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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacacaaacttcttcttttccattttttttttaatatactctttattgcagtttttggccctttaatttaatctgattctttgactttactgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG

Basic information

species Vitis vinifera
transcript Vv01s0011g05370.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 11
ctacacaaacttcttcttttccattttttttttaatatactctttattgcagtttttggccctttaatttaatctgattctttgactttactgct-----tgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG
    ||  ||    | |     |   || |        ||| || ||   ||  | |          | |  |    |   |||| | || || |     || ||||| ||||||||||| ||||| ||||||||||| || ||  |||| ||||| || |||||||||
----actgaccatatttgcagtaaacttctaagtcagaacttttaatgaaaggatgtaaaataccgctgtgctaccttatgttga-tctattgataaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCTCAAGTTCTTTGAG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 11
ctacacaaacttcttcttttccattttttttttaatatactctttattgcagtttttggccct-ttaatttaatctgattctttgactttactgctt-gtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG
 |    |   || ||| |  | | ||    |||  | ||   |   ||   |      |   |   ||| ||  |  ||| |      | | |  || ||||||| ||||| || |||||||| || |||||||||||||||||| | ||| ||||||| ||||||
ttcttgagcttttttcctagcaacttgaccttttgtgtaacttcatttcttgccaccagttttaccaatata--ccaattttaaattataaatattttgtagGAGCATGCCAACCTCTGCTGCCCTGGATGTTGTAGCCAAACATCTGAATTTGAAATTTTTTGAG
















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|30129214|gb|CB914553.1|CB914553
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|110388407|gb|EC953157.1|EC953157
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|30133454|gb|CB918793.1|CB918793
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|161709381|gb|FC059250.1|FC059250
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCT
EST: gi|30305224|gb|CB982018.1|CB982018
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGACGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|37188896|gb|CF608245.1|CF608245
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|32270099|gb|CD719258.1|CD719258
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|30137874|gb|CB923212.1|CB923212
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|37183515|gb|CF602869.1|CF602869
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|30305289|gb|CB982083.1|CB982083
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGACGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
EST: gi|161715091|gb|FC063627.1|FC063627
EST:     GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG                         GAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT
genomic: GCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAGgttctctatt ... ctgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcagtttttggccctttaatttaatctgattctttgactttactgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG
                                  ctttgac  putative branch site (score: 4)
                                        ctttact  CT-rich tract
                 tttaatttaatctgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacacaaacttcttcttttccattttttttttaatatactctttattgcagtttttggccctttaatttaatctgattctttgactttactgcttgtagGAGTATGCCCACATCTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- -cacaaac
- - - - - - - - - - ccatttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc