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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattggcacttcttatatattattgtttgctcatcaaaaaaatgttttatacccccaactgtagtgccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA

Basic information

species Vitis vinifera
transcript Vv08s0007g03850.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g19190.1 (Oryza sativa), 3'ss of exon 1
ttgattggcacttcttatatattattgtttgctcatcaaaaaaatgttttatacccccaactgtagt-gccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
 | | |  || ||  | |  | |    ||  |   |       |  ||||||    |    | | || | |||   |   || ||    |||  || |||||| ||||| || ||  | || ||||| || || || |||||||||||||||||||||||||| || ||||||||||| || |||||| | |||||||| |
-taaataacattttatgttgaatgccattcacgtttacgttttagattttattgtgctggatattgttggcacatttagttacatttatttctgttcgcagATCTTTCGCTTTTGCCGGTCAAAATGTCATAAAAATTTCAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCGTACAGGTGCTTGCATGGGA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g33050.2 (Oryza sativa), 3'ss of exon 1
ttgat-tggcacttcttatatattattgtttgctcatcaaaaaaatgttttatacccccaactgtagtgccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
   || |  || || || |   ||   | |    | |   |    | |   |  |       ||| |     ||  |  | | ||  | || |  | |||||| || || || ||  | || |||||||| || || || ||||||||||||||||||||||| || ||||||||||| || |||||  | |||||||| |
ggaatgtaacattttttttcccttgcagatcttcccttgcattcctataacaagctggattttgtcggtatgctg-taacaacattttttttcccttgcagATCTTCCGCTTTTGCCGGTCAAAATGCCATAAAAATTTTAAGATGAAGAGGAATCCTCGTAAGGTTAAATGGACAAAAGCATACAGATGCTTGCATGGGA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G19410.1 (Glycine max), 3'ss of exon 2
ttgattggcacttcttatatattattgtttgctcat---caaaaaaatgttttatacccccaactgta-gtgccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
 || | | ||      |   || | ||  |    ||   || |       || |   | |       |  |    |   || || |  | ||||| |    |||||||||||||| |||||||||||||||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||| || || ||  |||||||||
ctggtagacatccaagagtaatgaatgactatgtatgttcatagctccacttcacttcacatggcacatataattcaggtttctgacaactgttctt----cagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTCAAAATGAAGAGGAACCCTCGGAAAGTAAAATGGACAAAGGCATATAGACGAGTGCATGGAA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G30680.2 (Glycine max), 3'ss of exon 2
ttgattggcacttcttatatattattgtttgctcatcaaaaa---aatgttttatacccccaactgtagtgccac-tacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
 | |||     |  ||   | || ||||| | |||    | |   | ||||||| |       ||   || || | |  ||| | | |  | ||  ||| ||||||||||||||| |||||||||||||||||||||||||| || |||||||| ||||||||||| ||||||||||| ||||| ||  | ||  |||||||||
gtaattatg--taattgattgttcttgttggatcagttgagatttactgttttaaagtggtggctcaggttcctcatgattctttatt--tttttgttttgcagATTTTTCGGTTTTGTAGATCTAAATGCCACAAGAACTTTAAAATGAAGAGAAATCCTCGTAAGGTAAAATGGACCAAGGCATATCGTCGAGTGCATGGAA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G09780.1 (Glycine max), 3'ss of exon 2
ttgattggcacttcttatatattattgtttgctcatcaaaaa---aatgttttatacccccaactgtagtgccac-tacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
 | |||     |  ||   | || ||||| | |||    | |   | | ||||| |       ||   || || | |  ||| | | |  | ||  ||| ||||||||||||||| |||||||||||||||||||||||||| || |||||||| ||||||||||| ||||||||||| ||||| ||                 
gtaattatg--taattgattgttcttgttcgatcagttgagatttactattttaaagtggtggctcaggttcctcatgattctttatt--tttttgttttgcagATTTTTCGGTTTTGTAGATCTAAATGCCACAAGAACTTTAAAATGAAGAGAAATCCTCGTAAGGTAAAATGGACCAAGGCATATC---------------

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G09090.1 (Glycine max), 3'ss of exon 2
ttgattggcacttc----ttatatattattgtttgctcatcaaaaaaatgtttta-tacccccaactgtagtgccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
 || | | |||       | ||  |||||| | |     ||| | |     |  | | | |   ||    ||    |   || || |  | ||||| |    |||||||||||||| |||||||||||||||||||| ||||| || ||||||||||| ||||| |||||||||||||||||||| || || ||  |||||||||
ctggtagacacccaagagtaatgaattattatgtatgt-tcatagatccactccacttcacatgacacatgtaattcaggtttctgacaactgttctt----cagATTTTTCGGTTTTGTAGATCTAAATGCCACAAAAACTTTAAAATGAAGAGGAACCCTCGGAAAGTAAAATGGACAAAGGCATATAGACGAGTGCATGGAA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G05270.1 (Glycine max), 3'ss of exon 2
-ttgattggcacttcttatatattattgtttgctcatcaaaa---aaatgttttatacccccaactgtagtgccac-tacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
  |  |||    |  ||   | || ||||| | |||    |    || ||||||| |       ||    | || | |  ||| |   |  | ||  |||  |||||||||||||| |||||||| ||||||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||||| ||  | ||  |||||||||
agtagttgtg--taattgattgttcttgttggatcagatgagattaactgttttaaagtggtggctcagattcctcatgattctt---tgttttttgttttccagATTTTTCGGTTTTGTAGATCAAAATGCCACAAGAACTTTAAAATGAAGAGAAATCCTCGTAAGGTAAAGTGGACCAAGGCATATCGTCGAGTGCATGGAA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S43_13V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------ttgattggcacttcttatatattattgtttgctcatcaaaaaaatgttttatacccccaactgtagtgccactacttcctaaatagtgttcctttg-gcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
                                    || |     ||  |  | || ||| ||    |   |   | | | |    |   |||| | ||    |||  |       || |     || | |||| ||| |||| ||  | || |||||||||||||| || ||||||||  ||||||||||||| || || ||||| || || || |||  | | || || |
gtctgtttgctctcccaatgtggattcctatgctgctgacgtgatttggagttcat-gttggcgtggctgtaggttttgtgactgacgatactgaaatgttcgtacgcctctgtctgtttggtcatgcgaagATATTTAGGTTTTGCCGGTCGAAATGCCACAAGAATTTTAAGATGAAACGGAATCCTCGTAAGGTGAAGTGGACCAAAGCGTATAGGAAGCTTCACGGCA

upper sequence: Vv08s0007g03850.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ21089 (Selaginella moellendorffii), 3'ss of exon 1
ttgattggcacttcttatatattattgtttgctcatcaaaaaaatgttttatacccccaactgtagtgccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
                                             || | |   |  | |    ||        |    || | | |       |   |||| ||||| |||||  | || || ||||||||||| |||||||||||||| |||||||| || || || ||||| |||  |||  |   | | || || |
---------------------------------------------gtatgagcgcttcgatcacagatttctcgcgaaatataaaatcgctggctcttagATCTTTCGATTCTGCCGCTCCAAGTGCCACAAGAATTTCAAGATGAAGAGAAATCCTCGCAAGGTGAAGTGGACGAAGATCTATCGCAAGCTCCACGGCA

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|26262309|gb|CA813372.1|CA813372
EST:     CCACTGTATATCCAGGNCATGG--TTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|71876723|gb|DT025778.1|DT025778
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|71890437|gb|DT039492.1|DT039492
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|110418414|gb|EC984567.1|EC984567
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|351028971|gb|FQ434972.1|FQ434972
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|77587193|gb|DV222731.1|DV222731
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|71868891|gb|DT017946.1|DT017946
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|71866642|gb|DT015697.1|DT015697
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|110375172|gb|EC940133.1|EC940133
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATATAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
EST: gi|349823493|gb|FQ414903.1|FQ414903
EST:     CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAG                         ATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG
genomic: CCACTGTATATCCAGGGCATGGTATTCAGTTTGTTCGCAATGATGCCAAGgtagagaagt ... cctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttatacccccaactgtagtgccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA
                               tcctaaa  putative branch site (score: 2)
                                         tgttccttt  putative PPT
                                  taaatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattggcacttcttatatattattgtttgctcatcaaaaaaatgttttatacccccaactgtagtgccactacttcctaaatagtgttcctttggcagATTTTTCGGTTCTGTAGATCTAAATGCCACAAGAACTTCAAGATGAAGAGGAATCCTCGTAAAGTAAAATGGACAAAGGCCTACAGGCGGTTGCATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
-tgattgg
- - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -taccccc