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

...ctttatatctttgatttaactggaatattataatatataaataactgcaaggttaacaggttcttctttgttgagtgatcattattgttttcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g15050.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G43810.2 (Glycine max), 3'ss of exon 4
ctttatatctttgatttaactggaatattataatatataaataactg--caaggttaacaggttcttctttgttgagtgatcattattgtt-ttcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG
     | |  | |    ||  ||   |  |    ||||||||  ||   |  |  |      || |  | | || | ||||    ||| || ||  | || |||||| ||  |||| |  ||||||||||||||||||||||||||||| | |||||||||| | ||||| || ||| | |||||||| |
---agtctgataggcaaaatgggctcaagaagcaatataaattcctattcctgtcttttcttttttcttcttttcactgatatgaatttttgttttaatgtagCTATTCCTTTGTCTATCGATCACAAACCTGATAGATCTGATGAACGTCGAAGGATTGAACAGGCTGGGGGATTCATAATTTGGGCTG

upper sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38500.1 (Glycine max), 3'ss of exon 5
----------------------------------------ctttatatctttgatttaactggaatattataatatataaataactgcaag-gttaacaggttcttctttgttgagtgatcattattgtt-ttcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG
                                         ||  | |  | |    ||| ||   |  |    ||||||||  ||      ||       || |  | | || | ||||    ||| || ||  | || || | | ||  |||||| |||||||||||||||||||||  ||||||| |||||||||||| | ||||| || ||| | |||||| | |
gttttttgtaacttcaattctactaagttttcagtgttatgttagtttgataggcaaaacaggctcaagaagtgatataaattcctattcctgtctttcttttttcttcttttcactgatatgaatttttgttttaatgtagTTGTTCCTTTGTCCATTGATCACAAACCTGATAGATCCAATGAACGTCAAAGGATTGAACAGGCTGGTGGATTCATAATTTGGACCG
















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|110712077|gb|EE089286.1|EE089286
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351030454|gb|FQ432392.1|FQ432392
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|45368324|gb|CK906683.1|CK906683
EST:     TGTTGCAAATGTGGGAGA-TCTAGAGTGG-TGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351048563|gb|FQ448837.1|FQ448837
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|349815543|gb|FQ400699.1|FQ400699
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|161716302|gb|FC064648.1|FC064648
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|32245933|gb|CD711752.1|CD711752
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAATCCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351023467|gb|FQ432850.1|FQ432850
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351029448|gb|FQ436842.1|FQ436842
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|349817905|gb|FQ407894.1|FQ407894
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|352791261|gb|FQ474951.1|FQ474951
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351044250|gb|FQ447604.1|FQ447604
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|110371845|gb|EC935970.1|EC935970
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|349832452|gb|FQ421013.1|FQ421013
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|27584677|gb|CB007372.1|CB007372
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|349815027|gb|FQ410250.1|FQ410250
EST:     TGCTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351025872|gb|FQ427884.1|FQ427884
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351025088|gb|FQ433505.1|FQ433505
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351012826|gb|FQ430389.1|FQ430389
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351030991|gb|FQ439027.1|FQ439027
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|161717197|gb|FC066571.1|FC066571
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|349830246|gb|FQ420506.1|FQ420506
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351036088|gb|FQ463933.1|FQ463933
EST:     TGTTGCAAATGTGGGAGATTCAAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACACACCTGATAGATCTGATGAACGCCACA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|110711257|gb|EE087557.1|EE087557
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|161719283|gb|FC064823.1|FC064823
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351033310|gb|FQ446542.1|FQ446542
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351021784|gb|FQ437169.1|FQ437169
EST:     TGTTGCAAATGTGGGAGATTCCAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|351046056|gb|FQ441439.1|FQ441439
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
EST: gi|161715035|gb|FC063620.1|FC063620
EST:     TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAG                         CTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA
genomic: TGTTGCAAATGTGGGAGATTCTAGAGTGGTTGCTTGTAGAGCTGGTTCAGgtttctgcct ... tcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaggttaacaggttcttctttgttgagtgatcattattgttttcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG
     ggttaac  putative branch site (score: 3)
                                       ttgttttc  putative PPT
                                atcattattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttatatctttgatttaactggaatattataatatataaataactgcaaggttaacaggttcttctttgttgagtgatcattattgttttcaactgcagCTATCCCACTGTCCACTGATCACAAACCTGATAGATCTGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - aaataac