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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGAGTTTAGACCTAAATGGGACCCTATGCTTGCTTATTTTAAAATCTTGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaacgtaaaatttgaacacatgtactagtgatgtattgacttaatacttgttcccacaattttgagttgatatctcaactctctgtttattctgtttgcag

Basic information

species Vitis vinifera
transcript Vv05s0020g04870.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G121223_T02 (Zea mays), 5'ss of exon 4
TGATGAGTTTAGACCTAAATGGGACCCTATGCTTGCTTATTTTAAAATCTTGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaacgtaaaatttgaacacatgtactagtgatgtattgacttaatacttgttcccacaattttgagttgatatctcaactctctgtttattctgtttgcag
|| ||| ||| | |  || ||||| || |||||||| ||||  |||   ||||| || |||||||| |  |   |||  |||||||||||||||||||||||||||  | | |    | |     | |||       ||||      | ||  ||   | |||  || |||  ||  | |  ||                        
TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATATTGCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagcttctgttgt---tccctgtgt-----atgttcatgttaaactctcaattccaacatgttg--tttgttttccag-----------------------

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G124965_T02 (Zea mays), 5'ss of exon 3
TGATGAGTTTAGACCTAAATGGGACCCTATGCTTGCTTATTTTAAAATCTTGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaacgtaaaatttgaacacatgtactagtgatgtattgacttaatacttgttcccacaattttgagttgatatctcaactctctgtttattctgtttgcag
|| ||| ||| | |  || ||||| || |||||||| || |  |||   ||||| || |||||||| |  |   |||  |||||||||||||||||||||||||||  | | |    |         |   ||  | ||||      | ||  ||   | |||  || |||  ||  | |  ||                        
TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagcttctgtt--------gttccctgtttatgttcatgttaaactctcaattccaacatgttg--tttgttttccag-----------------------

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G01030.1 (Glycine max), 5'ss of exon 3
TGATGAGTTTAGACCTAAATGGGACCCTATGCTTGCTTATTTTAAAATCTTGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaacgtaaaatttgaacacatgtactagtgatgtattgacttaatacttgttcccacaattttgagttgatatctcaactctctgtttattctgtttgcag
|||||| ||| | |||||||||||  |||||||||| || |  ||| | |||||||||| ||||||||  | ||||||||||   |||||||| |||||||| | || | |  | |  || ||    | |  ||    || | |    |       |||| |  | | || | ||  |   |    |    |                
TGATGACTTTCGTCCTAAATGGGATGCTATGCTTGCATACTGCAAAGTATTGGAGGAATGCCCTCATAATGGGACAATGATTTCTCACTGGATTAAAAAGgtatcttcaccaaagatcttaaatttgtattttaagtgtgcaatagtatg------gttcactgattcttcatttactccttttgtttgtag----------------

upper sequence: Vv05s0020g04870.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G23080.2 (Arabidopsis thaliana), 5'ss of exon 4
TGATGAGTTTAGACCTAAATGGGACCCTATGCTTGCTTATTTTAAAATCTTGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaacgtaaaatttgaacacatgtactagtgatgtattgacttaatacttgttcccacaattttgagttgatatctcaactctctgtttattctgtttgcag
 ||||||||| |||||||||||||  ||||||||||||| || ||||  || ||||||   ||| | ||||  || |  ||||| || ||||| ||||||||              ||||     | |    | |||||  ||  || |  ||||  || |     | |  ||                                   
CGATGAGTTTCGACCTAAATGGGATACTATGCTTGCTTACTTCAAAACTTTAGAGGAAGATCCTAAGACAGGAACTACCATTGTTCATTGGATTAAAAAGgt--------------atttttctgctttccttcgtgattcatgaacatgttactaatttcttttgtctgcag-----------------------------------

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|161709868|gb|FC058054.1|FC058054
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|110685139|gb|EE063222.1|EE063222
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|30252882|gb|CB970433.1|CB970433
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|32271923|gb|CD721082.1|CD721082
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|30327353|gb|CD010615.1|CD010615
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|110384349|gb|EC948779.1|EC948779
EST:     AGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: AGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|32249475|gb|CD715294.1|CD715294
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|110389589|gb|EC954442.1|EC954442
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGAT
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGAT
EST: gi|161718153|gb|FC065659.1|FC065659
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|110361567|gb|EC925049.1|EC925049
EST:     TGGAGGATTTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|32248982|gb|CD714801.1|CD714801
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|161719072|gb|FC065699.1|FC065699
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|30324249|gb|CD007511.1|CD007511
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|71855922|gb|DT004977.1|DT004977
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|30325801|gb|CD009063.1|CD009063
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|33409613|gb|CF215240.1|CF215240
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|33409206|gb|CF214833.1|CF214833
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGA
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGA
EST: gi|27583867|gb|CB006562.1|CB006562
EST:     TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
genomic: TGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG
EST: gi|110398278|gb|EC964527.1|EC964527
EST:     AGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAG                         TTCCCTTTCTTCTGCAGTGATAGAGAA-ATATCATTGGTCGAAGAATTTGG
genomic: AGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaa ... ctgtttgcagTTCCCTTTCTTCTGCAGTGATAGAGAATATATCATTGGTCGAAGAATTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGAGTTTAGACCTAAATGGGACCCTATGCTTGCTTATTTTAAAATCTTGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaacgtaaaatttgaacacatgtactagtgatgtattgacttaatacttgttcccacaattttgagttgatatctcaactctctgtttattctgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA