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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgggattcctttcttgaattatttctgtgttcaatgtt...

Basic information

species Vitis vinifera
transcript Vv05s0049g01180.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G32470.1 (Glycine max), 5'ss of exon 4
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcattt---cctttatttgggattcctttcttgaattatttctgtgttcaatgtt
|||||||||||||||||||||||||||||| |||||||||||||| || || || ||||| ||||||||||||||||| || ||||| ||| |||||||||| ||  ||    |    |  |||  |       ||   |||   ||  |||||     ||  ||| | |||  |   |  |     || | | ||       
CCAGAATTGGATGGTTGTAAAAGGTGAAAAAATAGTATTTCCTGGAGGTGGGACTCATTTCCATTATGGAGCTGATAAGTACATTGCATCAATTGCAAATgtgagtctg-catctaactttactggttttggatataaaaaaatgaaaccatttatattttgtttttgaattggtagttctatgagattttatattatgca--

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G00880.2 (Glycine max), 5'ss of exon 4
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgg-gattcctttcttgaattatttctgtgttcaatgtt
|||||| |||||| |||||||||||||||||||||| |||||||| ||||| |||||||||||  | |||||||| || || ||||| ||| ||||||||||||||    | |    |  | |||| ||  | ||||  |    | | |||||   ||| |     | |  | |  ||| | |   | ||||||       
CCAGAACTGGATGATTGTAAAAGGTGAAAAGATAGTGTTTCCTGGAGGAGGGACACATTTTCACAAAGGAGCTGACAAGTACATTGCATCAATTGCAAATgtaagaggcttactggttacctctataaagcataatgaaatgatatatgcattctgtttttcaattggtagcatcattggacttcatgtgtgttatgcag-

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G00550.1 (Glycine max), 5'ss of exon 3
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgg-gattcctttcttgaattatttctgtgtt-caatgtt
|||||| |||||| |||||||||||||||||||||| |||||||| ||||| ||||||||||| || |||||||| || || ||||| ||  ||||||||||||| || |     | |  | |||| ||  | ||||  |    | | |||||   ||| |     |||    |  ||| | | | || |||||   | || 
CCAGAACTGGATGATTGTAAAAGGTGAAAAGATAGTGTTTCCTGGAGGAGGGACACATTTTCACTACGGAGCTGACAAGTACATTGCATCTATTGCAAATgtaaggtttactggttat--ctctataaagcataatgaaatgctatatgcattctgtttttcaactgatagaatcattggactttatccgtgttatgaagta

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G35120.4 (Glycine max), 5'ss of exon 4
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattg-atgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgggattc-----ctttcttgaattatttctgtgttcaatgtt
|||||||||||||  |||||||| |||||| ||||| |||||||| || || || |||||||||||||||||||| || || || || ||| ||||||||||| |  || ||    | ||||    ||   |   |    || |  | |  || |  ||| |||  || |       | | |   ||| | | ||||||       
CCAGAATTGGATGACTGTAAAAGCTGAAAAAATAGTGTTTCCTGGAGGCGGGACTCATTTTCATTATGGAGCTGACAAGTACATAGCATCAATTGCAAATgtatgtctgcatctgattttactggttttgcatataaaaaaatgacaccatatatattttgttttagaattgggagttctatgagattttatgtgtgttt------

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 4
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgggattcctttcttgaattatttctgtgttcaatgtt
||| || ||||||||||| ||||| || || ||    || ||||| ||||||||||||||||||||||| |||||||| |||||||| ||| | |||||||||||   | | |    |       |||    |||| |    |      ||| | | ||   ||  | |  |      ||||                  
CCAAAACTGGATGGTTGTTAAAGGAGAGAAAATCAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCAATGGCAAATgtaaggcagttactagatc------ttatgtggaatagaggtgtgtgtccatcttcatttactgatactattcatggaaattgcag--------------

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 4
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgg-gattcctttcttg-aattatttctgtgttcaatgtt
||| || ||||||||||| ||||| || |||||    || ||||| ||||||||||||||||||||||| |||||||| |||||||| ||  | |||||||||||   | | | ||       | |  || |||| |         |     ||| || |||||   |||   |||||| || | |||| |           
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttggtgtttgtacaagagaacgt--------atattattctttcatttgctaattgtattcttggaaatttttcag-----------

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 5'ss of exon 4
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgggattcctttcttgaattatttctgtgttcaatgtt
 ||||| ||||||||||  ||||| || || ||    ||||| || |||||||| ||||| ||||| || ||||||||||| ||||| ||  | |||||||||||| |  |   ||       ||||   |   ||                ||  || | || | |                                 
TCAGAACTGGATGGTTGAGAAAGGCGAGAAAATTTCTTTTCCCGGTGGAGGCACTCATTTCCATTACGGTGCTGATAAATACATTGCATCGATCGCAAATgtaagagtcttttgctcactttttatttctagtgataacttgtctctaatgattttttgactttgcag--------------------------------

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|110712757|gb|EE088080.1|EE088080
EST:     GCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|110384343|gb|EC948773.1|EC948773
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|71862752|gb|DT011807.1|DT011807
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|161710886|gb|FC058577.1|FC058577
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|71863911|gb|DT012966.1|DT012966
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|351017019|gb|FQ424446.1|FQ424446
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|77577655|gb|DV217568.1|DV217568
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|110724467|gb|EE100319.1|EE100319
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|349826528|gb|FQ418619.1|FQ418619
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|351025738|gb|FQ426752.1|FQ426752
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|349830601|gb|FQ416899.1|FQ416899
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|30251880|gb|CB969613.1|CB969613
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|110357412|gb|EC920933.1|EC920933
EST:     GCACACATTTTCATTATGGAGCTGATNAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAAGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|351027519|gb|FQ446682.1|FQ446682
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|71860356|gb|DT009411.1|DT009411
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|351024446|gb|FQ426255.1|FQ426255
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|349830626|gb|FQ416924.1|FQ416924
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
EST: gi|351015441|gb|FQ447270.1|FQ447270
EST:     GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAAT                         ATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT
genomic: GCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattga ... gtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgggattcctttcttgaattatttctgtgttcaatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaac