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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctcttggaaatgttcttttgtagattaatgtaatttatgatatatctggggatagtaggggtattagtgttttgatatcatctttctattaatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGGTGACAGCTACTATGAGTACTTAATTAAAGTGTGGCTTCAGCAGGGAGCT

Basic information

species Vitis vinifera
transcript Vv10s0003g03280.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g11850.1 (Oryza sativa), 3'ss of exon 2
----------------------tttctcttggaaatgttct---tttgtagattaatgtaatttatgatatatctggg-----gatagtaggggtattagtgttttgatatcatctttctattaatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGGTGACAGCTACTATGAGTACTTAATTAAAGTGTGGCTTCAGCAGGGAGCT
                      | | | |||| | |    |   ||   |   || || | | | | |   ||| |       |||| | | |||  |  || | | ||      |||||||  |||||| ||   ||||||| |||||| |||||||||||| || || ||||| ||||||||||| |||||||| ||| || | ||||| ||| ||||||| | |   
gtatgcattgcttgaacccttctgtgttttggcactaaattaagttcagaatatattgcattgtctaac-catcagaaaaattgatatttgaggtgattatgctctcattattgttttctat--atgcagTCCCTCCTCTGGTCAATTTAGTGGAGAAAATATTCGATTAGGATCTCGTGGTGACAGTTACTATGAATACCTATTGAAAGTATGGGTTCAGCAAGAAAGA

upper sequence: Vv10s0003g03280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G28910.2 (Glycine max), 3'ss of exon 2
tttctcttggaaatgttcttttgtagattaatgtaatttatgatatatctggggatagtaggggt--attagtgttttgatatcatctttctattaatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGGTGACAGCTACTATGAGTACTTAATTAAAGTGTGGCTTCAGCAGGGAGCT
     |       | || ||||||    |   |   | | |  | | |       | ||     |  | |    ||| ||||||     |   | ||||||||||||| ||||||||||||| ||||||||||||  |  ||||||| ||||||||||| ||||||||||||||||| ||||| |||||||||   ||||||
--caccccaattgtttttttttgtcacctttaggcttgtgtcttcttttcttttctcgtcattttctactgacttttagatatctctaataactaaatgcagCCCTCATTCTGGTGAATTTAGTGGAGAAAATATTAGACTGGGATCTCGTGGTGACAGTTACTATGAGTACTTAATCAAAGTATGGCTTCAGAGTGGAGCT

upper sequence: Vv10s0003g03280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G10130.1 (Glycine max), 3'ss of exon 2
------tttctcttggaaatgttcttttgtagattaatgtaatttatgatatatctggggatagtaggggtattagtgttttgatatcatctttctattaatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGGTGACAGCTACTATGAGTACTTAATTAAAGTGTGGCTTCAGCAGGGAGCT
       || | ||     | |    || |||  |  |||  ||| |  | | |||    ||  |     || |    ||| ||||||     |   | ||||||||||||| |||||||| |||| ||||||||||||  |  ||||||| ||||| ||||| ||||||||||||||||| ||||| |||||||||   ||||| 
accccaattgttttttttttatcacctt-taggcttgtgtctttttttcttt-tctcatcattttc----tactgacatttagatatctctaataactaaatgcagCCCTCATTCTGGTGAGTTTAGTGGAGAAAATATTAGACTGGGATCTCGTGGGGACAGTTACTATGAGTACTTAATCAAAGTATGGCTTCAGAGTGGAGCA

upper sequence: Vv10s0003g03280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G30000.1 (Arabidopsis thaliana), 3'ss of exon 2
tttctcttggaaatgttcttttgtagattaatgtaat--ttatgatata---tctggggatagtaggggtattagtgttttgatatcatctttctat-taatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGGTGACAGCTACTATGAGTACTTAATTAAAGTGTGGCTTCAGCAGGGAGCT
  |   | |    || |||||     || |||   ||  |  | || |    ||    | |     |||   |  || | |||  |  | ||||||  |  |||||||||||  | ||||| |||  ||| || |||||| | |||||||| |||||||| |||||||||||||| |||||||| |||||||||||||| ||||||
-gtaattcgtgtttgctctttcaactataaataccatgctagtaatttgctttcccttgctttcccgggctcttttgatctgacttgttgtttctacctggtgcagCCCTCAAACAGGTGACTTTGTTGGTGAGAATATCAGGTTGGGATCTCGTGGTGATAGCTACTATGAGTATTTAATTAAGGTGTGGCTTCAGCAAGGAGCT

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|30134610|gb|CB919948.1|CB919948
EST:     CATTTAAAGACTCTTCCAAAGGTGGAGGGACTGGTTCCAATCTATATAAG                         CCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGG
genomic: CATTTAAAGACTCTTCCAAAGGTGGAGGGACTGGTTCCAATCTATATAAGgtattggcat ... attaatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGG
EST: gi|110359036|gb|EC919849.1|EC919849
EST:     CATTTAAAGACTCTTCCAAAGGTGGAGGGACTGGTTCCAATCTATATAAG                         CCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGG
genomic: CATTTAAAGACTCTTCCAAAGGTGGAGGGACTGGTTCCAATCTATATAAGgtattggcat ... attaatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctggggatagtaggggtattagtgttttgatatcatctttctattaatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGGTGACAGCTACTATGAGTACTTAATTAAAGTGTGGCTTCAGCAGGGAGCT
                                            tattaat  putative branch site (score: 2)
                                      tctttctatt  CT-rich tract
                                     atctttctattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctcttggaaatgttcttttgtagattaatgtaatttatgatatatctggggatagtaggggtattagtgttttgatatcatctttctattaatgcagCCCTCACTCTGGTGAATTTAATGGAGAAAATATCCGTTTGGGATCACGTGGTGACAGCTACTATGAGTACTTAATTAAAGTGTGGCTTCAGCAGGGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- -ctcttgg