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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCTCAAGGCCAAGATCGAACTTCTTAATAAGACCAACATGGTTGACTATGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtactttttattttatacgtggtagggtttatggcttgtggtttgtgatttgttgcgatttttggcag

Basic information

species Vitis vinifera
transcript Vv00s0252g00070.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G156333_T01 (Zea mays), 5'ss of exon 4
ATCCTCAAGGCCAAGATCGAACTTCTTAATAAGACCAACATGGTTGACTATGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtactttttattttata--cgtggtagggtttatggctt--gtggtttgtga--tttgttgcgatttttggcag--------------------------------
       |||||||||||   || || ||    ||||||||||| ||||||||||||||||||||||||   || ||| ||||||| ||||| |   | |  |   |  |      |  || ||| |  |  | ||||   || | | | |      |  ||     | | |                                  
-----GGAGGCCAAGATCCGCCTCCTCAACGGCACCAACATGGTCGACTATGCCATGGACATCCACAAGTCCCTCTACGACACCGACGACGTGCTCGAGGACATGgtgaagcgccgagccgaggtcgtctcca-ggctcaggtcgctcgaggaggccgcagccccgctcgtcgccttcctccagaacccgctcgtcgccccgttca

upper sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 5'ss of exon 1
ATCCTCAAGGCCAAGATCGAACTTCTTAATAAGACCAACATGGTTGACTATGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtactttt---tattttatacgtggtagggtttatggcttgtggttt-gtgatttgttgcgatt-tttggcag-------------------------
||||| ||| | || ||| | ||| | ||  |||| ||||||||||| || |||||||| || ||||||||||| |||||||| || |||| ||||||||||| | ||   ||||     |  | || |  |      ||| | ||| |||   || |  | || ||||                             
ATCCTGAAGTCTAAAATCCAGCTTTTGAACCAGACGAACATGGTTGATTACGCCATGGATATTCACAAGAGTCTCTACCACACTGAAGACGCTCCTCAAGgtattcttgtgtattcctctctggatatgtctgtgaatttgcgtttttgtgtactggtttgtttgtttgatgatgaatgttgaaatttgtggtgatag

upper sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S363_21V6.2 (Physcomitrella patens), 5'ss of exon 1
ATCCTCAAGGCCAAGATCGAACTTCTTAATAAGACCAACATGGTTGACTATGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttt-------ttattttatacgtggtagggtttatggcttgtggt-ttgtgatttgtt--gcgatttttggcag----------------------
||| | ||  | || || || || ||    |||||||||||||| ||||| ||||||||||||||||||  ||| |||||||| |||||||||||||| |||   |        || |||| | | | | || |    ||   ||     ||| || | |||  | |  |||   |                        
ATCTTGAAATCGAAAATTGAGCTGCTGGCCAAGACCAACATGGTCGACTACGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacggggcgttgtttttttctttgaagtggccgtgaggtgaaacattgagagtggttttgtgggtttgttcgagttgtgcggtgaaggaggggaa

upper sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S73_26V6.1 (Physcomitrella patens), 5'ss of exon 1
ATCCTCAAGGCCAAGATCGAACTTCTTAATAAGACCAACATGGTTGACTATGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtactttttattttatacgtggtagggtttatggcttgtggtttgtgatttgttgcgatttttggcag--------------------------------
||||| |||||||| ||||| || ||    |||||||||||||| ||||| || ||||| ||||||||||| || ||||||||||| ||||| || ||||||      |       | ||  |       || | |  ||  ||   |||  | || |  || |                                    
ATCCTGAAGGCCAAAATCGAGCTGCTGGCGAAGACCAACATGGTCGACTACGCTATGGATATCCACAAGAGCCTCTACCACACCGAAGACGTCCCACAAGgtctgaaatggcggtgatgtaattttccaaattggtcttgcatttcaattcctagcaaaattagcttacttggttgcatctgagccactgttctttcatg

upper sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S9_109V6.1 (Physcomitrella patens), 5'ss of exon 1
ATCCTCAAGGCCAAGATCGAACTTCTTAATAAGACCAACATGGTTGACTATGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgt-actttttattttatacgtggtagggtttatggcttg--tggtttgtgatttgtt-----gcgatttttggcag------------------------
||||| || ||||| |||||  | ||    |||||||||||||| |||||||||||||||||||||||||| || |||||||||||||| || || |||||| | |        |  |  || |   ||||||  |||   |  ||| |  ||| ||     | | | | |||                           
ATCCTGAAAGCCAAAATCGAGTTGCTGGGCAAGACCAACATGGTGGACTATGCCATGGACATCCACAAGAGCCTGTACCACACCGAGGAAGTGCCGCAAGgttagtgcgcgcggtggagttgttgtcgtttatatctttatttatttattttttttttatagggggtgtctggtgatctgttgtgttttttctgtttttc

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|71875756|gb|DT024811.1|DT024811
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|161720928|gb|FC070668.1|FC070668
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|71874079|gb|DT023134.1|DT023134
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|71857038|gb|DT006093.1|DT006093
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|161710358|gb|FC061087.1|FC061087
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|71874542|gb|DT023597.1|DT023597
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|34543038|gb|CF511270.1|CF511270
EST:     TTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|71870368|gb|DT019423.1|DT019423
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|26261569|gb|CA812632.1|CA812632
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|110711525|gb|EE088102.1|EE088102
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|110377140|gb|EC942200.1|EC942200
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|110712956|gb|EE088454.1|EE088454
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|34542953|gb|CF511185.1|CF511185
EST:     CGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: CGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|110685212|gb|EE063375.1|EE063375
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|71858778|gb|DT007833.1|DT007833
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|294965851|gb|GW837334.1|GW837334
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|71861236|gb|DT010291.1|DT010291
EST:     TGCCATGGACGTCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|110712683|gb|EE087943.1|EE087943
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|352768501|gb|FQ467457.1|FQ467457
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|110711122|gb|EE087316.1|EE087316
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
EST: gi|110713232|gb|EE088975.1|EE088975
EST:     TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAG                         ATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG
genomic: TGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttttta ... tttttggcagATATGGTGGAGAGGAGGGCTGAGGTTGTGGCGAGGTTGAAGGCCTTGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCTCAAGGCCAAGATCGAACTTCTTAATAAGACCAACATGGTTGACTATGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtactttttattttatacgtggtagggtttatggcttgtggtttgtgatttgttgcgatttttggcag

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