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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccag

Basic information

species Vitis vinifera
transcript Vv05s0020g03080.t01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: LOC_Os11g04980.2 (Oryza sativa), 5'ss of exon 22
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgt-tcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccag
 | |||||||||||||||||||||||||| ||  | ||   ||| || || ||  | || |||| ||| || || ||||||||||||| | |    | ||||         ||||     | |||  ||  |  |       ||  ||   |  |  ||||                        
CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgttaattctgttgcaggagatctcgatacctaaggtgctaattctctatctcaa--tgatgttgcag-----------------------

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: LOC_Os12g04990.1 (Oryza sativa), 5'ss of exon 22
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccag
 | |||||||||||||||||||||||||| ||  | ||   |||||| || ||  | || |||| ||| || || ||||| ||||||| | |      | | | || |  ||| | ||    | | | |||  ||           |      ||   || |  ||| |               
CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAGgtaggcccgttaat-acaagttggaggagattt--ctacaccaggtac----------taattctctatctcaatgacttttgcag-----------

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 22
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccag
 | |||||||||||||| |  |||||||| ||||| ||||| |||||||||||  |||| |||| |||| | ||||| ||||||||||||||  || | | | || ||         |  |     | |     || |        |     |   |    ||| | | | ||  || |  |||
CTTAGAGGTTTTGAATTCGTAAAAGCTGTCACTTTAGTGCTCGAACCATTTACGTTGGAAAATGGTCTGTTGACTCCGACATTCAAGgcaagctttgagtcttaagatgatctgtttttcatttttaacc--tgcagtgtggcaataaatcatcttttgtgtatgtgcatgcaactttt--cag

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 22
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgt--tcttccag
 |||||||||||||||| |  ||||| || ||||||||||| |||||||||||  |||| ||||  ||| | ||||| ||||||||||||||  || | |   || || |       |  |     | |        |    |||||     | | ||  || | |   | ||||     || |||
CTGAGAGGTTTTGAATTCGTAAAAGCGGTCACTTTGGTGCTCGAACCATTTACGTTGGAAAATGGCCTGTTGACTCCGACATTCAAGgcaagctttgagtcctaagattttctgtttttcatttttaacctgttgtgtgtg-tggcaataaatca-tgttttgtgtatgtgcatgcaacttttcag

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 5'ss of exon 22
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaat--ctgagaaaataaaaccagagcagacacaataaaatggcaggctctt-actgcattatcttctttcatgttcttccag-
|||||||| || || ||||| || |||||||| |||||||| |||||||||||  |||| ||||   || | ||||| || ||||||| || | |   || | || ||   | |   ||   | |   |  ||  | |||   ||   ||    |  |  |  || |      |  | |   | ||| 
TTGAGAGGCTTCGAGTTTGCAAAGGCTGTGACATTGGTGCTGGAACCATTTACTCTGGAAAATGGCTTGTTGACTCCGACGTTCAAGgtaaatttcttatatgaatatacttcactcaaactagcttcaaaaggta-aattctatcttagttagtggaaaggtttgttcgacatggtatatgttcaga

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 22
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 24
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccag-------------------------------------------
||| |||||||||| ||||||||||||||||| ||| | | |||||||||  | || || ||||   ||||||| || ||  |||||| ||   |   |||||      |    || |  |      | ||| |  ||      ||||  | |   || ||| ||| |||   |||||  | |                                            
TTGCGAGGTTTTGAGTTTGCCAAAGCTGTGACGTTGATTCCTGAACCATTCTCAATAGAAAATGGATTGCTTACACCCACGCTCAAGgtaac--tctgatttattctcatccagaagtgcatttcctgaagaaatgat----ctgcag-ttttccttggattttctccttat-tgttcaactaataaatgaagatcaatgatttagaatgaatttgggtatgtgcag

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|71889597|gb|DT038652.1|DT038652
EST:     TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAG                         ATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
genomic: TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttc ... gttcttccagATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
EST: gi|110414986|gb|EC980854.1|EC980854
EST:     TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAG                         ATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
genomic: TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttc ... gttcttccagATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
EST: gi|110425425|gb|EC991810.1|EC991810
EST:     CTGCTTACTCCAACATTCAAG                         ATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
genomic: CTGCTTACTCCAACATTCAAGgcaagtgttc ... gttcttccagATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
EST: gi|71882993|gb|DT032048.1|DT032048
EST:     TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAG                         ATCAAGAGACCTCAAGCAAAGGCA
genomic: TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttc ... gttcttccagATCAAGAGACCTCAAGCAAAGGCA
EST: gi|46918400|gb|CN547729.1|CN547729
EST:     TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAG                         ATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
genomic: TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttc ... gttcttccagATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
EST: gi|30129022|gb|CB914361.1|CB914361
EST:     TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAG                         ATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG
genomic: TGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttc ... gttcttccagATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAGgcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA