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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtctgcttttatcatttagaatttgcttttatggccttctcacctaaaaagttatgtttttgtcttacttggaatgaatggatgcatgatatatcatgtgcag

Basic information

species Vitis vinifera
transcript Vv13s0019g04190.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G35560.1 (Glycine max), 5'ss of exon 3
GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtctgcttttatcatttagaatttgcttttatggccttctcacctaaaaagttatgtttttgtcttacttggaatgaatggatgcatgatatatcatgtgcag
|||||||||||||||||||||||| || || || || ||||||||||| ||   ||||| ||| |||||| |||||||| | || | |  |   |  |||    ||| ||  |||                  | ||||   ||| |     | |||| |  | || | || || | | |  |||||
GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCTGAAGgtca-atatttcttccgactatt----attagcggtta------------------aattatacctttct-----tgggaaaggtttgaagtataatctgttaattgcag

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 3
GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtctgcttttatcatttagaatttgcttttatggccttctcacctaaaaagttatgtttttgtcttacttggaatgaatggatgcatgatatatcatgtgcag
|||||||||||||||||||||||| || || || || ||||||||||| ||   ||||| ||| |||||| | |||||| | || | |  |   |  |||    ||| ||| |||                  | |||| | |||  |||      || |  | || | || || | | |  |||||
GAGGCCAGGTCAGAGCCGAATTACAACTCCTAGAAAGGAGACTGATACATGTAAAATATTTTCAGGAGTTTCCGAAGgtca-atatttcttccgactatt----attagctgtta------------------aattatatcttt--cttgagaaaaaaggtttgaagtataatctgttaattgcag

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 5'ss of exon 3
GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtctgcttttatcatttagaatttgcttttatggccttctcacctaaaaagttatgtttttgtcttacttggaatgaatggatgcatgatatatcatgtgcag
|||||| ||||||||| | || || || || || |||||||||||||||||||| ||||  ||||||||  ||||||||    |      || |||  || | | ||||  |||  |   || |  |  |         ||| || |  |  |||  ||  ||  ||                    
GAGGCCTGGTCAGAGCAGGATCACAACTCCTAGAAAAGAGACTGATACTTGCCGGATATCGTCTGGAGTCTCTGAAGgtctagttatacattctat--ttcatagtttgagttt--gattttgtttctcagc------cgttgttctaattgttgatatccataaatttgcag--------------

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|352790897|gb|FQ477345.1|FQ477345
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|71880899|gb|DT029954.1|DT029954
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|71877721|gb|DT026776.1|DT026776
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|71863219|gb|DT012274.1|DT012274
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|352778035|gb|FQ467088.1|FQ467088
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|71855293|gb|DT004348.1|DT004348
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|71861705|gb|DT010760.1|DT010760
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|71879200|gb|DT028255.1|DT028255
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|71880874|gb|DT029929.1|DT029929
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|352776661|gb|FQ465459.1|FQ465459
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|352777956|gb|FQ467009.1|FQ467009
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|351024445|gb|FQ426254.1|FQ426254
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAGTATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|352778092|gb|FQ467145.1|FQ467145
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|352763986|gb|FQ467556.1|FQ467556
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA
EST: gi|352768213|gb|FQ467352.1|FQ467352
EST:     ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAG                         GAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAAA
genomic: ACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtc ... tcatgtgcagGAATGACTACTGGATCACCAATAATGGTAAATGTACCTAATACTGATCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCCAGGTCAGAGCCGAATTACTACACCAAGGAAAGAGACTGATACTTGCCGAATATATTCTGGAGTTGCTGAAGgttagatgtctgcttttatcatttagaatttgcttttatggccttctcacctaaaaagttatgtttttgtcttacttggaatgaatggatgcatgatatatcatgtgcag

- - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG