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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttattctgcattctgtttgtttgtatttcatttgacatgctgcccttattattttattacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT

Basic information

species Vitis vinifera
transcript Vv01s0011g01420.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g52370.1 (Oryza sativa), 3'ss of exon 5
gtaaggttattctgc----attctgtt---tgtttgtatttcatttgacatgctgcccttattatttta--ttacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT
|||| ||  ||   |    ||| |  |   | |||  ||||| ||| ||||  |  || |   |||| |  | |||||||||  ||  |      || || ||||||||||| || ||||| || || || || |||||  |||| |||||||| || ||||||| ||||||||||||| |
gtaatgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT

upper sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 5
------gtaaggttatt---ctgcatt----ctgtttgtttgtatttcatttgacatgctgcccttattatttta--ttacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT
      |||| ||  ||   |  || |    || | | |||  ||||| ||| ||||  |  || |   |||| |  | |||||||||  ||  |      || || ||||||||||| || ||||| || || || || |||||  |||| |||||||| || ||||||| ||||||||||||| |
gtgatagtaatgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcagGTCCAAATAACACCGTACCTATTCATTGGTATATAATGACCAGCCCCTTCACCGATGACATCACTCGCAAATTCTTCGAAAGCCGTAAATACTTTGGCTT

upper sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G31070.2 (Arabidopsis thaliana), 3'ss of exon 5
--------------gtaagg-ttattctgcattc-------tgtttgt----ttgtatttcatttgacatgctgcccttattattttattacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT
                | || || ||||  ||||       | |||||    || |     ||||||||  ||   |    || | | |||| | ||||  ||  | ||   ||  |||| |||||||| |||||||| ||||||||||||||||| |  || || |||| |||    || || || |||||||| ||
gtgagtgagactactcatggcttcttctatattccaacagatatttgtaccgttatgccatatttgacactcttttccgcataatatcttacgttcagGTCCAATTCGTCCAGTTACAATACATTGGTATATTATGACTAGTCCATTTACTGATGAAGCGACACGAAAATATTTCTCGAGTCACAAGTACTTTGGTCT

upper sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ27144 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggttattctgcattctgtttgtttgtatttcatttgacatgctgcccttattattttattac-ttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT------
                        || || |     | |      |||  ||  |    | |  |  |   |  | ||||  |  | ||    || |  |||||||||||||||||||||||||| ||    |  || ||  |||| ||||||  | | || |||||||| ||      
------------------------gtatgcaagagttcttgagaactgttctagtgggctaaccaaatcaaatacacagGAAGGCTAGTCATGATCCCATGGTACATTATGACGAGTCCATTTACAGACACCGCTACTCGGCAATTCTTTGAAGCCAAAAAGTACTTTGGTCTTGAAGC

upper sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ33510 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggttattctgcattctgtttgtttgtatttcatttgacatgctgcccttattattttattac-ttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT------
                        || || |     | |      |||  ||| |    | |  |  |   |  | ||||  |  | ||    || |  |||||||||||||||||||||||||| ||    |  || ||  |||| ||||||  | | || |||||||| ||      
------------------------gtatgcaagagttcttgagaactgttcttctgggctaaccaaatcaaatacacagGAAGGCTAGTCATGATCCCATGGTACATTATGACGAGTCCATTTACAGACACCGCTACTCGGCAATTCTTTGAAGCCAAAAAGTACTTTGGTCTTGAAGC

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|110690672|gb|EE068034.1|EE068034
EST:     TGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG                         GCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTA
genomic: TGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGGgtaaggttat ... ttacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTA
EST: gi|110401181|gb|EC967782.1|EC967782
EST:     TGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG                         GCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTA
genomic: TGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGGgtaaggttat ... ttacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTA
EST: gi|161713618|gb|FC063422.1|FC063422
EST:     AAGACTTGCTGCTCAATCTACAAATGAGG                         GCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTA
genomic: AAGACTTGCTGCTCAATCTACAAATGAGGgtaaggttat ... ttacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTA
EST: gi|110728445|gb|EE104021.1|EE104021
EST:     TGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGG                         GCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTA
genomic: TGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGGgtaaggttat ... ttacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttgtttgtatttcatttgacatgctgcccttattattttattacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT
                  atttgac  putative branch site (score: 4)
                                        ttttatt  putative PPT
                                  ttattattttattact  TA-rich tract