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'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG

Basic information

species Vitis vinifera
transcript Vv11s0052g00320.t01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------ctcaaataggtttctaatatcttttatataa--aaaacatttttttatattttccccgctcttgttcgccttttttttttctttttt-ttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
                                      ||  |      ||||   |||  |  ||  | |  |      |  ||  | |  | |  ||  |   | |  ||||  | | || ||  |   | |||||||||| ||||||||||| ||||| ||   ||||||||| || || ||||| ||||| || || |||||  |||||||||||||||| |||||||| |||
gtacatacataattgggaattttgttttgaacaaataaaaggataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttagGCAGACATTGGTCTTGCTATGGGTATCCAAGGAACAGAAGTAGCTAAAGAAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
--------ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggactt--tagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
        ||| | ||   ||| |  || ||||  |  | ||||| | ||    || |||  |   | |  ||        | |||||| |    |  || ||||  ||||||||||| |||||  | ||||||||    ||||| || ||||| || ||||| ||||| || || |||||||||||||||||||| || || || | |
gtttatctctcgactaatgttccatcatgttttgaa--agaaacaatcttc---atgttcaacaaccataatc-----cagtctttcttatgcaatgctgaacttaatagGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
-----------------------------------------------------------ctcaaata-ggtttctaatatcttttatataaaaaacatttttttatattttccccgctctt----gttcgccttttttttttctttttt--ttttttggactt-tagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
                                                            | ||| | |   |   |  |   | ||||  ||   |       || ||| | | | | ||       |  ||||   |  |  ||  |    | |   ||||  ||||||||||||||||  |||||||||||   ||||| || ||||| || ||||| ||||| || |||||||||||||||||||| || ||||| || | |
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM2G391042_T01 (Zea mays), 3'ss of exon 25
-----------------------------------------------------ctcaaatagg---tttctaatatcttttatataaa------aaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggacttt--agGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
                                                      |   | | |   |||||| |  ||  ||| |||       || ||| |||  |||  |   |        |   | ||| ||  | |||       | || |  ||  ||||||||||||||||  ||||||| |||   ||||| || ||||| || ||||| ||||| || ||||||||||||||||||||||| || || || | |
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacat---cttttgttagtacttgagaaactctgaaacttgcagGCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
                                                |    ||  | || ||  |     ||| |   ||        || ||   |        || ||| |||| |   | |  |  || ||        | ||||||||||||||||| | ||||||||   ||||||||| || || ||||||||||| ||||| || ||  |||||||||||||| | || ||||| |||
gtacattcaatttgggagttcatattttaaatgaatacaagaattcaacatgcatgtgattatatgaagcactatttggtaatacagcacttctaacatgttgaggtttcttccccttctcaatcttatcattattcccacttatcagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM2G138195_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------ctcaaatagg---tttctaatatcttttatataaa------aaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggacttt--agGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
                                                      |   | | |   |||||| |  ||  ||| |||       || ||| |||  |||  |   |        |   | ||| ||  | ||        | || |  ||  || |||||||||||||  ||||||| |||   ||||| || ||||| || ||||| ||||| || ||||||||||||||||||||||| || || || | |
gtttgtggactgtagtctctatgaatttttaattactttgaaaccagcatcggtttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacat---cttttgttagtactcgacaaactctgaaacttgcagACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 27
ctcaaataggtttctaatatcttttata-taaaaaacatttt--tttatatttt----ccccgctcttgttcgcct--tttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
           |  ||  |||| || |  | | | |  ||||  || | ||| |     |  | | |||||  | |  || | |||     | | |||||||| ||||||| |||||||||||||||||||| ||   ||| ||||| ||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||| |||
---------tctattagaatctattgttctgacacattttttggttcaaattatgtgaactagtttttgttttcatggttgtgtttgtgactctatttttggagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 25
ctcaaataggtttctaatatcttttatataaaaa-acatttttttatat--------tttccccgctcttgttcgcctt-ttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
           |  ||  |||| || |  | | | |||||||||  |          |   |  | | |||||  | |  || ||||| |   | | |||| || ||||||| |||||||||||||||||||| ||   ||| ||||| ||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||| |||
----------ctattagaatctattgttcagacacacattttttggttcaaattaggtaaactagtttttgttttcatggttgtttttgtgactctatttttgagtttagGCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 24
ctcaaataggtttctaatatcttttatataaaaaacatttttttatatttt-----ccccgct--cttgttcgccttttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
       ||||||  | |||| |||  ||  |  |  |||| || || | |      |   ||  ||| |   |  ||||| |   | | |   ||||||| | ||||| ||||| |||||||||||||| ||   ||| ||||| ||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||| |||
-------aggtttgaactatcatttcaatgcaggagtttttgttctaatgtagtaaactaactagcttttattctgtttttgtaattctatacattttggaatatagGCCGATATAGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 24
ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttc-----cccgctcttgttcgccttttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
     | ||||||  | |||| ||   ||  | |   |||| || || |        |  ||| || |||   | || |  |||| |   ||||| ||| | ||||| ||||| ||||| |||||||| ||   ||| ||||| ||||| ||||||||||| || |||||||| ||||||||||||||||| |||||||| |||
----taaaggtttgaactatcattccaatgcagatgtttttgttctaatgcagtaaactagcttttattcttttcttgtaattctatacattttt-ggaatatagGCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 3'ss of exon 26
-----------------------------------------ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctc-----ttgttcgccttttttttttcttttttttttttggactt-tagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
                                         ||  |      |   | | ||||||    ||  |   |   |   | ||| | | ||       |  ||  |   ||  | ||   ||||||   || | ||  ||||||||||||||||||| ||||| ||  |||||||||| || || || ||||| || |||||||| |||||||||||||| ||||| ||||||||||||
gtatagtaatttactgaaatttaaactgataatgtcgaaagctacatctaactgaaagtttcttttggccaagtattttgcctacgtttttactcagcgagcggatcattatctcattggtgttaaattttttgagtgtatttgcagGCAGATATTGGTCTTGCTATGGGAATAGCAGGAACAGAAGTGGCTAAGGAGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 26
ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggacttt-agGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
 |  ||||  |||   | ||   |  |||    ||  |||    |||       | || || ||     |     ||||| | ||        ||||| |||||||||| ||||| |||||||| ||   ||| || || |||||||| || |  || ||||||||||||||||||||||| ||||  || ||||| |||
gttcaatacattt---acattcctcgtatgtgtaagctttaaaaata-------cactgttattgaggatcacactttctgtgttgccccccaactttcagGCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAG

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 26
---------------ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
                | | |     ||  ||    |||    | |     || |     | |  |   |  ||  | || |     |  |     |   || || | |||  |||| || ||||||||| ||||||| ||  ||||||| || || || ||||| || || |||||||||||| | |||||||||||  | || ||||| |||
gtaaaaggctacctattgatactttctttcaacggttttggcgtgatgtgtatgtcacagtttaattttctgtcgaggtcacgaggctgatg---gtacattattggcactgcagGCCGACATTGGTCTTTCAATGGGTATAGCAGGAACGGAAGTCGCGAAAGAAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG

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|30299117|gb|CB975911.1|CB975911
EST:     TGCTGTAACTGGAGATGGAACTAATGATGCTCCTGCACTACACGAG                         GCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAG
genomic: TGCTGTAACTGGAGATGGAACTAATGATGCTCCTGCACTACACGAGgtttggcgag ... tggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAG
EST: gi|110712227|gb|EE089604.1|EE089604
EST:     TTGTTGCTGTAACTGGAGATGGAACTAATGATGCTCCTGCACTACACGAG                         GCAGATATTGGTCTTGNCA-TGGGCATTTCAGGAACAGAGGTTGCAAAAGA
genomic: TTGTTGCTGTAACTGGAGATGGAACTAATGATGCTCCTGCACTACACGAGgtttggcgag ... tggactttagGCAGATATTGGTCTTG-CAATGGGCATTTCAGGAACAGAGGTTGCAAAAGA
EST: gi|30299189|gb|CB975983.1|CB975983
EST:     GAACTAATGATGCTCCTGCACTACACGAG                         GCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAG
genomic: GAACTAATGATGCTCCTGCACTACACGAGgtttggcgag ... tggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAG
EST: gi|30299258|gb|CB976052.1|CB976052
EST:     TGCTGTAACTGGAGATGGAACTAATGATGCTCCTGCACTACACGAG                         GCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAG
genomic: TGCTGTAACTGGAGATGGAACTAATGATGCTCCTGCACTACACGAGgtttggcgag ... tggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttccccgctcttgttcgccttttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG
       cccgctcttgttcgcc  CT-rich tract
                       ttttttttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcaaataggtttctaatatcttttatataaaaaacatttttttatattttccccgctcttgttcgccttttttttttcttttttttttttggactttagGCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- -aaatagg
- - - - - - - - - - - - - - taaaaaa