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

...aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttgtaacaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG

Basic information

species Vitis vinifera
transcript Vv16s0039g02240.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 3
aacatactttcttagaagtat-cttgttcatttttttcttctatt--tggtttttgtaacaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
   |       |  || |||| | ||  |||      || |  ||     || |  || |||   |  |||  |  |   ||    | | |||  || ||||||||||||| |||||||| |||||| ||||||| || |||||||| || || |||||||||
--tactgaaattcggatgtattcatgagcatacccaactacatttataaattgtaatagcaacttattcctatatgttatttttgcacgttctg-atttgcagATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g42940.3 (Oryza sativa), 3'ss of exon 3
---------aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttgta-acaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG----------------------------------------
          || |   ||  |  || || |  |  ||||||  | |   |     ||||  |      | ||  ||||  | | | ||| |||            ||||||||| || ||||||||| ||||| ||||||||||||| | ||| |  || || ||||||                                        
ttacagatccacgttgctttatttaattagcacgcacattttggtttcagaaacacttttcttgcgttgtaaattcctct-cttcttttgtaaact---------cgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGGTTTACATATATGTATAAATAATTTATTATGAGGCAGCAA

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 3
---------aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttgta-acaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
          || |   ||  |  || || |  |  ||||||  | |   |     ||||  |      | ||  ||||  | | | ||| |||            ||||||||| || ||||||||| ||||| ||||||||||||| | ||| |  || || ||||||
ttacagatccacgttgctttatttaattagcacgcacattttggtttcagaaacacttttcttgcgttgtaaattcctct-cttcttttgtaaact---------cgcagATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 3
-aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttgtaacaatgaagccctcaacctatgttga-aaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
   | |   ||| |  |  || | | |  | ||      | | || || |||  | |  | ||    | |      | || |   ||| ||  | | ||||||||||||| |||||||| |||||||| ||||||||||||||||| || || || ||||||
ctgcttttcttcctcaagataccgtttcaaattccagagttttttcgggttt-atgattacgacatacacggtgactctttatgcatgttcggtgt-tgcagATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G113995_T01 (Zea mays), 3'ss of exon 3
aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttg-taacaatgaagccctcaaccta--tgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
    | ||| |||   |  |  || |  |||      || | || ||||| || | |  |  |      ||   ||  | || |     || |  |  || ||||||| || |||||||| |||||||| ||||| ||||||||||| || || || ||||||
---tttcttccttgagataacattttaaattccagagttttgttgggtttatgattatgaccagttatacatggtaactctttatgcacgtttcgagttgtagATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 4
---------------------------------------------------aacatactttctt---agaagtatcttgtt----catttttttcttctatttggtttttgtaacaatgaagccctca----------acctatgttgaaa---------atg-gtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
                                                   | | |  | | ||   | ||||  ||| ||    ||| |  ||  ||  |   ||       | |   | | |  ||          | | | ||||| |         ||| ||  || ||||||||| ||||||||||||  ||||||||| ||||| || || |||||||||   || ||||||
gtgagaattagttttcatgccttttatctcggtgaaagaaaagttatgctgagcttgttgtttttcgaaaagttccttctttctccatatcattaatcagtccagtaggctggaaagaaaggtctacaggcacaaggtagcaaggttgatatatttgttgatgtgtgcatttatgcagATTTATGTTGTTGATAGCTTGGATCGTGAGAGAATAGGTAAAGCAAAGCAGGAATTTCAG

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------------------------------------------aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttgtaacaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
                                                                                                        |   | |  | | | | ||  ||||  || | |||   ||| |||   | || || | |  | |   | |  |||   | |  ||| |||     ||||||| || || || |||||||| |||||||||||||| || |||||||||  ||| ||||||
gtacgtatatagtttttttttcgatttttgctttcagtcagatacttaactttcaaggtttttccatctctatgttggcatatgttatcctatatttggttatgatgttgcagtatcatatgttgcttggccaatctttagatctttttccatctt-tatcgaccatggtataagactactct-atgatgctct-----tgcagATATACGTGGTGGATTCCTTAGATCGAGAGAGGATCGGGAAAGCAAAGCAAGAATTTCAG

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|26264563|gb|CA815626.1|CA815626
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|30296696|gb|CB973490.1|CB973490
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71879757|gb|DT028812.1|DT028812
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71880432|gb|DT029487.1|DT029487
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71880733|gb|DT029788.1|DT029788
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71878380|gb|DT027435.1|DT027435
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71880637|gb|DT029692.1|DT029692
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|30296765|gb|CB973559.1|CB973559
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71877999|gb|DT027054.1|DT027054
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|110716367|gb|EE091287.1|EE091287
EST:     TGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: TGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71880723|gb|DT029778.1|DT029778
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|33409512|gb|CF215139.1|CF215139
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|110729888|gb|EE106340.1|EE106340
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71878000|gb|DT027055.1|DT027055
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71879446|gb|DT028501.1|DT028501
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|71879383|gb|DT028438.1|DT028438
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|161707222|gb|FC055589.1|FC055589
EST:     AGAAACTCAGGCCACTCTGGAGGCATAACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGA
EST: gi|351036486|gb|FQ457199.1|FQ457199
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTCGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
EST: gi|110375930|gb|EC940960.1|EC940960
EST:     AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTG                         ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA
genomic: AGAAACTCAGGCCACTCTGGAGGCATTACTTTAATAATACTGATGGACTGgtaatcatta ... atatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttttgtaacaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG
     ttgtaac  putative branch site (score: 2)
                                          tctatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacatactttcttagaagtatcttgttcatttttttcttctatttggtttttgtaacaatgaagccctcaacctatgttgaaaatggtctatatatgcagATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
aacatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatg