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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA

Basic information

species Vitis vinifera
transcript Vv02s0012g02660.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 1
ttgcttgttcctgatg--tggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA
    ||  || || ||  || |  ||    |  |   || |||    ||  | | | || |  | || |  ||  || |        |   |||   | ||| |||||||  | ||||| ||| | ||  | ||||| |||||||| || ||||| ||||||||||||||||| || || ||||| || ||||| | |||  
aaatttactcttgttgtttgaaccttgcttaggtttgtaactgc-tgtgt-tgtgccttctgcgtttttgcaattctaacagcggcatccattctcctacagACGGGTGACACCCTCATACAGCTCTACAACAATTTCATCACTGATTTCGAGACGAAGATCAATCTTCTCAAACTTGCGCATTTCGCGGTCATCGCTTCGC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
---ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA
    ||  |||| |     |||||    | ||   | ||||   |       || |   |      |  |  ||  || |     ||  ||| ||     ||| | || ||  |  |||| ||| | ||  | ||||| ||| ||||||| ||||| ||||||||||||||||| || || || || || ||||| | |||  
tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcatt-cattctc--ccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 1
ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctt-tttatggttatctaa--aacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA
  | |   | ||  ||      |  | | | ||   || ||   || | |||  |  ||||   |||| |     ||  |   || |   | |  |||| ||||| ||||||||| | || || |||||||| ||||| ||||| ||||||||||| || ||||| ||||||||||| |||||||||||||| ||||||||| 
--gttgacttctattgaaacaatattcatactctg-atgtgcatattcttattatagtttaaatttatttgtttgacaaacggttcttcctataaattttcagGCTGGTGATGCTTTAATACAATTATATCACAATTTCATCACAGACTTTGAGACGAAAATCAACCTTCTCAAGCTTGCACATTTTGCTGTTATAGTTTCTC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTG--TCATAGTTTCTA-
              ||  | | | ||  ||||  ||  |  |     || |  ||||     |  |   ||   |       ||| |  ||    ||     |  |   |     |||| |  | |  |     |  |   |  ||| |||       |||      |||||     | |       |  |   ||   ||| 
-------------gtgatgctttaatacaattatatcacaatttcatcacagactttgagacgaaaatcaaccttctcaagcttgcacattttgctgttatagTTTCTCGGCAGTATTCTGAAAAAGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 1
ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctt-tttatggttatctaa--aacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA
 ||  | ||  |||     || || || | |   ||||   ||  | | |||  |  ||||    |||||     ||  ||  || |   | |  |||| ||||| ||||||||  | || || |||||||| ||||| ||||| ||||||||||| || ||||| ||||||||||| || ||||| ||||| ||||||||| 
-tgacttttattgaaaca-atatt-tgtactctgatatgcatgtgttcttattatagtttaaatgtatctgtttcacaaatggttcttcctataaattttcagGCCGGTGATGCATTAATACAATTATATCACAATTTCATCACAGACTTTGAGACCAAAATCAACCTTCTCAAGCTTGCGCATTTCGCTGTTATAGTTTCTC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
-ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA
 | | || |      | | |||    |   |||   |    ||   ||  | |  | || |    | ||       || | |  | | ||||||||| ||||| ||||||||| | |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||||||  | || ||| 
ttaggttttagggtttatagatcaattttgattgcttccaagtttttgtgtctgatcttaacctgtgtcattgttataatataattttttttcattt-cagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G19006.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgcttgttcctgat-gtggatgttatgaaattcaatatctgtgcatgcatatccttttta-tggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA
  |  | ||   | |    |||      ||| |||   |       |  | |   || ||| ||      |    | | ||  | |  ||  || ||||||||| || |||||| | || ||| | ||  | ||||| ||||||||||||||||| | |||||||||||| ||||| || ||||| |||||  |||| ||  
-cgaatattttagctcagagatacccaaaaactcagctttacaaggtttacagatttgttaatgacgtgtttccccctgtttatgttcataatc-tttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAGACGAGGATCAATCTTCTGAAGCTTGCGCATTTCGCTGTTGTAGTCTCCC

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S131_74V6.1 (Physcomitrella patens), 3'ss of exon 1
--------ttgcttgt-tcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA
        | | || | | ||   |||| | |||| |   |   |||  |||||   || |           | || |  |   |||  ||| ||     |  ||||||||||| ||| | ||  | ||| |||||||||| |||||    ||||||||||| ||||||||| | || |||||||| || ||||||||||| || || |
atcagagatggattttattctttggtggctcttattagggttggtat--gtgca---atttgtcacaagaactgatgttgagggtatggtttggtg----cgattgcagGCGGGGGATACCCTTGTACAGCTATATCATAACTTTATTCGGGACTTTGAGACCAAGATCAATTTGCTGAAGCTCGCCCACTTTGCTGTCATCGTATCGA

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|349823515|gb|FQ414925.1|FQ414925
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|351014718|gb|FQ437918.1|FQ437918
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110711237|gb|EE087522.1|EE087522
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110712189|gb|EE089526.1|EE089526
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110719329|gb|EE097178.1|EE097178
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110713457|gb|EE089396.1|EE089396
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|294965380|gb|GW837095.1|GW837095
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCGG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|351030871|gb|FQ438907.1|FQ438907
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110713832|gb|EE090100.1|EE090100
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110711790|gb|EE088671.1|EE088671
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|351027874|gb|FQ448444.1|FQ448444
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110729815|gb|EE106179.1|EE106179
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110711621|gb|EE088310.1|EE088310
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|161713729|gb|FC063754.1|FC063754
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATGACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|161720766|gb|FC070274.1|FC070274
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAACTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|351043427|gb|FQ451479.1|FQ451479
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110712204|gb|EE089557.1|EE089557
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|110711432|gb|EE087905.1|EE087905
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|349825445|gb|FQ419362.1|FQ419362
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|349825607|gb|FQ421706.1|FQ421706
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
EST: gi|161718279|gb|FC066030.1|FC066030
EST:     ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAG                         GCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG
genomic: ACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttccc ... tcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA
                    atctaaa  putative branch site (score: 3)
                                ttcttttgtattttc  putative PPT
                  ttatctaaaacttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
-tgcttgt
- - - - - - - -gtggatg
- - - - - - - - - - - - - -aaattcaa
- - - - - - - - - - - - - - - - - - - - - gcatgca