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

gtaatttgctaagcatttaactatatctttggtatattatgcgatgatgtcgatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g06640.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G414002_T02 (Zea mays), 3'ss of exon 14
gtaatttgctaagcatttaactatatctttggtatattatgcgatgatgtcgatatgtataaagttgttcatgtctt--taatcatctttt---ctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
    | || |     | |  || | ||| |  | | |  |        ||  | ||| |    |   ||||| ||||  |  |    ||||   || |||   ||||| | ||| || || ||  |       ||||||||||||||||||||||| ||||| || |||||||
---gtatggtctctctctctctctctctctc-tctctcttttctcacagtacacatgcaatgtgcccttcatttcttgttggttgaattttaaacttggttc-cagGGTAAAAAGGCTGACGCGTTGATCAAGTATTTTGGCGAGGATCCTGTCCGTTGCCCCTTCGAACAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G132810_T01 (Zea mays), 3'ss of exon 6
gtaatttgctaagcatttaactatatctttggtatattatgcgatgatgtcgatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
         || || |||   | | | ||    ||| ||  | |||    | || ||       ||  |  |   || ||| ||     || |||    |||| | ||| || |||||  |       |||||||| ||||||||||| |||||||| ||||||||||
--------gtatgcttttctttcttttttgctcatagtacac-atg----caatgtgctcttcatttcttgttggttgaattataaa--cttggttc-tagGGTAAAAAGGCTGATGCGTTGATTAAGTATTTTGGTGAGGATCCTGTTCGCTGCCCCTTTGAACAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA04G32990.1 (Glycine max), 3'ss of exon 19
gtaatttgctaagcatttaactatatctttggtatattatgcgatgatgtcgatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
       |  |     ||||| || ||||||| | ||||| |   | | |  |     |||||| |     |||         | |||| |  |||||||||| |||||||||||||||||||| ||||||||||| |||||||||  ||| || || ||||| ||||
-------gtaatatgcttaaccatctctttggaagattatacataggtataaagggacataaagat-----tgt--------gtgttttatttgtggacagGGTAGAAATGCAGATGCACTTGCCCTATATTTTGGTGAGGATCCTTCCCGTTGTCCTTTTGAGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 16
gtaatttgctaagcatttaactatatctttggtatattatgcgatgatgtcgatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
       |  |     |||||||| | | | ||| |||||||    || |  | |  |||||||         |  |  |  || | |        ||||||| |||| ||| ||||||||||||||||||||||| ||||||||||  || |||||| | || ||||
-------gtaatatgcttaactatctttgttgtacattatgcaccaatatgaagagatataaag--------attgtagaatatgtct--------gacagGGTAGAAGTGCTGATGCACTTGCACTATATTTTGGTGAGGATCCTGCTCGTTGCCCAATGGAGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 18
gtaatttgctaagcatttaactatatctttggtatattatgcgatgatgtcgatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
       |  |     |||||||| |   | ||| |||||||    || |  | |  |||||||         |  | |||    || |||     ||||||| ||||  || ||||||||||||||||||||||| ||||||||||  || |||||  | || ||||
-------gtaatatgcttaactatcttcgttgtacattatgcaccaatatgaagagatataaag--------attgtaaat----ttgtct-----gacagGGTAGAAGCGCTGATGCACTTGCACTATATTTTGGTGAGGATCCTGCTCGTTGCCCTATGGAGCAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaatttgctaagcatttaactatatctttggtatatt--atgcgatgatgtcgatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
||||||||  || |  |  |||| ||     |    ||      ||  |||| | |     | ||  || |  |    ||  |  |||| | | ||  | ||||| |||||||| ||||| ||||| |  ||||||||||||||||||  ||| || |||||||||||||
gtaatttgtcaacctct--actagattccaagcgcctttaccttgacaatgtggttgatcctgaaaatgatttttgtgttgtt--tcttatgttggacggcagGGAAGAAATGCTGATGCTCTTGCTCACTATTTTGGCGAGGATCCTAACCGTTGTCCATTTGAACAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 3'ss of exon 26
----------gtaatttgcta--agcatttaactatatctttggtatattatgcgatgatgtcgatat-gtataaagttgttcatgtcttt-aatca-tcttttct-cggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
            ||| |  ||  |  | |  | |  |  |    || ||| | | |||   | ||| | | |   | ||   | ||| ||| ||||| |||| | |  ||  ||||||| | |||||| |||||||||||||  ||||||||||||||||||  ||  |  ||||||||| |||
gtaatgtttgtcaatctcttattactagtagattccaagtgccttacattttacaatgtgtttgatcttgaaagtaattacacttgtttttgaatcaatcttatgtatggacgacagGGAAAAAATGCTGATGCACTTGCACACTATTTTGGCGAGGATCCTAACCATTATCCATTTGAAAAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT5G07770.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaatttgctaagcatttaactatatctttggta--tattatgcgatgatgtcgatatgtataaagttgttcatgtcttt--aatca-tcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
|||||||         |  |||| |      |    ||   |  |   ||||   |     | |  ||  |  | | |||  ||| | |||| |   ||  ||||| | | |||||| |||||||||||||  ||||||||||||||||||  ||  |  ||||||||| |||
gtaatttttgtcaacctctactagactccaagcgcctaacctttggcaatgtgtttgatcctgagattactttttttttttgaataaatcttatgatggacgacagAGAATAAATGCTGATGCACTTGCACACTATTTTGGCGAGGATCCTAACCATTATCCATTTGAAAAAG

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: PP1S13_282V6.2 (Physcomitrella patens), 3'ss of exon 16
gtaatttgctaagcatttaactatatctttggtatattatgcgatgatgtc-gatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
   |    | | |   |  |   | ||| || | |  | |  | |    |  | ||| | ||  | | | |||  |  | |  | |  | |   ||  ||||||||| ||||||||| ||||||| | |||||| ||||||||||| |   | || |||||||||||||
actaccgccaatggcctgcaacctttctgtgatgtggttttagtttgcatttggtatttgtattgat-tgcatagcaatgacaagcaatgcggtgtt-acagGGCAGGAATGCAGATTCACTTGCTCAATATTTCGGCGAGGATCCGGCGAGATGTCCATTTGAACAAG

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|110700830|gb|EE077830.1|EE077830
EST:     GTGTTGCTGAGGGACAGGTGGGGTCTGTGACAAATCTATATTCTGTGGTG                         GGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAAGATCCTGTCCGC
genomic: GTGTTGCTGAGGGACAGGTGGGGTCTGTGACAAATCTATATTCTGTGGTGgtaatttgct ... cggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGC
EST: gi|110700821|gb|EE077821.1|EE077821
EST:     GTGTTGCTGAGGGACAGGTGGGGTCTGTGACAAATCTATATTCTGTGGTG                         AGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGC
genomic: GTGTTGCTGAGGGACAGGTGGGGTCTGTGACAAATCTATATTCTGTGGTGgtaatttgct ... cggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGC
EST: gi|110700879|gb|EE077921.1|EE077921
EST:     GTGTTGCTGAAGGACAGGTGGGGTCTGTGACAAATCTATATTCTGTGGTG                         GGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAAGATCCTGTCCGC
genomic: GTGTTGCTGAGGGACAGGTGGGGTCTGTGACAAATCTATATTCTGTGGTGgtaatttgct ... cggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGC
EST: gi|110700824|gb|EE077817.1|EE077817
EST:     GTGTTGCTGAAGGACAGGTGGGGTCTGTGACAAATCTATATTCTGTGGTG                         GGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAAGATCCTGTCCGC
genomic: GTGTTGCTGAGGGACAGGTGGGGTCTGTGACAAATCTATATTCTGTGGTGgtaatttgct ... cggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtcgatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG
                            ctttaat  putative branch site (score: 4)
                                  tcatcttttctc  CT-rich tract
      atatgtataaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgctaagcatttaactatatctttggtatattatgcgatgatgtcgatatgtataaagttgttcatgtctttaatcatcttttctcggtggacagGGCAGAAATGCAGATGCACTTGCACTATATTTTGGCGAGGATCCTGTCCGCTGCCCATTTGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT