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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgtataatataagagcaatagctgtaaacctttttttttttttttttaatgtgtaaataaaaagcacataataaaaggggggcaacccatgtc...

Basic information

species Vitis vinifera
transcript Vv09s0002g00340.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os10g25130.1 (Oryza sativa), 5'ss of exon 8
GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgtataatataagagcaatagctgtaaacctttttttttttttttttaatgtgtaaataaaaagcacataataaaaggggggcaacccatgtc
|||||||||||||||||| |  ||||| ||||| ||||| || || |||||||| || ||||||||||| || || |||| ||| ||||||||  ||||||||||||| |  | | | ||  || |  |  ||   ||   ||  |  |     || |  ||| | | | |||  |  |   ||                
GATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttt-tgaattctcagcacattttcaatatggctgcattcatgctgcaccaaagcctaattgaga-gcattttgttttag----------------

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G088064_T03 (Zea mays), 5'ss of exon 8
GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgtataatataagagcaatagctgtaaacctttttttttttttttttaatgtgtaaataaaaagcacataataaaaggggggcaacccatgtc--
|||||| |||||||| || |  ||||| ||||| ||||| || || ||||||||||||||||||||||| || || || | ||| ||||||||  |||||||||||   |  | |     ||||  ||    ||     | | |  |  |   || ||| | ||| |    ||| |||  ||  | | |||     | ||  
GATGCAATTACTGATTAGGAATGAGAAAGATGGCATTCTGTGCCCAATTCCTCAGTACCCTTTGTACTCAGCCTCCATAGCTCTTCATGGTGGAGCTCTTgtatgtactttcatttgctcagcagaag----aatatggtctatagtactaaatattgtatcaatga----cacctaa--aatcgagcgcatgttctttcag

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA07G05130.1 (Glycine max), 5'ss of exon 8
GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgta-tgtttgtataatataagagcaatagctgtaaacctttttttttttttttttaatgtgtaa-ataaaaagcacataataaaaggggggcaacccatgtc
|||||| ||||| || ||| | || || ||||| ||||| ||||||||||| ||||||||| ||||||| || |||||||  || |||||||||   || ||| |||||     ||| |   |||  |    |||     |||  |   | | |  |||       |    |  |  | |||      | || | |  ||  
GATGCAATTACTCATTAGATCAGAAAATGATGGTATTCTGTGTCCCATTCCACAGTACCCTCTGTACTCAGCCTCAATTGCCCTCCATGGTGGCTGCCTGgtaatgttttctccatacagttgcataatgcataatttaatttggtcactatatagatgcaccctgttttgatgattttataggttatgtgccatctttg--

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA16G01630.2 (Glycine max), 5'ss of exon 6
GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgta-tgtttgtataatataagagcaatagctgtaaacctttttttttttttttttaatgtgtaa-ataaaaagcacataataaaaggggggcaacccatgtc
|||||| ||||| || ||| | || || ||||| ||||| ||||||||||| ||||||||| ||||||| || |||||||  || |||||||||   || ||| |||||     ||| |   |||  |    ||      |||  |   | | |  | |      ||    |  |  | |||      | || | |  ||  
GATGCAATTACTCATTAGATCAGAAAATGATGGTATTCTGTGTCCCATTCCACAGTACCCTCTGTACTCAGCCTCAATTGACCTCCATGGTGGCTTCCTGgtaatgttttctccatacagttgcataatgcatagtttaatttggtcactatatagaagcaccctattttgatgattttataggctatgtgccatctttg--

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G17290.1 (Arabidopsis thaliana), 5'ss of exon 8
GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgtataatataagagcaatagctgtaa-acctttttttttttttttttaatgtgtaaataaaaagcacataataaaaggggggcaacccatgtc---------------------------
||||||  | || ||||   | ||||| |||||||| |||||||| ||||||||||| || |||||||| ||||||||||  || || ||||| ||| | ||||||| ||    | |       ||     ||  |  ||      ||  | | | |  ||  || |  || |       |||           |  | |                            
GATGCAACTTCTCATAACTTCAGAGAAAGATGGAATCCTTTGTCCTATTCCTCAGTATCCATTGTACTCAGCTTCAATTGCCCTTCACGGTGGAACTTTGgtatgttcgttatctttgtttatgatgatgatatcattttgacgcattactatatcaaatgggaaaatgaatctgtctccaaagtttcttttgtctttcttctcattgtcgtcatgttcttctggtag

upper sequence: Vv09s0002g00340.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 5'ss of exon 8
GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgtataatataagagcaatagctgtaaacctttttttttttttttttaatgtgtaaataaaaagcacataataaaaggggggcaacccatgtc
||||||  | ||  | ||  | ||||| ||||| |||||||  || ||||||||||| || |||||||| ||||||||||  || ||||||||  || | |||||||  ||||||      | | ||    |     ||  |     |||||  ||| ||||  |   |                               
GATGCAACTTCTCTTGAGCTCAGAGAAAGATGGTATTCTTTCCCCGATTCCTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATGGTGGATCTTTGgtatgttcatataatcatcatggagtaatgttgttttttggtacaagtttttgaaatttgtacttcttag------------------------------

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|161710855|gb|FC058161.1|FC058161
EST:     CTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTT                         GTTCCTTACTATCTTGATGAAGCAACTGGGTGGGGCTTGGAGATTTCAGAA
genomic: CTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgt ... ggttttgcagGTTCCTTACTATCTTGATGAAGCAACTGGGTGGGGCTTGGAGATTTCAGAA
EST: gi|161710403|gb|FC059015.1|FC059015
EST:     CTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTT                         GTTCCTTACTATCTTGATGAAGCAACTGGGTGGGGCTTGGAGATTTCAGAA
genomic: CTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgt ... ggttttgcagGTTCCTTACTATCTTGATGAAGCAACTGGGTGGGGCTTGGAGATTTCAGAA
EST: gi|161717648|gb|FC066273.1|FC066273
EST:     CTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTT                         GTTCCTTACTATCTTGATGAAGCAACTGGGTGGGGCTTGGAGATTTCAGAA
genomic: CTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgt ... ggttttgcagGTTCCTTACTATCTTGATGAAGCAACTGGGTGGGGCTTGGAGATTTCAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgtataatataagagcaatagctgtaaacctttttttttttttttttaatgtgtaaataaaaagcacataataaaaggggggcaacccatgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggcaa