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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgtgtttcctctcacttgtgccattttttttttccttataaagttgccctgagtgtgatcttctgaaatttgaagaatttctcctctgtggtta...

Basic information

species Vitis vinifera
transcript Vv05s0077g00470.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: LOC_Os05g06690.2 (Oryza sativa), 5'ss of exon 17
GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatg-tgtttcctctcacttgtgccattttttttttccttataaagttgccctgagtgtgatcttctgaaatttgaagaatttctcctctgtggtta
|| ||||| ||||| || ||||||||||||||||| || ||| || | || ||||||||||| || |  |||||||||||||| | | | ||||||||||||   || |  ||  |||    | |  | ||| | | | |     |  | ||  | ||   |  |       ||||  | ||  ||   | ||||   | 
GAGACAGCCGATCATCTTCTCTACCCAAATCCTGGATCTGGATTGGTCCATGAACAGCATCTGCAATACTTCCATTTTCTTGGCAGTCTCCTTGGGAAGgtactttggttgtttatcttttctttttcttttctgtctactgctgactgatgtgcagaaccttgtagagcttaattaaatgatctttcacactgtatat-

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA17G04180.1 (Glycine max), 5'ss of exon 17
GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgtgtttcctctcactt--gtgccattttttttttccttataaagttgccctgagtgt-gatcttctgaaat-ttgaagaatttctcctctgtggtta------------------------------------------------------------------------------
|||||||| |||||||| || || || |||||||| || ||||||||||| ||||| ||| |||| |||||||| || ||||| ||| |||| |  |||||||    | |   |   || |    |   | ||| | ||| | |||||||| | |||  |  | ||    ||    | ||  |   ||| |     ||||||                                                                               
GAAACAGCGGATCACCTGCTTTATCCTAATCCTGGATCTGGAATGATACATGAACAACATTTCCAATTTTTCCACTTCCTTGGTACTCTTCTCGCAAAGgtatcccctctcctcctccattccctttttaatttctattttcctataaagtgggcctttgcattgaatgactatgctattctatcttttttgtcacgtggtttgaggtagtctgcatcctattcctatactgcttgcacttaattggaattttgcttcacagttactacttgcatgtgcag

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA07G36390.1 (Glycine max), 5'ss of exon 17
GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgtgtttcctctcacttgtgccattttttttttccttataaagttgccctgagtgt-gatcttctgaa---atttgaaga----atttctcctctgtggtta------------------------------------------------------------------------------------------
|||||||| |||||||| || ||  | |||||||| || ||||||||||| ||||| ||| |||| |||||||| || ||||| ||| ||||||  |||||||    | |   |   |  |       |  | | ||| || ||||||| | |||  |  | ||    |||||   | || || |    |||    || | | || |                                                                                          
GAAACAGCGGATCACCTGCTTTATGCTAATCCTGGATCTGGAATGATACATGAACAACATTTCCAATTTTTCCACTTCCTTGGTACTCTTCTTGCAAAGgtatcccctctcctccgcctttccctttctaatctcttttctaataaagtgggcctttgcattgaatgactgaatctacttcaaaatgctattctatcttttttgtcacgtggtttgagttagtctgcatcctattcctctactgcttgcacttaattggaattttgcttcacatttactacttacttgcatgtgcag

upper sequence: Vv05s0077g00470.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: AT3G17205.1 (Arabidopsis thaliana), 5'ss of exon 17
GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgt--gtttcctctcacttgtgccattttttttttccttataaagttgccctgagtgtgatcttctgaaatttgaagaatttctcctctgtggtta
|| || ||||||||| | || || || |||||||| |||||||||||||| ||||||||||||||||| || |||||||| || | | | || |  || ||||| | |  | ||  |  |  |  |||     | || |   |||  |  ||   ||   ||  | ||| |  |  | | | |         || |  |  
GAGACCGCTGATCACATGCTTTATCCTAATCCTGGATCAGGAATGATACATGAACAGCATCTCCAGTTCTTTCATTTTCTCGGCAGTCTCCTCGCAAAAgtatggtatttgattggtggccttgatgcggaactcttataatttaccattttttactcc-tgaaaacttttatatataggacagaaagcaaactataatg-

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|71889221|gb|DT038276.1|DT038276
EST:     ACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG                         GCCATGTTTGAAGGGATTCTTGTGGATATACCATTTGCAACATTCTTTTTG
genomic: ACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgtg ... cttcctgtagGCCATGTTTGAAGGGATTCTTGTGGATATACCATTTGCAACATTCTTTTTG
EST: gi|71884176|gb|DT033231.1|DT033231
EST:     ACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG                         GCCATGTTTGAAGGGATTCTTGTGGATATACCATTTGCAACATTCTTTTTG
genomic: ACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgtg ... cttcctgtagGCCATGTTTGAAGGGATTCTTGTGGATATACCATTTGCAACATTCTTTTTG
EST: gi|71881320|gb|DT030375.1|DT030375
EST:     ACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAG                         GCCATGTTTGAAGGGATTCTTGTGGATATACCATTTGCAACATTCTTTTTG
genomic: ACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgtg ... cttcctgtagGCCATGTTTGAAGGGATTCTTGTGGATATACCATTTGCAACATTCTTTTTG
EST: gi|110370035|gb|EC934210.1|EC934210
EST:     ACGAACAGCATCTCCAGTTTTTTCATTTTCTTGGAACTGTTCTTGGGAAG                         GCCATGTTTGAAGGGATTCTTGTGGATATACCATTTGCAACATTCTTTTTG
genomic: ACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgtg ... cttcctgtagGCCATGTTTGAAGGGATTCTTGTGGATATACCATTTGCAACATTCTTTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACAGCTGATCACCTACTCTACCCAAATCCTGGGTCAGGAATGATACACGAACAGCATCTCCAGTTTTTCCATTTTCTTGGAACTGTTCTTGGGAAGgtatgatgtgtttcctctcacttgtgccattttttttttccttataaagttgccctgagtgtgatcttctgaaatttgaagaatttctcctctgtggtta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctct