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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccctgttctcatgaaacagaattttttatttatttatttatttttttccagcataaaaagttaataaccagactgaagttctcctgttgtttttccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGATGTTACAAATCGAATGAATCTTACCCCTGTGGCCTTAATGGAGGGAACCT

Basic information

species Vitis vinifera
transcript Vv05s0051g00870.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA16G27210.1 (Glycine max), 3'ss of exon 11
tcccctgttctcatgaaacagaattttttatttatttatttatttttttccagcataaaaagt--taataaccagactgaagttctcctgttgtttttc-----cagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGATGTTACAAATCGAATGAATCTTACCCCTGTGGCCTTAATGGAGGGAACCT
     || | || | ||     | |   |||| ||||    | || |||      || | | |  | || ||     |  |  | | |||   |  ||       |||| |||||||| ||||| || | ||||||||||||||||||  | |||||||| ||||| ||||||||||| || || |||||||| ||||| | | | |
----atgctttcgtcaat---gactggatattgatttgaacaattgtttaagagctagagaatgattatgactcagttctaaatgttctgcgatcctttgtgtttagGTGGATGAGTATTCCCGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTAACTCCGGTGGCCTTGATGGAAGCATCGT

upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA02G08180.1 (Glycine max), 3'ss of exon 10
tcccctgttctcatgaaacagaattttttatttatttatttatttttttccagcataaaaagttaataaccagactgaagttctcc-tgttgtttt---tccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGATGTTACAAATCGAATGAATCTTACCCCTGTGGCCTTAATGGAGGGAACCT
     |  | || | || || | |  |||      || ||||     |   ||   |  |   | |     ||    || |  ||  || |  |||   |  |||| |||||||| ||| | || | ||||||||||||||||||  | |||||||| ||||| |||||||||||||| || |||||||| ||||| | | | |
gaatgtaatgtc-taaagcaaattgatttgaacgattgtttaaaagct---agagaatgattatgacgcatagttctaaatgttctgtgatcctttgtgtttagGTGGATGAGTATTCCTGCACAAGCATACCTAGCATATGGGCTGTGGGTGATGTCACAAACCGAATGAATCTTACTCCGGTGGCCTTGATGGAAGCATCGT

upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G24170.3 (Arabidopsis thaliana), 3'ss of exon 11
------------tcccctgttctcatgaaacagaattttttatttat----ttatttatttttttccagcataaaaagttaataaccagactgaagttctcctgttgtttttccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGATGTTACAAATCGAATGAATCTTACCCCTGTGGCCTTAATGGAGGGAACCT
            |||    ||  ||   |  | ||||| |  |  ||    || |   |   ||||  |   || |   |  |       ||     |    |    | |   ||||| || ||||| || || ||||| |||||||||||||||||  | || ||||  ||||| ||||| || ||||| ||||| || ||||||||||  ||||
gttttaacaatttcctaaatttgcagatactaaaatttatcctgaataaagttttccgtgactttctggggaaacattctcctcttgcagctactaattcagtacattatcctcagGTTGACGAGTATTCACGAACTAATATACCTAGCATATGGGCTGTAGGAGATGCCACAAACCGAATTAACCTTACACCTGTTGCGTTAATGGAGGCCACCT

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|46917982|gb|CN547311.1|CN547311
EST:     TGAACTTGGAAGTTGTAGGTGTGGAATTGGACAAGATGGGAGCTGTGAAG                         GTAGATGAGTACTCCCGGACTAACATACCTAGCATAT
genomic: TGAACTTGGAAGTTGTAGGTGTGGAATTGGACAAGATGGGAGCTGTGAAGgttgtctttt ... gtttttccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATAT
EST: gi|110729876|gb|EE106312.1|EE106312
EST:     TGAACTTGGAAGTTGTAGGTGTGGAATTGGACAAGATGGGAGCTGTGAAG                         GTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGAT
genomic: TGAACTTGGAAGTTGTAGGTGTGGAATTGGACAAGATGGGAGCTGTGAAGgttgtctttt ... gtttttccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGAT
EST: gi|161711343|gb|FC059926.1|FC059926
EST:     TGAACTTGGAAGTTGTAGGTGTGGAATTGGACAAGATGGGAGCTGTGAAG                         GTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGAT
genomic: TGAACTTGGAAGTTGTAGGTGTGGAATTGGACAAGATGGGAGCTGTGAAGgttgtctttt ... gtttttccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttccagcataaaaagttaataaccagactgaagttctcctgttgtttttccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGATGTTACAAATCGAATGAATCTTACCCCTGTGGCCTTAATGGAGGGAACCT
                  taataac  putative branch site (score: 1)
                                   ttctcctgttgttttt  putative PPT
         ataaaaagttaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccctgttctcatgaaacagaattttttatttatttatttatttttttccagcataaaaagttaataaccagactgaagttctcctgttgtttttccagGTAGATGAGTACTCCCGGACTAACATACCTAGCATATGGGCCATTGGTGATGTTACAAATCGAATGAATCTTACCCCTGTGGCCTTAATGGAGGGAACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
-cccctgt
- - - - -ctcatga
- - - - - - - - aacagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcctgt