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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtacgagttctgcttcattatttgatggctagagtctagttaaaagtttctgaaggtctgcttttggaacttaccattaagggatgcgtttctacagGAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGCCTTGCTGAACCCTTCAGCAGCAGGGCCCCTTGTCTGGCCATCACCTTTG

Basic information

species Vitis vinifera
transcript Vv08s0007g00200.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00200.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g02130.1 (Oryza sativa), 3'ss of exon 6
attgtacgagttctgcttcattatttga-tggctagagtctagttaaaagtttctgaaggtctgcttttggaacttaccattaagggatgcgtttctacagGAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGCCTTGCTGAACCCTTCAGCAGCAGGGCCCCTTGTCTGGCCATCACCTTTG
 |   | ||| |     |  || |   | | |       ||  |    | || |  | | |||||   ||    | |   | | ||  |  |||||  ||||||||| || ||| | |||||  ||||||  || ||||||||||||||||| |||||||||||| || |||||| |||| | || |||||||| ||  | 
-tcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccatgctctgccactgattttaattttaatggtttttgtttccccagGAGAATTCCCTATTCTGTTGCGCTGAAACGGAACCATGGAGCATGTGCAGCTTTGCTGAACCCTACATCAGCAGAGCCCATGGTGTGGCCATCCCCACTT
















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|30134585|gb|CB919923.1|CB919923
EST:     CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGG                         GAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGC
genomic: CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGGgtaaacctca ... gtttctacagGAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGC
EST: gi|110700513|gb|EE078637.1|EE078637
EST:     CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGG                         GAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGC
genomic: CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGGgtaaacctca ... gtttctacagGAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGC
EST: gi|18458145|gb|BM436423.1|BM436423
EST:     CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGG                         GAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGC
genomic: CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGGgtaaacctca ... gtttctacagGAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGC
EST: gi|30126246|gb|CB911585.1|CB911585
EST:     CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGG                         GAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGC
genomic: CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGGgtaaacctca ... gtttctacagGAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGC
EST: gi|110412439|gb|EC978189.1|EC978189
EST:     CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGG                         GAGAATACCATATACAGTTTGCCATGAAACACAAGCATGGAGCATGTGCAG
genomic: CGGGAATTGCTTGCATGGGGAGCAGATCGACTTCACCGAGATTCATCTGGgtaaacctca ... gtttctacagGAGAATACCATATACAGTT-GCCATGAAACACAAGCATGGAGCATGTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtttctgaaggtctgcttttggaacttaccattaagggatgcgtttctacagGAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGCCTTGCTGAACCCTTCAGCAGCAGGGCCCCTTGTCTGGCCATCACCTTTG
                         aacttac  putative branch site (score: 2)
                                            cgtttct  putative PPT
                                 attaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtacgagttctgcttcattatttgatggctagagtctagttaaaagtttctgaaggtctgcttttggaacttaccattaagggatgcgtttctacagGAGAATACCATATACAGTTGCCATGAAACACAAGCATGGAGCATGTGCAGCCTTGCTGAACCCTTCAGCAGCAGGGCCCCTTGTCTGGCCATCACCTTTG

- - - - - - ctgcttc
- - - - - - - - - - - - - gatggct
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgaagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggatgc