Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttcttttccttgggaacacgcggtaatgaagttatatggtgctgttaaatttgcatgggtttccgtttaagctgaaatctctggaatggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAGTCCGTCAAAAACATATGAACATGGTTTCCGAGTAGGGTTTAAAGGAAAT

Basic information

species Vitis vinifera
transcript Vv09s0002g02140.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------tctttcttttccttgggaacacgcggtaatgaagttatatggtgctgttaaatt--tgcatgggtttccgtttaagctgaaatctctggaatggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAGTCCGTCAAAAACATATGAACATGGTTTCCGAGTAGGGTTTAAAGGAAAT
                                                    |||  ||   |||  || |  |  |       |       ||    ||  ||  ||| | |  |||| || |  ||  || ||||| | || |  ||||||||| ||||||||||||| ||||| |||||||| |||||||||||||||||||  |||| |||||||||||||||||| || || ||||| |||||||| 
gtaagtggttaaatgtattggagctagtgcttagttatgtagtatgagttcatttaattagtttgctaagattcattggcctgatgggtgcttgtctataggtttctgctttgtattcccttgacccttgaagctctgaattgaacatgcagGATTTTGGATAACCTTCCAGTTGCTGTTCATAGACAAAGGAGGGATGGAAGTCAATCAACAACATATGAACATGGTTTTCGTGTTGGGTTCAAAGGAAAC

upper sequence: Vv09s0002g02140.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------tctttcttttccttgggaacacg---cggtaatgaagttatatggtgctgttaaatttgcatgggtttc--cgtttaagctgaaatctctggaatggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAGTCCGTCAAAAACATATGAACATGGTTTCCGAGTAGGGTTTAAAGGAAAT
                                                     |  ||  ||| ||  |   ||     | ||   |   || | |   | | |    |||| ||     |   |  || || ||||  ||||| | || |  ||||||||| ||||||||||||| ||||| |||| ||| ||||||||||||||| |||  |||| |||||||||||||||||| || || ||||| |||||||| 
gtaagtggtaaatgtattggagctagtgcttagttatgtagtataggtgtatttaattagtttgctgagattcattggcctgttgggtgcttgtctataggtttctgctttgaatttcccttgacccttgagttgaag-ctctgaattgaacatgcagGATTTTGGATAACCTTCCAGTTGCTGTTCGTAGACAAAGGAGGGATGGAGGTCAATCAACAACATATGAACATGGTTTTCGTGTTGGGTTCAAAGGAAAC
















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|161705906|gb|FC054812.1|FC054812
EST:     GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
EST: gi|110691298|gb|EE069240.1|EE069240
EST:     GCTGCAAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
EST: gi|71862773|gb|DT011828.1|DT011828
EST:     GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
EST: gi|351033128|gb|FQ446481.1|FQ446481
EST:     GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
EST: gi|71865270|gb|DT014325.1|DT014325
EST:     GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
EST: gi|351030399|gb|FQ432337.1|FQ432337
EST:     GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
EST: gi|349833072|gb|FQ416450.1|FQ416450
EST:     GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
EST: gi|34546863|gb|CF515095.1|CF515095
EST:     GCTGCAAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTGTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
EST: gi|161713929|gb|FC062883.1|FC062883
EST:     GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACAT                         GATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG
genomic: GCTGCGAAGAATTTTAAGGAAAAAATTGATGATGAATATCGAGTAAACATgtaagtacca ... ggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaaatttgcatgggtttccgtttaagctgaaatctctggaatggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAGTCCGTCAAAAACATATGAACATGGTTTCCGAGTAGGGTTTAAAGGAAAT
     aattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttcttttccttgggaacacgcggtaatgaagttatatggtgctgttaaatttgcatgggtttccgtttaagctgaaatctctggaatggatgtgcagGATTCTGGATAACCTTCCGGTTGCAGTTCATAGGCAAAGGAGGGATGGAAGTCCGTCAAAAACATATGAACATGGTTTCCGAGTAGGGTTTAAAGGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - ttccttg
- - - - - - - -ggaacac
- - - - - - - - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgga