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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGAAACTTGCCAAGAAATACCATGCCTTTTTAGCATCAGAGGCTGTTATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcatatgattatggcacctgttgttagttactataacttgcaattaatatgagcgcttatttggtcatgttagatatgatgtatgtggaggacta...

Basic information

species Vitis vinifera
transcript Vv06s0080g00400.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 2
----TCAAGAAACTTGCCAAGAAATACCATGCCTTTTTAGCATCAGAGGCTGTTATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcatatgattatggcacctgttgttagttactataacttgcaattaatatgagcgctta--tttggtcatgttagatatgatgtatgtggaggacta
    | |||||||| || || || ||||||||||||||||| || || || || ||||||||||| || |||||||| || ||||| |||||||||||||||| ||||  | | |  ||  |       || | |  |  |   ||     |    | |  | | ||   ||  ||  | ||| ||    | ||  || |      
TTGGTGAAGAAACTAGCTAAAAAGTACCATGCCTTTTTAGCTTCTGAAGCAGTCATTAAGCAGATTCCTCGTCTTTTGGGTCCTGGTCTCAACAAGGCAGgcatgtattgcctttttttcggttttggattttgaacttttcggacaaatgagagtttttggtgatttgcttctgtttttttaaatcatttttacatgaa------

upper sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G35450.2 (Glycine max), 5'ss of exon 4
----TCAAGAAACTTGCCAAGAAATACCATGCCTTTTTAGCATCAGAGGCTGTTATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcatatgattatggcacctgttgttagttactataacttgcaattaatatgagcgcttatttggtcatgttagatatgatgtatgtggaggacta-
    | ||||| || || || ||||||||||| ||||||||||| || || || ||||||||||| || |||||||| || ||||| |||||||| ||||||| ||||  |   |  |||||     | | |||    | | | |  |    |  | |   |   || |||||| || |      | || | | |  |  | || 
TTGGTGAAGAAGCTAGCTAAAAAATACCATGCTTTTTTAGCATCTGAAGCAGTCATTAAGCAGATTCCTCGTCTTTTGGGTCCTGGTCTCAACAAAGCAGgcatgtattgc-cgtagttatgtt-tttctggtttaggattttgatcttttttggacaaatgatgttttttggtgattt---gctttattttttttaatcattat

upper sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 3
----TCAAGAAACTTGCCAAGAAATACCATGCCTTTTTAGCATCAGAGGCTGTTATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcatatgattatggcacctgttgttagttactataacttgcaattaatatgagcgcttatttggtcatgttagatatgatgtatgtggaggacta
    | || ||||| ||||| ||||| |||||||||||||| || || || || || |||||||| || ||||| || || ||||| |||||||||||||||| || |    |||  || |||    ||    |  ||   | |  ||  |   ||  ||     ||  ||| |    | |  ||    |    | |  |  | 
TTGGTGAAAAAACTAGCCAAAAAATATCATGCCTTTTTAGCCTCTGAAGCAGTCATCAAGCAGATTCCTCGTCTCTTGGGACCTGGTCTCAACAAGGCAGgcatgttt----tattgttttggattttgaatctcttttggacattttagagagaacttggtgatttgcttgttttaataacttacatcggtcattgctgtgtt

upper sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G31040.2 (Glycine max), 5'ss of exon 3
----TCAAGAAACTTGCCAAGAAATACCATGCCTTTTTAGCATCAGAGGCTGTTATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcatatgattatggcacctg---ttgttagttactataacttgcaattaatatgagcgcttatttggtcatgttagatatgatgtatgtggaggacta
    | || ||||| ||||| ||||| ||||||||||| || || || || || || |||||||| || ||||| || || ||||| |||||||||||||||| || |    |||  || |||    ||    |  |||  | | ||    | | ||  |       ||  |||| | |  | | ||  |   | ||  | |     
TTGGTGAAAAAACTAGCCAAAAAATATCATGCCTTTTTGGCCTCTGAAGCAGTCATCAAGCAGATTCCTCGTCTCTTGGGACCTGGTCTCAACAAGGCAGgcatgttt----tattgttttggattttgaatctcgtagacattttagagagtacttggtgatttgcctgttttgataacttcacatcggtcat-tgctgtgttt--

upper sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G08360.1 (Arabidopsis thaliana), 5'ss of exon 4
----TCAAGAAACTTGCCAAGAAATACCATGCCTTTTTAGCATCAGAGGCTGTTATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcatatgattatggcacc--tgttgttagttactataacttgcaattaatatgagcgcttatttggtcatgttagatat-gatgtatgtggaggacta----------------------------------------------------------------------------
    ||||||| ||||| |||||||||||||| || || || || ||| |||| ||||||||||| || |||||| | || ||||| || ||||||||||||||||      ||    ||     ||  |||| ||  ||||      ||  | ||   ||  |   ||| | |   || |    | |  |||| | |     || |                                                                            
CTCGTCAAGAAGCTTGCAAAGAAATACCATGCTTTCTTGGCCTCTGAGTCTGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTTAACAAGGCAGgcaagttctggctacagctaatattccattgttcttctttacatccgttttgattttggataggt-tttagtagtctatttcttttgtcaatgtctttttgatacaatgccaatcctttatcctgtgagattatgcttctttgatgattcttaagtaacattcctttgctttactttacacag

upper sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 4
----TCAAGAAACTTGCCAAGAAATACCATGCCTTTTTAGCATCAGAGGCTGTTATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcatatgattatggcacctgttgttagttactataacttgcaattaatatgagcgcttatttggtcatgttagatatgatgtatgtggaggacta
    | ||||| ||||| ||||||| |||||| ||  | || || ||  |||| ||||||||||| || |||||| | || ||||| |||||||||||||||| || | | |  | |   |      ||   |  |||  | || | |    |  ||||||      |||   || ||     |||||   |||   ||     
CTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTTTCCTTGCTTCTGAATCTGTCATTAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGgcatgtctctaaccttacc-taatctttgc-atatgttcttgtatcctc---tctatatgatgctacattaaatcttgactcttatgaacaatgaacag-----

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|71868912|gb|DT017967.1|DT017967
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71867230|gb|DT016285.1|DT016285
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71868681|gb|DT017736.1|DT017736
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|161710675|gb|FC059046.1|FC059046
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|110386493|gb|EC951092.1|EC951092
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71868840|gb|DT017895.1|DT017895
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|30298813|gb|CB975607.1|CB975607
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|77583338|gb|DV220702.1|DV220702
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71869642|gb|DT018697.1|DT018697
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|77586494|gb|DV222363.1|DV222363
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|110689031|gb|EE067943.1|EE067943
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71880113|gb|DT029168.1|DT029168
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71872587|gb|DT021642.1|DT021642
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|77581865|gb|DV219896.1|DV219896
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|110693837|gb|EE070417.1|EE070417
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|110686483|gb|EE064171.1|EE064171
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|30126576|gb|CB911915.1|CB911915
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|77577254|gb|DV217332.1|DV217332
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|110723348|gb|EE100554.1|EE100554
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|37189916|gb|CF609265.1|CF609265
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|110686797|gb|EE064845.1|EE064845
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71875077|gb|DT024132.1|DT024132
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|110394329|gb|EC959115.1|EC959115
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71865803|gb|DT014858.1|DT014858
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT
EST: gi|71879518|gb|DT028573.1|DT028573
EST:     ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGTAA                         G----TT
genomic: ATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcata ... tattagcaagAAAAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGAAACTTGCCAAGAAATACCATGCCTTTTTAGCATCAGAGGCTGTTATTAAGCAGATCCCCCGTCTTTTAGGCCCTGGGCTCAACAAGGCAGGCAAgtatatcatatgattatggcacctgttgttagttactataacttgcaattaatatgagcgcttatttggtcatgttagatatgatgtatgtggaggacta

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT