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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagtcaacttaagtaattaagtaataattattaagttttaccaaatgcccacttagtctctgtttaacttttgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG

Basic information

species Vitis vinifera
transcript Vv06s0004g02820.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 2
----------aaagtcaacttaagtaattaagtaataattattaagttttaccaaatgcccacttagtctctgtttaacttttgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG
          |    |  || |   ||    ||  | |||  |   |  || |   | |     | |   |           ||  || |   ||| ||  |   |  || |||||||| || |||||||| || || || |||||||| |||||||| |||||||| ||||||||||||||
gttagtgtttatcaactcctcacacaaactcgtcttgattgctgt-tcatatctctttctgggattgctacctcaagcaacatgactcgtacctctatttcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 3
--aaagtcaacttaagtaattaagtaataattattaagttttaccaaatgcccactt----agtctctgtttaacttt---tgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG
   |  |    | || |  | |   ||       |   ||       ||  |   ||      |  |||  |||       ||  || ||  ||| ||  |   |  || |||||||| || |||||||| || || || |||||||| |||||||| |||||||| ||||||||||||||
gttagtttttatcaactgctcacacaaactccccttgattgctgttcatatctctttctcggattgctgcctaaaacaacatgactcattcctctatttcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 2
----------aaagtcaacttaagtaattaagta-ataattattaagttttaccaaatgcccacttagtct----ctgtttaacttttgtttcttttttctttta----ttacatca---agATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG
              |||  || | |  | |  || | |||  ||   || |      |  |   |||   |    ||| || ||| | ||| | |||   |||||    ||  |||    |||||||||||||| || ||||| || ||||| ||||| ||  | |||||||| ||||| ||||||||||||||
gtttagacatttcttcatattgaatcgtcagctagagaatggttgtattgtggggtttatcgttttaacttttaactgatttactctcgttgcatttcgtttttaatcgttgtatcgtttagATATGGAGATGAACATAAGCTTGCTGGATTTTCAGCTACTCTTCAAGCTATTATTTCTTTTGTGGAGAATGG

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S55_143V6.1 (Physcomitrella patens), 3'ss of exon 4
--aaagtcaacttaagtaattaagtaata-attattaagttttaccaaatgcccacttagtctctgtttaacttttgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG
   |   |        ||||||   | |  | ||||  |||     |  |      ||||  ||| || | ||  | |   |   |    || ||      ||||| || |||||||||||||| ||||| |||||||| ||||||||||||||||| || ||||| || ||  |
tctattccgggagggataattatccattttagtatttcgttacgttagtt--ttgattaggttct-ttaacctgatatcattccgtgtggtttttttgagcagATACGGGGATGAGCACAAGCTTGCAGGTTTCTCAGCGACATTGCAAGCTATCATGTCTTTTGTTGAAAACAG

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S452_21V6.1 (Physcomitrella patens), 3'ss of exon 4
aaagtcaacttaagtaattaagta-----ataattattaagttttaccaaatgcccacttagtctctgtttaacttttgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG
     ||| |   ||  |||  ||       ||| | ||  | |    ||||    |  || | | | |||     |  |  | | |   || | ||      |||||||| ||||||||||| |||||||| |||||||| ||||| ||||||||||| || ||||| || ||| |
--tagcaattcttgtgtttatatacgttggaaatgactatatatataaaaatatatatgta-tatatattttgaggtcatcccatgtgatttcttttgagc--agATATGGGGATGAGCACAAACTCGCAGGTTTCTCAGCGACATTACAAGCTATCATGTCTTTTGTTGAAAATAG

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ34812 (Selaginella moellendorffii), 3'ss of exon 3
aaagtcaacttaagtaattaagtaataattattaagttttaccaaatgcccacttagtctctgtttaacttttgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG
                                               |     ||  ||||||||       ||||  |  | ||  || ||      ||||||||||||||||||||| | || || ||||| |||||| | || || ||||| ||||||||    | | |
-----------------------------------------------gtgtggtttttctctgttgctacgctgttcttgatctccattgttt-----agATATGGAGATGAGCACAAGTTGGCTGGCTTCTCCGCAACACTACAGGCAATCATGTCGTTTGTAATAACTAG

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ23517 (Selaginella moellendorffii), 3'ss of exon 3
aaagtcaacttaagtaattaagtaataattattaagttttaccaaatgcccacttagtctctgtttaacttttgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG
                                               |     ||  ||||||||       ||||  |  | |   || ||      ||||||||||||||||||||| | || || ||||| |||||| | || || ||||| ||||||||    | | |
-----------------------------------------------gtgtggtttttctctgttgctacgctgttcttgatcttcgttgttt-----agATATGGAGATGAGCACAAGTTGGCTGGCTTCTCCGCAACACTACAGGCAATCATGTCGTTTGTAATAACTAG

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|110699831|gb|EE077188.1|EE077188
EST:     AAGAAGCACTTTTTCATTCTGAGTCACTCTGGGAAACCAATATATTCCAG                         ATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTAT
genomic: AAGAAGCACTTTTTCATTCTGAGTCACTCTGGGAAACCAATATATTCCAGgtgtggttct ... ttacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcccacttagtctctgtttaacttttgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG
                 gtttaac  putative branch site (score: 3)
            tctctgtttaactttt  CT-rich tract
                  tttaacttttgtttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagtcaacttaagtaattaagtaataattattaagttttaccaaatgcccacttagtctctgtttaacttttgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
aaagtcaa
- - - - - - - - - - - - - - - - - - - -taccaaa
- - - - - - - - - - - - - - - - - - - - - - - - cccactt