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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAACTGCAGGAGTGAAGCATATTGTGTTGGTTGGGTCTATGGGAGGAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgattcttttttatttttgttcagaaaattacttactctctttaacaatttgggtgtcatgtttgtgaaaatgagttctcatttttatgaatgct...

Basic information

species Vitis vinifera
transcript Vv08s0007g00530.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G068244_T01 (Zea mays), 5'ss of exon 4
CAAAAACTGCAGGAGTGAAGCATATTGTGTTGGTTGGGTCTATGGGAGGAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgattcttttttatttttgttcagaaa-attacttactctctttaacaatttgggtgtcatgtttgtgaaaatgagttctcatttttatgaatgct
| ||| |||| |||||||||||||||||| |||| || ||||||||||||||| | |  ||||||||  |||||||| |||| ||||| ||||| |||||  |  |   |||     ||   |    ||  | || | ||    | ||  | |  |    | ||  |||   | ||  | | |                
CTAAAGCTGCTGGAGTGAAGCATATTGTGCTGGTGGGATCTATGGGAGGAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaaatttggctcttccataggcaactactattcacaaattgtagaagtgggatcttgattattgcatatatctgctatag--------------

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G39930.2 (Glycine max), 5'ss of exon 4
CAAAAACTGCAGGAGTGAAGCATATTGTGTTGGTTGGGTCTATGGGAGGAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgattcttttttatttttgttcagaaaattacttactctctttaacaatttg-----ggtgtcatgtttgtgaaaatgagttctcatttttatgaatgct-------------------------------------------------------------------------------------------
| ||  |||| ||||||||||| |||||||| || ||||||||||| |||||||| || |||||||| |||||||||||||| ||||||||||| |||||| || ||  |||||  |||   |  |   || ||| | || ||  ||||| | ||     | | | || |   |  |  |     ||||| || ||| |   |                                                                                           
CTAAGGCTGCTGGAGTGAAGCACATTGTGTTAGTAGGGTCTATGGGTGGAACAGATCTTAACCATCCTTTGAACAGCTTGGGTAATGGGAATATACTGgttagtaatgttttttcctttacttcta---aactacctcct-tccataacattctgtcattgcttttatatgattagagcttgcaactcatcttaatgcaaaatgcaagtttggtgtaaatgcctaaatggatatgttttacttcccccatgccctttgatattcctcctttgataggaagaatgttgattgcag

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G15960.1 (Glycine max), 5'ss of exon 4
CAAAAACTGCAGGAGTGAAGCATATTGTGTTGGTTGGGTCTATGGGAGGAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgattcttttttatttttgttcagaaaattacttactctctttaacaatttgggtgtcatgtttgtgaaaatgagttctcatttttatgaatgct
| ||  |||| ||||||||||| |||||||| || ||||||||||| ||||| ||||| |||||||| |||||||||||||| |||||||||||  ||||| || ||  ||| |  ||| | |    |  |   |   |      |       | | | | || |   |  |  |      |||| || ||| |   |
CCAAGGCTGCTGGAGTGAAGCACATTGTGTTAGTAGGGTCTATGGGTGGAACGGACCTTAACCATCCTTTGAACAGCTTGGGTAATGGGAATATATTGgttagtaatgttttctcctttatttctgaactacctccctcctagcattctgccattgcttttatatgattagagcttgcaagtcatcttaatgcaaaat

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G37660.1 (Arabidopsis thaliana), 5'ss of exon 4
CAAAAACTGCAGGAGTGAAGCATATTGTGTTGGTTGGGTCTATGGGAGGAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttg-tgattcttttttatttttgttcagaaaattacttactctctttaacaatttgggtgtcatgtttgtgaaaatgagttctcatttttatgaatgct
| ||  |||||||||| ||||| ||||| ||||||||||| |||||||||||| || | || || ||  | || ||  | || ||||  || || |||||  |   | ||||| |   |||| || |  | |    | | | ||      ||| |        | | ||  |     ||                    
CTAAGGCTGCAGGAGTTAAGCAGATTGTTTTGGTTGGGTCGATGGGAGGAACAAACATTAATCACCCTCTCAATAGTATTGGCAATGCTAACATTCTGgtgagactactctttctctgttttcttgaacacagagatgagtttcacggcaaatgttcacagtctttatgcaatttgtag--------------------

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|349811666|gb|FQ409663.1|FQ409663
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|349810529|gb|FQ402772.1|FQ402772
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|28959045|gb|CB339524.1|CB339524
EST:     GGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|351016336|gb|FQ446196.1|FQ446196
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|349821239|gb|FQ404371.1|FQ404371
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|110700744|gb|EE077667.1|EE077667
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|110385557|gb|EC950093.1|EC950093
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|110731770|gb|EE106470.1|EE106470
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|352786365|gb|FQ478974.1|FQ478974
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAAGAAA-GCTGAACAGTATTTATCGGACTCTGGAATACCTTA
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGA-GAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTA
EST: gi|45771772|gb|CN007624.1|CN007624
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAGCAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|351023663|gb|FQ448214.1|FQ448214
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|352790186|gb|FQ481385.1|FQ481385
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|351051751|gb|FQ449565.1|FQ449565
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|351054211|gb|FQ450293.1|FQ450293
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|351028714|gb|FQ433144.1|FQ433144
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|110692043|gb|EE070833.1|EE070833
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC
EST: gi|351055225|gb|FQ440564.1|FQ440564
EST:     GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTG                         GTTTGGAAGAGAAAAGCTGAACAGTATTTAGCGGACTCTGGAATACCTTAC
genomic: GAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgatt ... cattttacagGTTTGGAAGAGAAAAGCTGAACAGTATTTAGCAGACTCTGGAATACCTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAAACTGCAGGAGTGAAGCATATTGTGTTGGTTGGGTCTATGGGAGGAACAGACCTAAACCATCCCTTGAACAGCTTGGGAAATGGGAATATCCTGgtttgtgattcttttttatttttgttcagaaaattacttactctctttaacaatttgggtgtcatgtttgtgaaaatgagttctcatttttatgaatgct

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatg