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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtatttgttatttgtgctgtttatttatctttttcaaacttgatggtaacagttctagtaggagatgcttcagccttttgtctagctctgggattt...

Basic information

species Vitis vinifera
transcript Vv01s0137g00580.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 6
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtattt-gttatttgtgctgtttatttatctttttcaa--acttgatggtaacagttctagtaggagatgc-ttcagccttttgtctagctctgggattt--------------------------------------------------------------------------------------
|||||||||||||| |||||||| |||||||||| ||| |||||||| ||| |||  ||||| || ||| ||| || |||||||||||||||| ||||||||||||     |||  || || |  |  | |  |      ||  |   |||    |   ||||   |  |  ||| | | | | |  ||  |   |||    ||                                                                                      
GGACCAAGCTTATATGATTTTCTGCGGAAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcag

upper sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G063792_T04 (Zea mays), 5'ss of exon 6
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtattt-gttatttgtgctgtttatttatcttttt----caaacttgatggtaacagttctagtaggagatgctt--cagcct----tttgtctagctctgggattt--------------------------------------------------------------------
|||||||||||||| ||||||||  ||||||||||||| |||||||| ||| |||  ||||| || ||| ||| || |||||||||||||||| ||||||||||||     ||| ||| |  |     |    |  | |    || |     | ||        |  |  | | ||| |  ||||||    ||  || |   ||     ||                                                                    
GGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttctttctattacccctcctgcactataatgcatatacattagttttgtgcattatctgtgctgcattgcagcctgtcattaatccattactcatgcttgtactccagggagtatctaacatcatgtgatgtttttgtatttaccctctctctgtaatgtgttgcag

upper sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G179308_T01 (Zea mays), 5'ss of exon 6
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtat-ttgttatttgtgctgtttatttatctttttcaaacttgatggtaacagttctagtaggagatgctt-cagcctttt-gtctagctctgggattt-----------------------------------------------------------------------------
|||||||||||||| |||||||| ||| |||||| ||| |||||||| ||| |||  ||||| || ||||||| || |||||||||||||||| ||||||||||||     ||| ||  |  | |   |    |  | | |  | |     | |   || |  |   | ||   | |||| || | | ||| |  |      |                                                                             
GGACCAAGCTTATATGATTTTCTGCGGGAAAACAGTTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGATTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcacagttcttcctattatcgctcctgcactataatgcatatacattagtttttttttgcaatatatgtgcagcattgtagcctatcattaatccatattactactcatgcttaaggaatatctaacatcatgggatgtttatgtatttaccctctctctgtaatgtgttgcag

upper sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S425_6V6.2 (Physcomitrella patens), 5'ss of exon 6
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgt-atttgttatttgtgc-tgtttatttatctttttcaaacttgatggtaacagt-tctagtaggagatgcttcagccttttgtctagctctgggattt--
|| ||||| || |||||||||||||| ||||||||||||||  | ||| | |  ||||| || || ||  ||||| | ||||| ||||| | |||||| |||  || || | || | |||   | |||    ||  | |   |  ||  |     |||| | | |  |   ||   | | |   ||    ||   |  ||| |  
GGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCTTGGAGTCTGTAGCTTgtaagtcatattttgtatgtatatatttgcaaataatatatgattttcct-----cagtgtatggatgtgtatttcttatctgattcatcagaaatatgatctgt

upper sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 5'ss of exon 8
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgt-atttgttatttgtgctgtttatttatctttttcaaacttgatggtaacagttctagtaggagatgcttcagccttttgtct--agctctgggattt-------------------
||||| |||||||||||||| ||||| ||||||||||||||  ||||| | |  ||||| || |||||  ||||| | || |||||||| |  ||||| |||| || | ||||    | || |  ||   ||| |     ||  ||||  | |  |    | |  |||  |  |   |   | |||    |   | |  ||||                   
GGACCGAGCTTATACGATTTCCTTCGAAAAAACAATTATCGACCATTTTCTGCAGATCTCGTTCGCGACTTTGGCCGCCAGCTGTTGGAGTCCGTAGCTTgtgagttacttgtgggatctgttcattgaatatgtcgcgtaa-tttgacagcagaatcaattggcggaattattgatgttatatgttgtgaaagcggtaatttatgttcctgattgttgcag

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|110709438|gb|EE084898.1|EE084898
EST:     AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCAT                         TCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
genomic: AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtattt ... aaatttgcagTCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
EST: gi|110732680|gb|EE108178.1|EE108178
EST:     AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCAT                         TCATGCATGATTTGGACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
genomic: AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtattt ... aaatttgcagTCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
EST: gi|161716341|gb|FC064657.1|FC064657
EST:     AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCAT                         TCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
genomic: AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtattt ... aaatttgcagTCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
EST: gi|110698778|gb|EE076668.1|EE076668
EST:     AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTCTAGCAT                         TCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
genomic: AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtattt ... aaatttgcagTCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
EST: gi|110712429|gb|EE090038.1|EE090038
EST:     AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTATAGCAT                         TCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC
genomic: AGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtattt ... aaatttgcagTCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGTTGGAATGTGTAGCATgtgtgtatttgttatttgtgctgtttatttatctttttcaaacttgatggtaacagttctagtaggagatgcttcagccttttgtctagctctgggattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggagatg