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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT

Basic information

species Vitis vinifera
transcript Vv04s0023g03830.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os02g01170.1 (Oryza sativa), 3'ss of exon 7
gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgc---tttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
                                 | |||| |  | | |   |    ||| ||   ||       ||| | | |||  ||| | ||||  || | |   ||| ||| |||| || |||||||  |||||||| || ||||| || |||||||||||||| ||  | |||||||| ||| ||||||| ||||| ||| | ||     
--------------------------------gtaagtgcgctatatg-catttcaatatctga-attggccttctgtaag-tttagttact-taattgctctacatgtttgtagCTACTCGAGATCATGGCTGAATTCACCCCAGAGCAACAACATGCATTCTGCCAGTTTGTAACTGGTGCTCCTCGGCTTCCGCCTGGTGGTTTAGCTGCCC

upper sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G049141_T02 (Zea mays), 3'ss of exon 14
gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatata---ttgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
                                    ||  |   |   |  |  |  ||| || | | ||   ||       | |||||  | ||   |    | || |||  |||| ||||| ||||||| |||||| |||||||||||||| ||||| |||||||| ||  | || ||||| ||| ||||||| ||||| ||| ||||     
------------------------------------gtaagtttccctgcttctttgtaattcatttgtaggtttcgtaagtttatttggatgtttctaatgttgtgttttgcagTTTCTTGAGATCATGGCAGAATTTACTCCTGAGCAGCAACATGCTTTCTGCCAGTTTGTGACCGGTGCTCCTCGGCTTCCACCTGGGGGTTTGGCTGCTC

upper sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G374574_T01 (Zea mays), 3'ss of exon 14
gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
||||| |  ||| |        |  |  |   ||   |     |||   |  | |  |   | ||    | ||      || ||  || ||| |  |||  ||| ||| ||| |||| || ||  ||  ||||||||| ||||||||||||||||| |||||||| ||  | || ||||| ||| ||||||| | ||| ||  ||||     
gtaagctcattcgtcctcacatgctacatctcttacat-----aca---tccagttgtggtttttgagaagtg------tggttccttgattct--tgctcttg-tttgtagCTACTCGAGATTTTGTCAGAATTCACCCCTGAGCAGCAGCATGCGTTCTGCCAGTTTGTAACCGGTGCTCCTCGGCTTCCACATGGTGGATTGGCTGCCC

upper sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 14
gtaagattcttcctatatttg---gggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
||| | || ||  |   | |    || || |||  |||  | |||||             ||    |  ||||||   |||   |  ||| |  ||  ||         ||  ||||||| ||||| |||||||||||||| || |||||||||| ||| ||||| |||||  ||||||||||||||||||| |||||||| || |||||| |  
gtatgtttttttattcctgtagaaggacaattgtgttt--ttggaaatt-----------taggcttgttatatttggtgctgaacctgtatgatgctat---------tttcagTTACTCGAAATTATGGGAGAATTCACACCAGAGCAGCAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCTCCTGGTGGACTGGCAGTTC

upper sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 14
gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
             ||| |||    | |    |||    |  | |  | || | ||   || |   |  || | |     |    || || |  |  ||  |    ||| |||||||||||||| |||||||| ||||| || |||||||| | ||| ||||| |||||  ||||||||||||||||||| || |||||||| |||||| |  
------------gtatgtttttttcctcctaattataagtaatattgtgtattatagaaaattagagctagttataatttatgatgcttgtcctgttggatgctattt-tagTTACTTGAAATTATGGGAGAGTTCACACCAGAGCAGCAACGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCACCTGGAGGGCTGGCAGTTC

upper sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA06G00600.2 (Glycine max), 3'ss of exon 14
gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgat-ttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
             |||  ||    |   |   | ||  || | |  | || | | |  || |   |  || | | |  |||||  ||||   |   ||||  || |     ||||||||||||| |||||||  ||||| || |||||||| | ||| ||||| |||||  ||||||||||||||||||| || |||||||| |||||| |  
------------gtatgcttttttcccctaattataa-ggaatattgtgtatgacggaaaattagagctagtta-tatatgatgctgttctgttggatgctatttc-----agTTACTTGAAATTATGGGAGGGTTCACACCAGAGCAGCAACGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGCTGCCACCTGGAGGGCTGGCAGTTC

upper sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA11G11490.2 (Glycine max), 3'ss of exon 14
gtaagattcttcctatatttg--gggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
||| | |||||       | |  || ||||||  |||  | |||||             ||    |  ||||||   |||   |  |      | | ||||  ||    |  ||||||| | ||| |||||||||||||| || ||||| |||| ||| ||||| |||||  ||||||||||||||||| | |||||||| || |||||| |  
gtatggttcttttccccatagaaggacatttgtgttt--ttggaaatt-----------taggcttgctatatttgatgctgaacct-----ctatgatgctatt----ttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTC

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|110702937|gb|EE079346.1|EE079346
EST:     ACATAAAGTTTGATCATGGATACACTGCCAAGAGCCCTGCGATTATCAAT                         TTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGC
genomic: ACATAAAGTTTGATCATGGATACACTGCCAAGAGCCCTGCGATTATCAATgtaagattct ... tgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGC
EST: gi|27580872|gb|CB003567.1|CB003567
EST:     ACATAAAGTTTGATCATGGATACACTGCCAAGAGCCCTGCGATTATCAAT                         TTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGC
genomic: ACATAAAGTTTGATCATGGATACACTGCCAAGAGCCCTGCGATTATCAATgtaagattct ... tgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGC
EST: gi|30321585|gb|CD004847.1|CD004847
EST:     ACATAAAGTTTGATCATGGATACACTGCCAAGAGCCCTGCGATTATCAAT                         TTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGC
genomic: ACATAAAGTTTGATCATGGATACACTGCCAAGAGCCCTGCGATTATCAATgtaagattct ... tgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
           tattgac  putative branch site (score: 2)
                                       tgcctttgctttct  putative PPT
                        atttgtttattgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattcttcctatatttggggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG