Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAGACTTGAGGAAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgttatattttccatattgtgtggcaaaatcttagagggtcttcttatcagtttctaagatctagagcatcgtctgtttgaagtttttttccttt...

Basic information

species Vitis vinifera
transcript Vv01s0244g00070.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0244g00070.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G44630.1 (Glycine max), 5'ss of exon 5
CTCAGACTTGAGGAAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgttatattt-tccatattgtgtggcaa--aatcttagagggtcttcttatcagtttctaagatctagagcatcgtctgtttgaagtttttttccttt-
|||||||| |||||||| |||||||||||  |||||||||||||||| |||||||| || |||||  |   | | ||| |   || |     | |    |  ||| |     |   |||    |||| |  | | |    |||  ||||    |||  |        
CTCAGACTCGAGGAAGACAGATGCAAGGAATCAGAGGCCAGAGTTAGGGAGCTTGAAAAGCAGgtgctgactttgtttatttttagtacacagtactttagtttacacatattgactatggtcttctgaattatgg----tcgcttgttcttggttgatgcaacagg

upper sequence: Vv01s0244g00070.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G13260.1 (Arabidopsis thaliana), 5'ss of exon 5
CTCAGACTTGAGGAAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgttatattttccatattgtgtggcaaaatcttagagggtcttcttatcagt-ttctaagatctagagcatcgtctgtttgaagtttttttccttt
|| || |||||||| |||| ||||||||| ||||| || || || ||||||||||| |||||||| | ||    | |  |  ||| |  |       | || |    | ||  ||  | | |||| |  | |    ||   |||                    
CTTAGGCTTGAGGATGAGAAATGCAAGGAAGCAGAAGCTAGGGTGAGAGAGCTTGAAAAACAGgtaactggacaaatacctgtat-gcataattttttttttgctcttttttgtaatattgttctcacctttgagacaaaatctag------------------
















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|352798824|gb|FQ478459.1|FQ478459
EST:     AAGGGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAG                         GTTGCTGCTCTTGGAG
genomic: AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCTGCTCTTGGAG
EST: gi|351024338|gb|FQ423761.1|FQ423761
EST:     AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAG                         GTTGCTGCTCTTGGAGAGGGGGTATCTCTGGAAGCTA
genomic: AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCTGCTCTTGGAGAGGGTGTATCTCTGGAAGCTA
EST: gi|30256262|gb|CB972105.1|CB972105
EST:     GCTTGAG-AACAG                         GTTGCTGGANCTTGGAGAGGGTGTATCTGANGGAAGCTAAATTGCTGAGCA
genomic: GCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCT-GCTCTTGGAGAGGGTGTATCT-CTGGAAGCTAAATTGCTGAGCA
EST: gi|351037721|gb|FQ464162.1|FQ464162
EST:     AAGGGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAG                         GTTGCTGCTCTTGGAGAGGGTGTACCTCTGGAA-CTAAA
genomic: AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCTGCTCTTGGAGAGGGTGTATCTCTGGAAGCTAAA
EST: gi|351036830|gb|FQ459352.1|FQ459352
EST:     AAGGGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAG                         GTTGCTGCTCTTGGAGA
genomic: AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCTGCTCTTGGAGA
EST: gi|351031918|gb|FQ460175.1|FQ460175
EST:     AAGAGAGATGCAAGGATGCAAAGGCCAGAGTTAGAGAGCTTGAGAAACAG                         GTGGCTGCTCTTGGAGAGGGTGTATCTCTGGAAGC
genomic: AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCTGCTCTTGGAGAGGGTGTATCTCTGGAAGC
EST: gi|351037441|gb|FQ460640.1|FQ460640
EST:     AAGGGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAG                         GTTGCTGCTCTTGGAGAGGGTGTATCTCTGGAAACTAAATTGCTGAACAGA
genomic: AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCTGCTCTTGGAGAGGGTGTATCTCTGGAAGCTAAATTGCTGAGCAGA
EST: gi|351047980|gb|FQ441152.1|FQ441152
EST:     AAGGGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAG                         GTTGCTGCTCTTGGA
genomic: AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCTGCTCTTGGA
EST: gi|161717169|gb|FC066567.1|FC066567
EST:     AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAG                         GTTGCTTCTCTTGGAGAGGGTGTATCTCTGGGAGCTAAATTGCTGAGCAG
genomic: AAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgtta ... gagtcttcagGTTGCTGCTCTTGGAGAGGGTGTATCTCTGGAAGCTAAATTGCTGAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAGACTTGAGGAAGAGAGATGCAAGGATGCAGAGGCCAGAGTTAGAGAGCTTGAGAAACAGgttattgttatattttccatattgtgtggcaaaatcttagagggtcttcttatcagtttctaagatctagagcatcgtctgtttgaagtttttttccttt

- - - - - -  AAGAGA
- - - - - - - -  GAGATG
- - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcaaaa