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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactggatacagttaggaattggctgtgcagattttgtagttccataaatggtcttatgttacagcatgtcaagtttctaaccatatttccatcctgcagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTATGTAGATTTGAAG

Basic information

species Vitis vinifera
transcript Vv06s0004g04940.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G14760.1 (Glycine max), 3'ss of exon 8
----------------------------------------------------------------------------gactggatacagttaggaattggctg--tgcagatttt-------gtagtt-ccataaatggtcttatgttacagcatgtcaagtttctaaccatatttccatcctg--------cagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTATGTAGATTTGAAG
                                                                            |  ||      ||    ||||| |||  ||| | ||||       |||| | ||   |  | |    | | |||     |  |  |  |     ||||| | |            ||||||||||||||| || ||  | ||||||||||||||||| || || || ||||| |||||||||
gtaagatttacattagacttggtttggcttgacaattatatttaatgggttgtgtgtgtactctatcttgttgctagtatgtgggtggtagataattgtctgtctgctgttttttcaatgagtagatgccgggagagattccctctaacaatccctttacatcttgtttttattttcttaaaaaataaaatcagGTGGCGTGATGTTAAGCTTTGTGCTTTTGATAATGCAAATCATCGGACATATGTGGATTTGAAG

upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 8
gactggatacagttaggaattggctgtgcagattttgtagttccataaatggtcttatgttacagcatgtcaagtttctaaccatatttccatcctg-----cagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTATGTAGATTTGAAG
            ||  |  ||   || | |  |     | ||   ||  | |  ||   ||    ||   |   | | |       |||      ||     ||||||||||||||| ||||| |  ||||||||||||||||| || || || || || |||||||||
-----atcgtgtttttgccttacttgagtacctgggagatttatttattttgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG

upper sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G07540.1 (Arabidopsis thaliana), 3'ss of exon 7
--gactggatacagttaggaattggctgtgcagattttgtagttccataaatggtcttatgttacagcatgtcaagtttctaaccatatttccatcctgcagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTATGTAGATTTGAAG
   |||  ||    |  |         ||  |    ||  | |||||| |||  | |  |   | |   |   ||| || |      || || ||| |||||||||||||| || ||| ||||||||||||||||||| || ||||| ||||| || |||||||||
gtaactaaattttttatgttcaccaaagtataagactta-atttccatcaataat-tggttcaagatagttctaagattgttgt-gcatatctatc-tgcagGTGGCGTGACGTAAAATTGCGAGCTTTTGATAATGCTAAGCACCGTACTTACGTTGATTTGAAG

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|110405748|gb|EC971296.1|EC971296
EST:     TCTGAAGTGGAGGCACTAGTTCAAGCAGTCGAGAAACTCGGAACTGGAAG                         GTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTA
genomic: TCTGAAGTGGAGGCACTAGTTCAAGCAGTCGAGAAACTTGGAACTGGAAGgtatttttta ... catcctgcagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTA
EST: gi|30302294|gb|CB979088.1|CB979088
EST:     TCTGAAGTGGAGGCACTAGTTCAAGCAGTCGAGAAACTTGGAACTGGAAG                         GTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTA
genomic: TCTGAAGTGGAGGCACTAGTTCAAGCAGTCGAGAAACTTGGAACTGGAAGgtatttttta ... catcctgcagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTA
EST: gi|30330590|gb|CD013852.1|CD013852
EST:     TCTGAAGTGGAGGCACTAGTTCAAGCTGTCGAGAAACTTGGAACTGGAAG                         GTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTA
genomic: TCTGAAGTGGAGGCACTAGTTCAAGCAGTCGAGAAACTTGGAACTGGAAGgtatttttta ... catcctgcagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTA
EST: gi|110390056|gb|EC954941.1|EC954941
EST:     TCTGAAGTGGAGGCACTAGTTCAAGCAGTCGAGAAACTTGGAACTGGAAG                         GTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTA
genomic: TCTGAAGTGGAGGCACTAGTTCAAGCAGTCGAGAAACTTGGAACTGGAAGgtatttttta ... catcctgcagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatggtcttatgttacagcatgtcaagtttctaaccatatttccatcctgcagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTATGTAGATTTGAAG
                              ttctaac  putative branch site (score: 1)
                                         tttccatcct  putative PPT
         ttatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactggatacagttaggaattggctgtgcagattttgtagttccataaatggtcttatgttacagcatgtcaagtttctaaccatatttccatcctgcagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTATGTAGATTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - tggctgt
- - - - - - - - - - - - - - - - - - - - - ccataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaccata