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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgagaaatgatgggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT

Basic information

species Vitis vinifera
transcript Vv02s0012g00530.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 3
actgagaaatgatgggttgaacaatctacgtcatttctaaattg-gatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
|      | ||  |   |   |||| |     |    |   ||  |   |   |   |  |  | |  | | | ||     |    | |  | || ||||| ||||||| |||||||| || || || |||||||| || ||| | || ||  |||| |||||| ||||||| ||||  ||||||||||||||  | ||  
agaatatattgtcgaagttctcaatttgttgaagacttgtgttatggcacagcactctggctagcatgtcaaaactaacaaaagcatttcctgct-ttcagTCTCAAGGCCGTGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACAGAAGCTGGTGCGAACCGTGTCCTTGTATGTGATCTTCATTCCAGTCAAG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G16400.3 (Glycine max), 3'ss of exon 3
-actgagaaatgatgggttgaacaa--tctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
 | |||    |  |   || |      | | | |  || || |||  ||||  || ||||    | || ||   |         | ||   |  |||||  ||||||||||||||||||| ||||| |||||||||||||| ||  |||| || ||||| || || |||||||||||||||||||| |||||||| |||||||
tattgaatttttttacctttagttggttttgcatttttgctcaat--gatgtgagcaattggattttacatggaactaatggagtttgc-ctcctctctatagACTCAAGGGCGTGAATCAATTGCGGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTTGCTTGTGACCTTCATTCAGGGCAGT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G06110.1 (Glycine max), 3'ss of exon 3
-actgagaaatgatgggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
 | |||    |  |   || ||     |    |||||        ||||  |  || |    |  | ||  || ||  |  | || | ||   |||  ||||||||||| |||||||| ||||| |||||||||||||| ||  |||| || ||||| || || ||||||||||| |||||||| |||||||| |||||||
tattgaatttttttaccttcaattggtttttgcattttgcttgatgatgtcaacaaatgggtttcacat-gcaactaatggagcttttttcccctcggcagACTCAAGGACGTGAATCAATTGCTGCTAAACTTGTTGCGAACCTTATTACAAAAGCTGGGGCAGACCGTGTTCTCGCTTGTGACCTTCATTCAGGGCAGT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G35390.3 (Arabidopsis thaliana), 3'ss of exon 2
--actgagaaatgatg-ggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttct--------tcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
  |  |     |  || |||| | | |  | |      | |  |  |  || |   || |||  | |   | |  | ||||        |  | ||| ||  |   | ||||| |||||||||||||||||||| || ||| | ||||||||| |||||||  |||| ||||| || || ||||||||||||||||||||||| || ||||
gtaaagtctctttgtgtggtttagctactttcacatgatatggagggtttgttgataacttagctattggtaatcttttctggataaaattgtatgttttgctgcttgcagACACAAGGGCGTGAATCCATTGCTGCCAAATTGGTTGCAAATCTTATCACTGAAGCTGGTGCAGATCGAGTTCTTGCTTGTGATCTTCATTCAGGACAGT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G32380.1 (Arabidopsis thaliana), 3'ss of exon 3
actgagaaatgatgggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
                  | |   |||   |   ||||  | |||  | || |   |  || |||| || |||||  |  ||||  |||  | | ||||||| |||||||||||||| ||||| || ||| | || |||||  |||| ||  |||| ||||| ||  | ||||| ||||||||||||||||| || || |
------------------gtaggttctttttgtcttcttcaatggtagatacagtatgtcaagtaattt-catctgatgtatct--attgatgttttcagACACAAGGGCGTGAATCTATTGCTGCCAAATTGGTAGCAAACCTTATAACAGAAGCCGGTGCAGATAGGGTTCTGGCTTGTGATCTTCATTCAGGACAAT

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ12994 (Selaginella moellendorffii), 3'ss of exon 2
actgagaaatgatgggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
                                          | |   || |  ||  |  | |   || ||   |   | || || |  |  | ||||||||||||| |||||||| |||||||| || ||||| |||||| || | ||  |||| |||||| ||||||||||||| || ||  | || || |||||| 
-----------------------------------------gtagtcact-gtgatccagctttttctttcaatctacacgtc-gtgtgatgtttttcagACTCAAGGACGTGAATCGATTGCAGCAAAGCTTGTAGCAAATCTTTTGACAGAAGCCGGTGCGAACCGTGTTCTTGCATGCGACTTACACTCGGGGCAGG

upper sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ14005 (Selaginella moellendorffii), 3'ss of exon 2
actgagaaatgatgggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
                                          | |   || |  ||  |  | |   || ||   |   | || || |  |  | ||||||||||||| |||||||| |||||||| || |||||||||||| || | ||  |||| |||||| ||||||||||||| || ||  | || || |||||| 
-----------------------------------------gtagtcact-gtgatccagctttttctttcaatctacacgtc-gtgtgatgtttttcagACTCAAGGACGTGAATCGATTGCAGCAAAGCTTGTTGCAAATCTTTTGACAGAAGCCGGTGCGAACCGTGTTCTTGCATGCGACTTACACTCGGGGCAGG

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|351052954|gb|FQ453941.1|FQ453941
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATGGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|351033460|gb|FQ462111.1|FQ462111
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|161719281|gb|FC064821.1|FC064821
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTG
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTG
EST: gi|110376340|gb|EC941395.1|EC941395
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|30253361|gb|CB970912.1|CB970912
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|30253440|gb|CB970991.1|CB970991
EST:     CAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|110698297|gb|EE075660.1|EE075660
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|352789974|gb|FQ479584.1|FQ479584
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|30129654|gb|CB914993.1|CB914993
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|161721761|gb|FC071122.1|FC071122
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|351030850|gb|FQ438886.1|FQ438886
EST:     CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAG                         ACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC
EST: gi|110719024|gb|EE096529.1|EE096529
EST:     CTGTCACAGCAGTAGTTTCGTATTTTGGCTATGCCAGATCTGAAA-AAAG                         AATCAAGGGCCTGAATCCATTGCAGCCAAACTTGTTGCAAAGGTTATCACC
genomic: CTGTCACAGCAGTAGTTCCGTATTTTGGCTATGCCAGATCTGATAGAAAGgcaagtttta ... ttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT
                         catcttcttcatctgt  CT-rich tract
       aaatttacatgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgagaaatgatgggttgaacaatctacgtcatttctaaattggatgctagaaatttacatgtaaattacatcttcttcatctgtatttttctcttcagACTCAAGGGCGTGAATCCATTGCAGCTAAACTTGTTGCAAATGTTATCACCAAAGCAGGTGCGGACCGTGTTCTTGCTTGTGATCTTCATTCTGGGCAGT

- - -gaaatga
- - - - - - -gggttga
- - - - - - - - - - - - - - - - - - - - - -ggatgct
- - - - - - - - - - - - - - - - - - - - - - - - - agaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtaa