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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaatctgaaaaagtataaatgtgtgatccttgatttgtaatcatgcatttgctttctgtcttcttttatttttttaacttctatagtacttgctcagGTTCTTGGCTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGGAAACTCTGACTTCCTGGAGTATGTTTTGGTGCGAACTGATTTGGACACA

Basic information

species Vitis vinifera
transcript Vv05s0020g04100.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G24080.1 (Glycine max), 3'ss of exon 8
-----tttgaatctgaaaaagtataaatgt-gtgatccttgatttgtaatcatgcatttgctttctgtcttcttttatttttttaacttctatagtacttgctcagGTTCTTGGCTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGGAAACTCTGACTTCCTGGAGTATGTTTTGGTGCGAACTGATTTGGACACA
         | ||||      | |   ||| |  || | |  ||  |  |  || ||||    | ||  |  ||| |   ||| ||||| ||     | |    |||| ||| ||||||||||| ||  ||||||| ||||||||| || |||| || || ||   ||| ||||||||||| ||||| || ||||||||||| |||
taaataacaagtctgtgtctctgtgtgtgtagaaatacatacttcattgtattggattta---tatgagtattttaaacatttcaacttttact---cctctctagGTGCTTAGCTGATGAGACAGCTGTCCTACTTCTTTACTCATTGTTGCAAGGGAATTCCACCTTTCTGGAGTATGTCTTGGTCCGGACTGATTTGGATACA

upper sequence: Vv05s0020g04100.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G04200.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------tttgaatctgaaaaagtataaatgtgtgatccttgatttgtaatcatgcatttgctttctgtctt-----cttttatttttttaacttctatagtactt-----gctcagGTTCTTGGCTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGGAAACTCTGACTTCCTGGAGTATGTTTTGGTGCGAACTGATTTGGACACA
                     |||   |||  || | | ||  | |||  |  | ||  || | || || ||    ||  |   |       || |||  |  |   |  ||  | | |          ||||| || |||||||||   ||| || | || || |||||| || |||| || || || |||||   ||||||||| |||||||||||||||||||| || 
gtaagttatattttcttgagctttttctctacaataatttatttttgtattgatagagatgca-tcctgtatcaaattcttaattcaatgctttctatgctactgtgtaataacgcaatctggcaatgtagGTTTTTAGCTGATGAGGGCGCCGTCTTGCTCCTCTACTCATTGTTGCAAGGGAATTCCGACTTTAAGGAGTATGTGTTGGTGCGAACTGATTTGGATACT
















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|352769603|gb|FQ468531.1|FQ468531
EST:     GGTCCACTTGTGAGATTACCTTTTGCTTCGTTGTTTGACACTCTTGGCAT                         GTTCTTGGCTG
genomic: GGTCCACTTGTGAGATTACCTTTTGCTTCGTTGTTTGACACTCTTGGCATgtgagtctct ... acttgctcagGTTCTTGGCTG
EST: gi|352780977|gb|FQ466290.1|FQ466290
EST:     GGTCCACTTGTGAGATTACCTTTTGCTTCGTTGTTTGACACTCTTGGCAT                         GTTCTTGGCTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGG
genomic: GGTCCACTTGTGAGATTACCTTTTGCTTCGTTGTTTGACACTCTTGGCATgtgagtctct ... acttgctcagGTTCTTGGCTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGG
EST: gi|161714238|gb|FC064147.1|FC064147
EST:     GGTCCACTCGTGAGATTACCTTTTGCTTCGTTGTTTGACACTCTTGGCAT                         GTTCTTGGGTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGG
genomic: GGTCCACTTGTGAGATTACCTTTTGCTTCGTTGTTTGACACTCTTGGCATgtgagtctct ... acttgctcagGTTCTTGGCTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatttgctttctgtcttcttttatttttttaacttctatagtacttgctcagGTTCTTGGCTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGGAAACTCTGACTTCCTGGAGTATGTTTTGGTGCGAACTGATTTGGACACA
                             ttttaac  putative branch site (score: 2)
                                              cttgctc  putative PPT
                  ttcttttattttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgaatctgaaaaagtataaatgtgtgatccttgatttgtaatcatgcatttgctttctgtcttcttttatttttttaacttctatagtacttgctcagGTTCTTGGCTGATGAGACTGCCATCCTACTGCTTTACTCACTGGTGCATGGAAACTCTGACTTCCTGGAGTATGTTTTGGTGCGAACTGATTTGGACACA

- - - - tgaaaaa
- - - - - - - - - - - tgtgtga
- - - - - - - - - - - - - - - - - - - - - -tcatgca