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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatctagttgttagtgcacccccctatagaaaccatgttgttatctcttacttggttttatttgtttgagaagttaattctttatttttctatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTGTAGTTGTTGATCGAGCAACCCCCAAG

Basic information

species Vitis vinifera
transcript Vv07s0031g00600.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g00600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G05940.1 (Glycine max), 3'ss of exon 8
--gatctagttgttagtgcacccccctatagaaaccatgttgttatctcttacttggttttatttgtttgagaagttaattctttatttttctatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTGTAGTTGTTGATCGAGCAACCCCCAAG
    |    || ||        |   | | |    |    |  |      |  | |     ||  || | |     ||         | || | | || |||| |||||||| |||||||||   ||||| |||||||||||||| |||||||| || ||||||||||| || || |||
ctacttgcattattttgatttacttttttggttctcggactactgaaatattgtggagaggat--gtctcaatcactataaagaagatgttttgtcttgcagATTCTGTGGAGAATTTGATGTCAGAAACCCATGAACTGGGAGGTTCTGCTGTGGTGGTTGATCGAGCTACTCCTAAG

upper sequence: Vv07s0031g00600.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G39330.1 (Glycine max), 3'ss of exon 8
gatctagttg--ttagtgc-acccccctatagaaaccatgttgttatctcttacttggttttatttgtttgagaagttaattctttatttttctatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTGTAGTTGTTGATCGAGCAACCCCCAAG
   ||| |||  ||| |   |    | | |      | ||   || |    || |  |       ||| | |   | |||        ||||   | || |||| |||||||| |||||||||   ||||| |||||||||||||| |||||||| || ||||||||||| || || |||
-tgctacttgcattattttgatttacttctttggttcttggacttctgaaatattgtggagaggatgtctcaattgctaaaaggaagatttt--gtcttgcagATTCTGTGGAGAATTTGATGTCAGAAACCCATGAACTGGGAGGTTCTGCTGTGGTGGTTGATCGAGCTACACCTAAG
















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|110415764|gb|EC981696.1|EC981696
EST:     TGGATCAAAAGGGCATCGTGGAATTGGGTTTATCACATTTGCAAGTGCAG                         AATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTACTG
genomic: TGGATCAAAAGGGCATCGTGGAATTGGGTTTATCACATTTGCAAGTGCAGgtcaatatat ... tatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTG
EST: gi|349818091|gb|FQ408866.1|FQ408866
EST:     CACATTTGCAAGTGCAG                         AATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTACTG
genomic: CACATTTGCAAGTGCAGgtcaatatat ... tatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTG
EST: gi|110429617|gb|EC996114.1|EC996114
EST:     TGGATCAAAAGGGCATCGTGGAATTGGGTTTATCACATTTGCAAGTGCAG                         AATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTACTG
genomic: TGGATCAAAAGGGCATCGTGGAATTGGGTTTATCACATTTGCAAGTGCAGgtcaatatat ... tatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTG
EST: gi|351020076|gb|FQ445683.1|FQ445683
EST:     CACATTTGCAAGTGCAG                         AATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTACTG
genomic: CACATTTGCAAGTGCAGgtcaatatat ... tatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTG
EST: gi|349811719|gb|FQ409716.1|FQ409716
EST:     CACATTTGCAAGTGCAG                         AATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTACTG
genomic: CACATTTGCAAGTGCAGgtcaatatat ... tatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTG
EST: gi|349818104|gb|FQ408879.1|FQ408879
EST:     CACATTTGCAAGTGCAG                         AATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTACTG
genomic: CACATTTGCAAGTGCAGgtcaatatat ... tatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttacttggttttatttgtttgagaagttaattctttatttttctatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTGTAGTTGTTGATCGAGCAACCCCCAAG
                                ttctttatttttctat  CT-rich tract
          ttttatttgtttgaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatctagttgttagtgcacccccctatagaaaccatgttgttatctcttacttggttttatttgtttgagaagttaattctttatttttctatgttacagAATCTGTGGACAATTTGATGGTTGAAACTCATGAACTGGGAGGGTCTGCTGTAGTTGTTGATCGAGCAACCCCCAAG

- - - - - - - - - cccccct
- - - - - - - - - - - - - - -aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - tacttgg