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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttcagtgggccaaactgtttaatataaaagtactgcaactattgctttgaaatttcaggtaactgttttgacacatttatgtcaatcattttccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAGCTGCCTGTGCTATGCATGGATGTTTCATCAGATGGAGATTTGCTTGTCA

Basic information

species Vitis vinifera
transcript Vv08s0007g04690.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g04690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G37050.1 (Glycine max), 3'ss of exon 3
--atgtttcagtg-ggccaaactgtttaatataaaagtactgcaactattgctttgaaatttcaggtaactgttttgacacatttatgtcaatcattttccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAGCTGCCTGTGCTATGCATGGATGTTTCATCAGATGGAGATTTGCTTGTCA
  || || || |  |  |     ||     ||     | |   | |   |  |||   |||||| | |  | ||||  ||   | || ||| ||||||| ||||||  ||||   ||  |  ||||||| ||||| || |||||||| |||||||||||||| || || |||||| | |||||||||||||||||  |||| |
cgattttgcactatgagcttgtggtcactcatgtttatgcattagcc-ctattttactatttcaagcatttttttt--cattataatttcattcatttttcagGTTCACTTTGCAGACACATTCAAATTCTTCCTTTCATTATATGGCCACAAGCTGCCTGTTCTGTGTATGGATATCTCATCAGATGGAGATTTAATTGTAA

upper sequence: Vv08s0007g04690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G34360.1 (Glycine max), 3'ss of exon 5
---atgtttcagtgggccaaactgtttaatataaaagtac-tgcaactattgctttgaaatttcaggtaactgttttgacacatttatgtcaatcattttccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAGCTGCCTGTGCTATGCATGGATGTTTCATCAGATGGAGATTTGCTTGTCA
   |   ||  |||     | ||  |   | |  |  ||      |    |  |||   |||||| |||  | |||    | | || | |   ||||||| ||||||  ||||   ||  |  ||||||| ||||| || |||||||| |||||||||||||| || || |||||| | || ||||||||||||||  |||| |
ttgacaattttgtgctatgagcttctggttgttcatttatgcattagccctattttactatttcaagtattt-tttaattataatttttt---tcatttttcagGTTCACTTTGCAGACACATTCAAATTCTTCCTTTCATTATATGGCCACAAGCTGCCTGTTCTGTGTATGGATATCTCCTCAGATGGAGATTTAATTGTAA

upper sequence: Vv08s0007g04690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G21540.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------atgtttcagtgggccaaactgtt--taatataaaagtact---------gcaactattgctttgaaatttcaggtaactgttttgacac--atttatgtcaatcattt----tccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAGCTGCCTGTGCTATGCATGGATGTTTCATCAGATGGAGATTTGCTTGTCA
                                         |  |||||||  | || |    |  ||   |||    | |         | | |||| |  ||   ||||    | ||   | | ||||  | ||||||   | || |    | ||||||||||  ||||||||||| ||||| | ||| ||||||||||| |||||| |||||||| | ||||| ||  | |||||||||||||| ||| |||| |
gtagattttctgtttatggcatatgtaaatgagaaaataataattttcagtacgtcatataaatgatacgctaaccacattcttataatcgtatctatcgtattatcatttacattgacgtatgtaacactaacttatgtaccttatattggtttcagGTTTTCTACATGGATTCCCTAAAATTCTACCTCTCCTTATATGGCCACAAGTTGCCTGTGATGTGCATTGACATCTCATCAGATGGAGAGTTGATTGTTA

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|349826686|gb|FQ418777.1|FQ418777
EST:     GTCCCGATGCTAAGTATATCGCAGCTGCATTGTTGGATTGTACAGTGAAG                         GTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAG
genomic: GTCCCGATGCTAAGTATATCGCAGCTGCATTGTTGGATTGTACAGTGAAGgtgagatgac ... cattttccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAG
EST: gi|351013542|gb|FQ425573.1|FQ425573
EST:     GTCCCGATGCTAAGTATATCGCAGCTGCATTGTTGGATTGTACAGTGAAG                         GTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAG
genomic: GTCCCGATGCTAAGTATATCGCAGCTGCATTGTTGGATTGTACAGTGAAGgtgagatgac ... cattttccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAG
EST: gi|351016863|gb|FQ424290.1|FQ424290
EST:     GTCCCGATGCTAAGTATATCGCAGCTGCATTGTTGGATTGTACAGTGAAG                         GTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAG
genomic: GTCCCGATGCTAAGTATATCGCAGCTGCATTGTTGGATTGTACAGTGAAGgtgagatgac ... cattttccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctttgaaatttcaggtaactgttttgacacatttatgtcaatcattttccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAGCTGCCTGTGCTATGCATGGATGTTTCATCAGATGGAGATTTGCTTGTCA
                        ttttgac  putative branch site (score: 3)
                                            tcattttcc  putative PPT
     ttgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtttcagtgggccaaactgtttaatataaaagtactgcaactattgctttgaaatttcaggtaactgttttgacacatttatgtcaatcattttccagGTTTTCTTTATGGATTCCCTCAAATTTTTCCTGTCCTTATATGGTCACAAGCTGCCTGTGCTATGCATGGATGTTTCATCAGATGGAGATTTGCTTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - -ccaaact
- - - - - - - - - - - - - - -aaaagta
- - - - - - - - - - - - - - - - - - ctgcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgacac