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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatttatctattgccatccattttctgaagttggttttctcatcaccacttctctttctgaaatatgatgggtgtaacgttttggttgtagTTCTCCATCCCTGGTGGTCGACATGCTGTGCACCATGCGACCCTTTTGCAGAGCGTGGGAGCAGCACGGGTTCTACGTGGTGCAGCTGCAGCAGCAACTG

Basic information

species Vitis vinifera
transcript Vv15s0021g01810.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA18G48840.1 (Glycine max), 3'ss of exon 11
gtagatttatctattgccatccattttctgaagttggttttctcatcaccacttctctt---tctgaaatatgatgggtgt-aacgttttggttgtagTTCTCCATCCCTGGTGGTCGACATGCTGTGCACCATGCGACCCTTTTGCAGAGCGTGGGAGCAGCACGGGTTCTACGTGGTGCAGCTGCAGCAGCAACTG
|||  | || | | |  || |   |   | |  ||  | ||   |||   | ||   ||   | |  |   |  |  ||||  |  |||   ||| ||||  | || |||||||| ||||||||  |||||||||| | |||  |||||||| |||||||| || | ||||| ||||||||||| |||||||||||||
gtaactatagcaagtagcaaca--tacttaattttcctctttatatctatatttgatttgaattttgatgctcctatgtgttgatctttcaattgcagTTTACAATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAGAGCTTGGGAGCACCAAGAGTTCTGCGTGGTGCAGCCGCAGCAGCAACTG

upper sequence: Vv15s0021g01810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G37720.1 (Glycine max), 3'ss of exon 12
gtagatttatctattgccatccattttctgaagttggttttctcatcaccactt--ctc---tttctgaaatatgatgggtgtaacgttttggttgtagTTCTCCATCCCTGGTGGTCGACATGCTGTGCACCATGCGACCCTTTTGCAGAGCGTGGGAGCAGCACGGGTTCTACGTGGTGCAGCTGCAGCAGCAACTG
|||  | || | | |  || |   |   | |  ||  ||||   |||   | ||   ||   |||  |   |   ||| || | |  |||   ||| ||||  |||| |||||||| ||||||||  |||||||||| | |||  |||| ||| |||||||| || | ||||| |||||||||||||| ||||||||||
gtaactatagcaagtagcaaca--tacttaattttcttttttatatctatatttggttcaaattttggcgttcctatgtgt-tgatctttcaattgcagTTTACCATTCCTGGTGGACGACATGCCATGCACCATGCTAGCCTCATGCAAAGCCTGGGAGCATCAAGAGTTCTGCGTGGTGCAGCTGCTGCAGCAACTG
















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|110387852|gb|EC952550.1|EC952550
EST:     GAAATCCTTCTTCCATACTCAAGTCATGTGCTGCTTTTGCTCTTCTCCAG                         TTCTCCATCCCTGGTGGTCGACATGCCGTGCACCATGCGACCCTTTTGCAG
genomic: GAAATCCTTCTTCCATACTCAAGTCATGTGCTGCTTTTGCTCTTCTCCAGgtagatttat ... ttggttgtagTTCTCCATCCCTGGTGGTCGACATGCTGTGCACCATGCGACCCTTTTGCAG
EST: gi|110374892|gb|EC939833.1|EC939833
EST:     GAAATCCTTCTTCCATACTCAAGTCATGTGCTGCTTTTGCTCTTCTCCAG                         TTCTCCATCCCTGGTGGTCGACATGCCGTGCACCATGCGACCCTTTTGCAG
genomic: GAAATCCTTCTTCCATACTCAAGTCATGTGCTGCTTTTGCTCTTCTCCAGgtagatttat ... ttggttgtagTTCTCCATCCCTGGTGGTCGACATGCTGTGCACCATGCGACCCTTTTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcatcaccacttctctttctgaaatatgatgggtgtaacgttttggttgtagTTCTCCATCCCTGGTGGTCGACATGCTGTGCACCATGCGACCCTTTTGCAGAGCGTGGGAGCAGCACGGGTTCTACGTGGTGCAGCTGCAGCAGCAACTG
                                   gtgtaac  putative branch site (score: 3)
                        aaatatgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatttatctattgccatccattttctgaagttggttttctcatcaccacttctctttctgaaatatgatgggtgtaacgttttggttgtagTTCTCCATCCCTGGTGGTCGACATGCTGTGCACCATGCGACCCTTTTGCAGAGCGTGGGAGCAGCACGGGTTCTACGTGGTGCAGCTGCAGCAGCAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG