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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaagcagatagattaatttttaaagcttttccttaaaaaataaccatattgttgtccatggcagTGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGAAAAG

Basic information

species Vitis vinifera
transcript Vv14s0219g00280.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0219g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G24070.1 (Glycine max), 3'ss of exon 11
gtaaggaagcagatagattaatttttaaagctt-ttccttaaaaaataaccatattgttgtccatggcagTGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGAAAAG
||||||||||  ||  |||     |||    |  || ||||    || |  ||  | |||||  |||||||||| |||||||||||||||||||| ||||||| |||||||||||||||||| ||
gtaaggaagctaattaatttcaccttatttttcattgcttatcttatgaaaatcatattgtctgtggcagTGGGTGGAAGAAACAGGAAAGTTGCTGAGGCTTATGCAAGGAATGGAGGGAAGAG

upper sequence: Vv14s0219g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G07410.2 (Glycine max), 3'ss of exon 8
gtaaggaagcagatagatt-------aatttttaaagcttttccttaaaaaataaccatattgttgtccatggcagTGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGAAAAG---------------------------------------------
||||||||||  ||   ||       | |||| |  |||| || ||  ||||   ||| |||||   | ||||||||||| |||||||| ||||||||||| ||||||| |||||||||||||||||| ||                                             
gtaaggaagctaattagtttcaccctatttttcattgcttatcttttgaaaa---ccaaattgt---ctatggcagTGGGTGGAAGAAATAGGAAAGTTGCTGAGGCTTATGCAAGGAATGGAGGGAAGAGGTTGTTTTGTATTTCTTTCTCTTTTGTTCATATTTCTAGGGAGAG

upper sequence: Vv14s0219g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G07410.1 (Glycine max), 3'ss of exon 8
gtaaggaagcagatagatt-------aatttttaaagcttttccttaaaaaataaccatattgttgtccatggcagTGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGAAAAG
||||||||||  ||   ||       | |||| |  |||| || ||  ||||   ||| |||||   | ||||||||||| |||||||| ||||||||||| ||||||| |||||||||||||||||| ||
gtaaggaagctaattagtttcaccctatttttcattgcttatcttttgaaaa---ccaaattgt---ctatggcagTGGGTGGAAGAAATAGGAAAGTTGCTGAGGCTTATGCAAGGAATGGAGGGAAGAG

upper sequence: Vv14s0219g00280.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G23190.1 (Glycine max), 3'ss of exon 9
gtaaggaagcagatagattaatttt-taaagcttttccttaaaaa-ataaccatat--------------tgttgtccatggcagTGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGAAAAG
|||||||  | |||  ||| | ||        ||||| ||    | ||| ||   |              | || |   |||||||||| || ||||| ||||||||||| || |||| ||| || ||||||||||| ||
gtaaggacactgattaattgacttcaccttatttttcattggtcatatatcctggtttcatttaaaaccatattatttgtggcagTGGGTGGGAGAAATAGGAAAGTTGCCGATGCTTATGCCAGAAATGGAGGGAAGAG

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|122690719|gb|EC956681.1|EC956681
EST:     CAGTACCTTCTTTGAGAGCTGTGGCATAGCTGATCTCATCACTACATGCT                         TGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGA
genomic: CAGTACCTTCTTTGAGAGCTGTGGCATAGCTGATCTCATCACTACATGCTgtaaggaagc ... tccatggcagTGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattaatttttaaagcttttccttaaaaaataaccatattgttgtccatggcagTGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGAAAAG
                            aaataac  putative branch site (score: 2)
     aatttttaaagctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaagcagatagattaatttttaaagcttttccttaaaaaataaccatattgttgtccatggcagTGGGAGGAAGAAACAGGAAAGTTGCAGAGGCTTTTGCAAGGAATGGAGGGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG