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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaagaacatgaacttactgtttatacaatgttttacctatttcttttttaccccagtaaatggataaaaaagtgtatgagtattgcatgggtaa...

Basic information

species Vitis vinifera
transcript Vv00s0260g00060.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0260g00060.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 4
GGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaagaacatgaacttactgtttatacaatgttttacctatttcttttttaccccagtaaatggataaaaaagtgtatgagtattgcatgggtaa
|| ||||| || |||||||| ||||||||||| || | |||||| |||||||| ||||| |||||| | || | ||| ||||| || ||||||   |||    ||||      || | | |    ||| |||  | | ||| | | |   |  | |     |  | |                        
GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgattaattggcatgtctactctttgtgttggttgtgttatgtttctctgtctgaattcctttatctactctatag-----------------------

upper sequence: Vv00s0260g00060.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA03G21680.1 (Glycine max), 5'ss of exon 4
GGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaagaacatgaacttactgtttatacaatgttttacctatttcttttttaccccagtaaatggataaaaaagt-gtatgagtattgcatgggtaa--
|| |||||||| |||||||||||||| ||||| || ||||||||   | | |||||||| ||||| ||||||| ||| ||||| || ||||||||||   | | |   |  | | || | |  ||| || |   |  |  ||   ||    ||| | | | |       | || ||  ||||  |||   |   
GGAAAACTCACTGATGGAACTGTTTTCGATTCTAGCTTTGAAAGAAATAATCCAATTGAATTTGAGCTTGGTACTGGTCAAGTGATCAAAGgtatgttgtgcataaacaacttcagtctgt-taattttctggtt--tcattacctataaaagtgactagctgctgtgcttgtttgcttatttaatgaaaatga

upper sequence: Vv00s0260g00060.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G10750.1 (Glycine max), 5'ss of exon 4
GGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgt-------aaagaacat--gaacttactgtttatacaa-tgttttacctatttcttttttaccccagtaaatggataaaaaagtgtatgagtattgcatgggtaa
|| |||||||| |||||||||||||| ||||| || ||||||||   | | |||||||| ||||| ||||||| ||| ||||| || ||||||||||       ||| ||| |  |   | | |   |||| || ||  |  |   | |  || ||  |  | | | || | |  |||||   |   ||            
GGAAAACTCACTGATGGAACTGTTTTCGATTCTAGCTTTGAAAGAAATAATCCAATTGAATTTGAGCTTGGTACTGGTCAAGTGATCAAAGgtatgttgtgcataaacaacttctggtttcattacctataaaagtgactagctgctgtgcttgtttacttatttattgaaaatgaaagtaagtagataaa----------

upper sequence: Vv00s0260g00060.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G25220.1 (Arabidopsis thaliana), 5'ss of exon 4
GGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaaga-------acatgaacttactgtttatacaatgttttacctatttcttttttaccccagtaaatggataaaaaagtgtatgagtattgcatgg-gtaa
|| ||  | || ||||||||||| |||||||| |||||||| || |||||||| ||||||||||| ||||| | ||| ||||| ||   |||| |||    |        ||| ||||   | ||| | |   ||| |   ||  | ||||||  |  |  |||| ||    || |   || | |     |||  | | 
GGAAAGTTAACTGATGGAACTGTCTTTGATTCAAGTTTTGAGAGAGGTGACCCTATTGAGTTTGAGCTTGGAACTGGTCAAGTCATCCCAGgtttgttgctatttcatcgcatcaactccatctttttccttcgttattgttaccttttttttgactgacaaaattgaaggtaatgca-attaattcgaaatgttgcag

upper sequence: Vv00s0260g00060.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G48580.1 (Arabidopsis thaliana), 5'ss of exon 5
GGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaagaacatgaacttactgtttatacaatgttttacctatttcttttttaccccagtaaatggataaaaaagtgtatgagtattgcatgggtaa
|||||||| || ||||||||||| || ||||| ||||||||||||||||| ||  |||||||| || | || ||||| || || || ||||||| || |    | |     |  ||  |||    | | ||   ||    ||| |||   |  | ||||| |||      || |   | |||||       
GGGAAACTTACTGATGGAACTGTATTCGATTCGAGTTTTGAAAGGGGTGATCCGTTTGAGTTTAAATTAGGAAGTGGTCAGGTTATCAAAGgta-gtgacttgcttttggcttttgagtatctcttttctt--ttaacattttcttaattccttcaatgg-taattttcggttt---tgttgcag------

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|26265898|gb|CA816961.1|CA816961
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110701184|gb|EE078492.1|EE078492
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110703071|gb|EE079606.1|EE079606
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|32458485|gb|CD799659.1|CD799659
EST:     GGGGTGACACCCAATTGAGTTTGAACTCGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: GGGGTG--ACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110371550|gb|EC935661.1|EC935661
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110419372|gb|EC985591.1|EC985591
EST:     TTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
genomic: TTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|26263918|gb|CA814981.1|CA814981
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|26257413|gb|CA808476.1|CA808476
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|254917519|gb|GR903171.1|GR903171
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110361110|gb|EC924563.1|EC924563
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110689576|gb|EE065919.1|EE065919
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|33409428|gb|CF215055.1|CF215055
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110377725|gb|EC942807.1|EC942807
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|51051736|gb|CO819206.1|CO819206
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|33410553|gb|CF216180.1|CF216180
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|351024512|gb|FQ426321.1|FQ426321
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|34416224|gb|CF414978.1|CF414978
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110694325|gb|EE071332.1|EE071332
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|33408493|gb|CF214120.1|CF214120
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|26258199|gb|CA809262.1|CA809262
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|33409349|gb|CF214976.1|CF214976
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA
EST: gi|110386208|gb|EC950788.1|EC950788
EST:     AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAG                         GATGGGACCAAGGATTGTTGGGGATGTGCGTGGGTGAGAAGCGAAAGCTGA
genomic: AAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaag ... tcttttgcagGATGGGACCAAGGATTGTTGGGGATGTGTGTGGGTGAGAAGCGAAAGCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAAACTCACAGATGGAACTGTTTTTGATTCCAGTTTTGAAAGGGGTGACCCAATTGAGTTTGAACTTGGTAGTGGCCAAGTAATTAAAGgtatgtaaagaacatgaacttactgtttatacaatgttttacctatttcttttttaccccagtaaatggataaaaaagtgtatgagtattgcatgggtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa