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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattataggtttgattttatggggagaatatttgcaatgagtttctccaaaattaattggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA

Basic information

species Vitis vinifera
transcript Vv01s0011g02820.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
ctattataggtttgattttatggggaga-atatttgcaatga-gtttctccaaaattaattggaaat--ttgacggcatggaatatttaa--catttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
      | | |    ||| |||     | ||  ||   |||  | || |  || |  |  ||| | |  |||| |   |   |  ||| |  |  |||  ||||||   || |   |||| ||||| || ||||| || |||||||||||||| ||||||||||| || || || |||||||| |||||||||||||||||     
------ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctggtattgattgaagtattaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g30060.1 (Oryza sativa), 3'ss of exon 5
ctattataggtttgattttatggggagaatatttgcaatgagtttctccaaaattaattggaaatttgacggc-atggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
 | | ||   ||  |   |   |  |     | ||||   |   | | | |  ||| ||| || | | |      |  | |  |||   |   |  | |||   ||||||||  | || || || || ||||| || ||||||||||||||||||||||| || || || |||||||||||||| ||||| |||||| | |
ttttgatgtattataggatgctgaaatctgttctgcatgaatcatatgctatgtta-ttgaaattgtaaaatttgtatacttattagtttcccctctccagCAATCACGTCCTATAACCAAGTTTACAGAGGACTTCGATTTCATGGCAATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTCGGTAAAAGCA

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G341027_T01 (Zea mays), 3'ss of exon 5
ctattataggtttgattttatggggagaatatttgcaatgagtttctccaaaattaattggaaatttgacggcatggaatatttaa---catttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
   ||| |       | || ||     | |   |   | ||  ||||      |  | | |   |||       || | | || |    ||||  |  | |||   || | |||  | || || ||||| ||||| |||||||||||||||||||||||||| ||||| || |||||||||||||| |||||||||||| | |
--cttaaaatgcctctgttctgttttcagtccct-tgaggacattctttgttgtcgacttgcttttttttaaactgtagtcttcactgtcattctctctacagCAATCGCATCCCATAACCAAGTTCACAGAGGACTTTGATTTCATGGCAATGAATGAGAAGTTCAACAAAGATGAAGTATGGGGCCATCTTGGTAAAAGAA

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 5
---ctattataggtttgattttatggggagaatatttgcaatgagtt-tctccaaaattaattggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
     | |||  || |   ||   ||  |  ||  | | | ||| |  | |    || || ||  |  |  ||     ||  || |||     |||| ||||||   ||||   | || |||  ||||||||| || |||||||||| ||| ||||||||||| || || || |||||||||||||| |||||||||||     
gagggagtatttgtataccttg--ggaaatgatgctaggattgaataatattgttaaatagttaaatgtcagatttgttg--atgtttgtatcttgctttgcagTTTTCACAGTCTGTAACAGCATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTTGGTAAGAAAT

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 5
ctattataggtttgattttatggggagaatatttgcaatgagtt-tctccaaaattaattggaaatttgacggcatgg--aatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA-
  | |||  || |   ||   ||  |  ||  ||| | ||| |  | |      |||| | |  |  || | |  | |  ||| |||     || | ||||||   ||||   |||| |||| ||||||||| || |||||||||| ||| ||||||||||| || || || |||||||| |||||||||||||| ||||  | 
-gagtatttgtataccttg--ggaaatgatgcttggattgaataatatttgttgttaaatagttaagtgtcagatttgttaatgtttgtatcttcctttgcagTTTTCACAGTCAGTAACAACATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGG-AAAGAAAT

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
-ctat-tataggtttgattttatggggagaatatttgc-aatgagtttctccaaaattaattggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
  ||| |  |  | || ||||||          | |    ||| | || |    | |  |      | ||||   |||| || |||  |    ||| |||||||| | ||  ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||| |||
tatatctgcaaatatgcttttatttttttcccttctattgatgggattat---gattgtaacattcagttgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G17050.1 (Glycine max), 3'ss of exon 6
-ctat-tataggtttgattttatggggagaatatttgcaatgagtttctccaaaattaattggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
  ||| | ||  | || ||||||        |  || || |||     |    | |  |      | ||||   |||| || ||| ||    ||| |||||||| |  || ||||| ||||||||||| |||||||||||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||||||| |||
tatatctgtaaatatgcttttatttttct--tccttccattgatgggattatgattgtaacattcagttgagttcatgaaaaattcaattaatgctttgcagGGTTTGCGCCCAGTCACAAAATTCACAGAGGATTTTGATTTTATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G11300.2 (Glycine max), 3'ss of exon 6
-ctat-tataggtttgattttatggggagaatatttgcaatgagtttctccaaaattaattggaaatttgacggcatggaatatttaacatttgcctt-gcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
  ||| | ||  | |  |||||||       |  |    ||| | || |    | |  |      | ||||   |||| || ||| ||    ||| || |||||| |  |  ||||| ||||||||||||||||||||||||||||  |||||||||||||| ||||| |||||||||||||||||||||||||||||| |||
tatatatgtaaatatacttttatgtttttccttctattgatgggattat---gattgtaacattcagttgagttcatgaaaaattcaattaatgcttttgcagGGTTTGCACCCAGTCACAAAATTCACTGAGGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G11320.2 (Glycine max), 3'ss of exon 5
ctattataggtttgattttatggggagaatatttgcaatgagtttctccaaaatta-attggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
| |  | |   |  || || ||       | | | | ||   |      | ||||  | |    | ||||   |||| || |||| |    ||  |||||||| |  ||  |||| |||||||||||||| |||||||||||||  |||||||||||||| ||||| |||||||||||||||||||||||||||||| |||
ccagaaaattgtcaatattttgattttgttttcttctattgataagattataattgtaatattcagttgagttcatgaaaaatttgattaatgt-ttgcagGGTTTCCGCTCAGTCACAAAATTCACTGAAGATTTTGATTTCACAGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGTCATCTTGGTAAAAGTA

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------ctattataggtttgattttat-ggggagaatatttgcaatgagtttctccaaaattaattg-gaaatttgacggcatggaatatttaacatttgccttg-cagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
                                     ||   |||| |||||    ||| || || | | |   ||||    |||||   |   ||| |||  |    |    || | |   ||    ||| ||| | ||||  | ||| |  ||||||||||| |||||||||||||  |||||||| || || ||||| |||||||||||||||||||||||||| ||  |||
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctacca---gttt----aaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA

upper sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ13073 (Selaginella moellendorffii), 3'ss of exon 5
ctattataggtttgattttatggggagaatatttgcaatgagtttctccaaaattaattggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGT--AAAGGTA-
                                      |  ||||   | |  ||   |      |||  || ||  |   ||| | ||    | || |  ||   | || |   || || || || ||||| |||||||||||||| |||||||| || ||||| ||||| || || |||||| | |||||   ||||||  
-------------------------------------gtatgtttactcgagcttttcttctttcttg-tggtatttat--tttgatat----catggacagCCTTC-TCAACGTACGAACTTTACGGAGGACTTTGATTTCATGGCGATGAATGAAAAGTTCAACAAGGACGAGGTTTGGGGTGAGCTTGGAGGAAAGGTTG

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|110730095|gb|EE106779.1|EE106779
EST:     CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAAGAACANGG                         GGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
genomic: CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACAGGGgtaattttct ... tgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
EST: gi|110699080|gb|EE077314.1|EE077314
EST:     CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACAGGG                         GGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
genomic: CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACAGGGgtaattttct ... tgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
EST: gi|161714152|gb|FC064417.1|FC064417
EST:     CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACATGG                         GGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
genomic: CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACAGGGgtaattttct ... tgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
EST: gi|110685265|gb|EE063492.1|EE063492
EST:     CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACAGGG                         GGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
genomic: CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACAGGGgtaattttct ... tgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
EST: gi|110690673|gb|EE068036.1|EE068036
EST:     CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACAGGG                         GGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG
genomic: CTCCTTTCCAAGGTCGTCATGGTTACCGGGGACGTGGAAGAGGAACAGGGgtaattttct ... tgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccaaaattaattggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
                                   atttaac  putative branch site (score: 3)
                                           tttgcctt  CT-rich tract
     aaattaattggaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattataggtttgattttatggggagaatatttgcaatgagtttctccaaaattaattggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - -ttatggg
- - - - - - - - - - - - - - - - - -caatgag
- - - - - - - - - - - - - - - - - - - - - - - - - aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgga