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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgatacttgacttggtacttcttgtgtagtctgatcgtaaagaccaatgccaattttcattattcttggaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATTGTATCTTTGCCCGGGAGAGCACACACCCACCTGGAGCTTTTGTAGTTCA

Basic information

species Vitis vinifera
transcript Vv08s0007g02270.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 13
gtaagtgatacttgacttggtacttcttgtgtagtctgatcgtaaag---------accaatgccaattttcattattcttggaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATTGTATCTTTGCCCGGGAGAGCACACACCCACCTGGAGCTTTTGTAGTTCA
||||||    ||   ||| ||  || | |  || | |    ||| |           |   | | ||      ||     ||||| | ||||||||||||||||| ||  |||||||||||||||||  |||| |  |||  | |  | | ||| || | |||||   |     ||   | |  |   ||| 
gtaagtttacctctgcttagtttttttcgcttatttttcatgtatattaatatcttgctggtactaaaaggtttttaatatggaaatatcagGGATGGAGAAGAAAAAAGCCTAGTGGCAGGTTCCAATTGTCTACATGAGGTATGGCGTAGCCTGGAAAAGCACTTTCTGGAGTGAGCCATCGGGGATTCC

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 12
---------------gtaagtgatacttgacttggtacttcttgtgtagtctgatcgtaaagaccaatgccaattttcattattcttggaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATTGTATCTTTGCCCGGGAGAGCACACACCCACCTGGAGCTTTTGTAGTTCA
                |||||  |  |   |||  |  ||| ||| || |   ||| |   |           |||| | |||    |||| | ||||||||||||||||| ||  |||||||||||||||||  |||| |  |||                                                    
gtgagtttacctctgctaagtttttttccgcttatt-tttcatgtatattaatatcttgctggtactaaaaggtttttaatat----ggaaatatcagGGATGGAGAAGAAAAAAGCCTAGTGGCAGGTTCCAATTGTCTACATGA----------------------------------------------------

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 13
---------------gtaagtgatacttgacttggtacttcttgtgtagtctgatcgtaaagaccaatgccaattttcattattcttggaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATTGTATCTTTGCCCGGGAGAGCACACACCCACCTGGAGCTTTTGTAGTTCA
                |||||| || |   |    || || |  ||||   | ||        |   | | ||      ||     ||||| | ||||||||||||||||| ||  |||||||||||||||||  |||| |  |||                                                    
gtaagtttacctctgctaagtgttattctccccc-tatttttcatgtatgttaatatcttg--cttgtactaaaaggttttgaatatggaaatatcagGGATGGAGAAGAAAAAAGCCTAGTGGCAGGTTCCAATTGTCTACATGA----------------------------------------------------

upper sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 13
gtaagtgatacttgacttggtacttcttgtgtagtctgatcgtaaagaccaatgccaattttca------ttattcttggaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATTGTATCTTTGCCCGGGAGAGCACACACCCACCTGGAGCTTTTGTA-GTTCA---
||||||  | | |          ||||| | || | ||   || ||      |||  ||  | |      ||    |||||| | |||||||||||||||||  |  |||||||||||||||||  ||||    | ||    ||    ||  || || |    |  | |   |||||  |||    |||    
gtaagtt-tgcctatggaaaattttcttttctattgtgcatgttaatgttcttgctgatactgaagggttttgagtttggaaatatcagGGATGGAGAAGAAAGAAGCCTAGTGGCAGGTTCCAATTGTCTTCATAAAGAAAATA---GCATGGAAGGGTGT-CTTCTAAAGGGAGCCATTGAGTATTCTTGT

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|30299809|gb|CB976603.1|CB976603
EST:     TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTT                         GGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
genomic: TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTTgtaagtgata ... gaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
EST: gi|110413748|gb|EC979554.1|EC979554
EST:     TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTT                         GGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
genomic: TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTTgtaagtgata ... gaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
EST: gi|32267836|gb|CD716995.1|CD716995
EST:     TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTT                         GGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
genomic: TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTTgtaagtgata ... gaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
EST: gi|110361016|gb|EC924466.1|EC924466
EST:     TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTT                         GGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
genomic: TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTTgtaagtgata ... gaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
EST: gi|22009162|gb|BQ794196.1|BQ794196
EST:     TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTT                         GGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT
genomic: TCGCATTTATTGTTCTTGCCGGATTGACCTTCGTATATTATGCGGCCTTTgtaagtgata ... gaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtagtctgatcgtaaagaccaatgccaattttcattattcttggaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATTGTATCTTTGCCCGGGAGAGCACACACCCACCTGGAGCTTTTGTAGTTCA
     gtctgat  putative branch site (score: 4)
                                                ctttc  putative PPT
                            aattttcattattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgatacttgacttggtacttcttgtgtagtctgatcgtaaagaccaatgccaattttcattattcttggaactttcagGGATGGAGAAGAAGAAGACCTAGTGGCAGGTTCCAGCTGTCCAGTTGAATTGTATCTTTGCCCGGGAGAGCACACACCCACCTGGAGCTTTTGTAGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT