  | |      | ||      |     |    ||| ||||       || ||  ||||   ||| ||| | ||||||||||| || ||||| ||||| ||||||||||| ||||| || |||||| |||| |||||  || | |||||||| ||||| || || |||||||
-------------gtaagaacagat-ttacaagctaggagctgcaacagttcttttgtatcttttgttaaactgga-------acccaccatttgcattt-gtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G39800.3 (Arabidopsis thaliana), 3'ss of exon 12
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
              | ||||      ||   || ||  | |      | ||      |     |    ||| ||||       || ||  ||||   ||| ||| | ||||||||||| || ||||| ||||| ||||||||||| ||||| || |||||| |||| |||||  || | |||||||| ||||| || |         
-------------gtaagaacagat-ttacaagctaggagctgcaacagttcttttgtatcttttgttaaactgga-------acccaccatttgcattt-gtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAG---------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ17662 (Selaginella moellendorffii), 3'ss of exon 12
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
                                                             |  |  | |  |   || |   |    || || ||    || | | |||||||| ||||| || ||||| || || |||||||| ||||||||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
-------------------------------------------------------------gtaactatactttcgtgctgttagctcgt-ttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
                                                             |  |  | |  |   || |   |    || || ||    || | | |||||||| ||||| || ||||| || || |||||||| ||||||||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |
-------------------------------------------------------------gtaactatacttttgtgctgttagctcgt-ttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG

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|33402539|gb|CF208166.1|CF208166
EST:     AGAGAGGAGA-CCCTAATCTCCTCAAG                         CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
genomic: AGAGAGGAGATCCCTAATCTCCTCAAGgtgagctgat ... tgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
EST: gi|110362804|gb|EC926359.1|EC926359
EST:     AGAGAGGAGATCCCTAATCTCCTCAAG                         CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
genomic: AGAGAGGAGATCCCTAATCTCCTCAAGgtgagctgat ... tgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
EST: gi|110728239|gb|EE103633.1|EE103633
EST:     AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAG                         CTTGATGATGTGATCGACCTTGTAATCCCAAGAAGCAGCAATAAACTTGTT
genomic: AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAGgtgagctgat ... tgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
EST: gi|110701185|gb|EE078493.1|EE078493
EST:     AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAG                         CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
genomic: AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAGgtgagctgat ... tgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
EST: gi|161709197|gb|FC060516.1|FC060516
EST:     AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAG                         CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
genomic: AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAGgtgagctgat ... tgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
EST: gi|29783302|gb|CB349405.2|CB349405
EST:     ATCTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAG                         CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
genomic: AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAGgtgagctgat ... tgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
EST: gi|110414936|gb|EC980800.1|EC980800
EST:     AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAG                         CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT
genomic: AACTAATTGGACTTGTGACTTCAAGAGAGGAGATCCCTAATCTCCTCAAGgtgagctgat ... tgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG
                                    tttttgtttt  CT-rich tract
                                agtatttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG

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