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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctcactctattttctttcattttgtcattttatagtgcttttaactggtattgtttgtcttcaagtttttatgtggtgaaacattgttttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTATTAAGGTCTGATTTCCAAGTTGCGGCACAAAACTGTTGGATTCGGAGAGG

Basic information

species Vitis vinifera
transcript Vv06s0004g04800.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G04290.2 (Glycine max), 3'ss of exon 2
tttctcactctattttctttcattttgtcattttatagt-gcttttaactggtattgtttgtcttcaagttttta--tgtggtgaaacat-tgttt---tgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTATTAAGGTCTGATTTCCAAGTTGCGGCACAAAACTGTTGGATTCGGAGAGG
        ||| ||     | | ||| |||  ||||  | | | |    |||  |||    |    | ||||| |   ||| | | | || |||||   | || |||| ||||| || || ||||| |||||||| |||||| | |||||||||||  |  |  |||||||||| ||| ||||||||||||||||| |||| | |||
-------ttcttttgcaaataagtttatcaaattatttttgttgtctcttggcgttggcaatgacgatgttttgaagcgtgctaataaatgtgtttcacttttacagAAGTTGTTGTGAGCCCTCCTTTTGTGTTCCTTCCTGTTGTAAAAAGTTTGCTGCGCCCTGATTTCCATGTTTCGGCACAAAACTGTTGGGTTCGCAAAGG
















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|110415564|gb|EC981483.1|EC981483
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCATCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|351028511|gb|FQ444792.1|FQ444792
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|30129525|gb|CB914864.1|CB914864
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|294965195|gb|GW837026.1|GW837026
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCATCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|110378426|gb|EC943557.1|EC943557
EST:     TTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: TTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|110692722|gb|EE068329.1|EE068329
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|110395870|gb|EC961544.1|EC961544
EST:     GCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|349826936|gb|FQ419027.1|FQ419027
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|161710111|gb|FC059796.1|FC059796
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|110726667|gb|EE102647.1|EE102647
EST:     GCTGAAGTTCCATCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|71871008|gb|DT020063.1|DT020063
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|294963951|gb|GW836826.1|GW836826
EST:     GATTGTTACTGTTTCGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAGGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|161720486|gb|FC070598.1|FC070598
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
EST: gi|161714171|gb|FC062916.1|FC062916
EST:     GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGG                         AGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT
genomic: GATTGTTACTGTTTTGAATGAGGCTGAAGTTCCGTCCGAAGACATTGTGGgtgagttgag ... tttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactggtattgtttgtcttcaagtttttatgtggtgaaacattgttttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTATTAAGGTCTGATTTCCAAGTTGCGGCACAAAACTGTTGGATTCGGAGAGG
 ttttaac  putative branch site (score: 2)
                                         ttgtttt  putative PPT
                    aagtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctcactctattttctttcattttgtcattttatagtgcttttaactggtattgtttgtcttcaagtttttatgtggtgaaacattgttttgttgcagAGGTTGTGGTAAGTCCTCCATTTGTGTTTCTTCCTTTGGTAAAAAGTTTATTAAGGTCTGATTTCCAAGTTGCGGCACAAAACTGTTGGATTCGGAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- -ctcactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacat