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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaataccaaacttaatcttttatgctgttgctggcttaagcgttctctttgaaaataagttataattctgtgcaggttttatttcacattctgtcatcttatatatgttattaaaagttaaagttttcaatgcctatag

Basic information

species Vitis vinifera
transcript Vv05s0077g01200.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA07G37040.1 (Glycine max), 5'ss of exon 12
GTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaataccaaacttaatcttttatgctgttgctggcttaagcgttctctttgaaaataagttataattctgtgcag-gttttatttcacattctgtcatcttatatatgttattaaaagttaaagttttcaatgcctatag
|| | ||||||| | |||||||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||  |      ||  |  || |  |||     ||  | ||    | |    ||     ||||   ||||| |||  ||  | |||    |  |  ||     |                                        
GTTTATTTCTTACACGAGTTTTGTAGTTTGAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTTTTTAGgtatgttacatttgaa--tggtcatc-atgacacagcctgttttgctgcttgtcttt----taagaactaattttgttaagcatattaaaagaactggtgctgcttc---------------------------------------

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA17G03570.1 (Glycine max), 5'ss of exon 14
GTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaataccaaacttaatcttttatgctgttgctggcttaagcgttctctttgaaaataagttataattctgtgcaggttttatttcacattctgtcatcttatatatgttattaaaagttaaagttttcaatgcctatag
|| | ||||||| | |||||||||||||| ||||||||| ||||||||||||||||||||||||| ||||||||||        ||| || ||   | ||| ||   | | ||     | |   | |     ||||   |||||  ||     |  ||    |   | | | | || |                                      
GTTTATTTCTTACACGAGTTTTGTAGTTTGAGCAAGAGCCTGCAGATGGTCCAGCAGCTTCGGCTTTTTAGgtatgt------taaatttgattggtcatggtgagacagcctgttttgctgcttgtcttt-taagaattaatttcgtaagactgatagcagaatatttattaactaa--------------------------------------

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA09G04260.1 (Glycine max), 5'ss of exon 14
GTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaataccaaacttaatcttttatgctgttgctggcttaagcgttctctttgaaaataagttataattctgtgcaggttttatttcacattctgtcatcttatatatgttattaaaagttaaagttttcaatgcctatag
||   ||||||  |||||||||||||||||||||||||||| |||||||| || ||||||||||| ||| |||||| |    |   | |      | |   |  |||   |  | ||| |  | |         ||||    ||||    |  ||||   |||  | || |  | | ||                                     
GTCCGTTTCTTGCATGAGTTTTGTAGTTTAAGCAAGAGCTTACAGATGGTTCAACAGCTTCGGCTTTTTTGgtatgtagcatctggagtggtgaatcttgacaattgacagtgtcagcctgttatgc-------agtttgtgttctcca-attttttgaatcaattgctattgtttgat-------------------------------------

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA15G15270.1 (Glycine max), 5'ss of exon 13
GTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaataccaaacttaatcttttatgctgttgctggcttaagcgttctctttgaaaataagttataattctgtgcaggttttatttcacattctgtcatcttatatatgttattaaaagttaaagttttcaatgcctatag
||   ||||||  | |||||||||||||||||||||||||| |||||||| || ||||||||| | ||| |||||| |    |   | |      | |   | ||||   |  | | | |  | |         ||||    ||||    |  |||    |||  |||| |  | | ||                                     
GTTCATTTCTTGCACGAGTTTTGTAGTTTAAGCAAGAGCTTACAGATGGTACATCAGCTTCGGTTTTTTCGgtatgtagcatctggagtagtgaatcttgacagttgacagtgtcaacctgttatgc-------agtttgtgttctcca-aattttagaatcagtttctattgtttgat-------------------------------------

upper sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT3G06670.2 (Arabidopsis thaliana), 5'ss of exon 15
GTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaatacca-aacttaatc--------ttttatgctgttgctggcttaagcgttctctttgaaaataagttataattctgtgcaggttttatttcacattctgtcatcttatatatgttattaaaagttaaagttttcaatgcctatag-----------------
|||| ||||||  | || ||||||||||||||||||||| | ||| |||| |||||||| || || |||||||||| |  ||| | ||| ||||         | ||   | ||| ||| ||| ||     |  | | |  ||   ||  ||  |||      ||| |||  ||     |  | | | |   ||  || |  ||     | |  | || || |                   
GTATATTTCTTGCACGAATTTTGTAGTTTAAGCAAGAGCCTCCAGGTGGTGCAGCAGCTGCGACTTTTTAGgtatgtatttacaagaacctaattacgactggtgtttatcagttactgacttcagaacatttgtagtagctattatagtatcgtgtctgctctttctttgtcaagtgcttctttaagaatagtctttgatggtctttttctctattggctgtcttttcaatgatttttcag

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|32248391|gb|CD714210.1|CD714210
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|32267561|gb|CD716524.1|CD716524
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|30324963|gb|CD008225.1|CD008225
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|110711495|gb|EE088040.1|EE088040
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|32272042|gb|CD721201.1|CD721201
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|32270535|gb|CD719694.1|CD719694
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|32269076|gb|CD718235.1|CD718235
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|30326297|gb|CD009559.1|CD009559
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|32270540|gb|CD719699.1|CD719699
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|30325174|gb|CD008436.1|CD008436
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|30324365|gb|CD007627.1|CD007627
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|30325851|gb|CD009113.1|CD009113
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
EST: gi|30327653|gb|CD010915.1|CD010915
EST:     TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAG                         GGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG
genomic: TGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaat ... atgcctatagGGATCTTGTGAATGAAGGCATCTTTGACATCGTATCTGATGCTTTGCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTTTTCTTATATGAGTTTTGTAGTTTAAGCAAGAGCTTGCAGATGGTCCAGCAGCTTCGGCTATTTAGgtatgcaaataccaaacttaatcttttatgctgttgctggcttaagcgttctctttgaaaataagttataattctgtgcaggttttatttcacattctgtcatcttatatatgttattaaaagttaaagttttcaatgcctatag

- - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT