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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC

Basic information

species Vitis vinifera
transcript Vv02s0025g00310.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g35090.1 (Oryza sativa), 3'ss of exon 2
gtatcttacttat-tctctcactttaaccacgatttgctgtga--ttcagtgtgttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
      |  |  | | | ||| |  | |       |||   ||   |||   ||    || || ||  |  |  | || | ||  | |||  | |      || | ||||||||||    ||||| || ||||||||||| || ||||| || ||  | |||||||| ||||| |||||||| |||||| | |||||||||||||||||
---cgctgttggtgtatgtcagtacagcgttcgcatgccaagaggctcaaactgaaagtgattgtaggtgctggttttaacttggtgtatgctgt------tgttgcagAGGGAGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCGAACCTGCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G43110.1 (Glycine max), 3'ss of exon 2
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
                                    | || | | |   |  || |  | || |  | |    |||  |||| ||  |      |||||| ||||||||||||||||| |||||| ||||||| |||||| ||||| || || || || ||||| |||||||||||||| || ||| |||||||||||||||| ||
----------------------------------gtccgttagttaacattgtc-tcctcttgtgctttacggttgtgtttaaattgtaacgtgtgtttgattcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATCTGGCGAAGCACCCGGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATC

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G02410.2 (Glycine max), 3'ss of exon 2
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
                          ||   | ||    |  ||  || |  || |||  || |    || | || |  || ||   | | | | ||||| ||||||||||||||||| |||||| ||||||| |||||| || || || || || || ||||| |||||||||||||| || ||| |||||||||||||||| ||
------------------------gtccgttagttaacattgtt--gtctcctcttgtgctt-tacagttgtgttaaaattgtaaggtgtgtgt-gtttgattcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATC

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 2
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC--------------------
                          ||   | ||    |  ||  || |  || |||  || |    || | || |  || ||   | | | | ||||| ||||||||||||||||| |||||| ||||||| |||||| || || || || || || ||||| |||||||||||||| || ||| |||||||||||||||| ||                    
------------------------gtccgttagttaacattgtt--gtctcctcttgtgctt-tacagttgtgttaaaattgtaaggtgtgtgt-gtttgattcagagggagtttgctttgcgaagAAGGACTTCAATCTGGCAAAGCACCCAGAGATTGATGTGCCGAATCTGCAGGTGATAAAGCTGATGCAGAGCTTCAAATCCAGAGAGTATGTGAGGGAGA

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G02070.1 (Glycine max), 3'ss of exon 2
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatata-ttttttcttgtt--tgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
                            | |       |   |||| || | | | || |     ||     ||  || |||  |  |||||||||  |   | | ||||||||||||||| |||||| ||||||| |||| | ||||| || || || || || || |||||||||||||| || ||| |||||||||| ||||||||
--------------------------gtaggtgccttagaatttcattggggttacgtctcg---ttgaagaatgaatcttaccttcttttttcttaatgtcggtgcagAGGGAGTTTGCTTTGCGAAGAAGGACTTCAATTTGGCGAAGCACCCTGAGATTGACGTGCCGAATCTGCAGGTGATTAAGCTGATGCAGAGTTTCAAGTC

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G37470.1 (Glycine max), 3'ss of exon 2
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatatattttttct-tgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
            | |  |  | || | ||||| |     |  |||  |  | | | || |     ||     ||  || |||  | |  ||  | | | || | |||||||||||||||  ||||| ||||||| |||| | || || || || || ||||| || |||||||||||||| || ||| |||||||||| ||||||||
-------gtaggtgccttagcatttatcacgaatcatcttcgttcgttagggttacgtctcg---ttgaacaatgaatcttacctttcgttggtgtttatggtgcagAGGGAGTTTGCTTCGCGAAGAAGGACTTCAATTTGGCCAAGCACCCTGAGATCGACGTGCCGAATCTGCAGGTGATTAAGCTGATGCAGAGTTTCAAGTC

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G41520.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgatt--------ttatat---------------attttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGA---TGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
||| | |  | |||    |   | || |  | | |  | |   | | || ||| |||  |     ||  ||  ||||||        || ||                |||  ||||| ||   | ||||||| ||||  | ||| |||||||| | |||  |  |  |||||||    || ||   ||| || |||||||| |||||||||||||||||||| |||||   
gtaccattttgatttgagcttatgaatctagttgtcttctacgttaatgggtttatgcatgatgattgattggttgattcaagagaattgtacttagaaatggttggaattggttctttttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGATTGAGAGTGTTCCAAATCTGCAAGTTATCAAGTTGATGCAGAGTTTCAA---

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G41520.2 (Arabidopsis thaliana), 3'ss of exon 2
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgatt--------ttatat---------------attttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGA---TGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
||| | |  | |||    |   | || |  | | |  | |   | | || ||| |||  |     ||  ||  ||||||        || ||                |||  ||||| ||   | ||||||| ||||  | ||| |||||||| | |||  |  |  |||||||    || ||   ||| || |||||||| |||||||||||||||||||| ||||| | 
gtaccattttgatttgagcttatgaatctagttgtcttctacgttaatgggtttatgcatgatgattgattggttgattcaagagaattgtacttagaaatggttggaattggttctttttgtgtgcagagGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGATTGAGAGTGTTCCAAATCTGCAAGTTATCAAGTTGATGCAGAGTTTCAAAT-

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ29946 (Selaginella moellendorffii), 3'ss of exon 1
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
                       | |    ||| |    |      | | | ||  | |      ||  |     ||    || | |      ||||| |   ||||||| ||   ||| || || ||||||||||||||| | || || || || ||||||||||| ||||| ||||| |||||| | |||||||||||||||||
----------------------gtgag-gggatctagcttctcctggcgcgctcgcgctcacgcatttctaatccga---gatttctccccaattgttcggcgcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC

upper sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ25099 (Selaginella moellendorffii), 3'ss of exon 1
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgt-gttcatgtttttattttattttattgattttatatattttttc--ttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
                                      ||||     | | | ||  |  ||| |    ||||  | ||   | || | |   |  ||||| |   ||||||| ||   ||| || || ||||||||||||||| | || || || || ||||||||||| ||||| ||||| |||||| | |||||||||||||||||
--------------------------------------gtgaggggatctagctcgcgcatttctcccttttttctaatccgagatttctccccaattgttcggcgcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCTCCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC

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|37189141|gb|CF608490.1|CF608490
EST:     ATTATTCCTGAGAAGAACCGCAGGGAGATCTCCAAGTATCTCTTTCAAG                         AGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATA
genomic: ATTATTCCTGAGAAGAACCGCAGGGAGATCTCCAAGTATCTCTTTCAAGgtatcttact ... tttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
                    tattgat  putative branch site (score: 3)
                                   ttttttcttgtttgct  putative PPT
      tttttattttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgattttatatattttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGATGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT