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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagaacttctttggtttttcttttgaatttactttctaaaccttttgcagttattttacagtgagatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACC

Basic information

species Vitis vinifera
transcript Vv12s0035g01060.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G00400.2 (Glycine max), 3'ss of exon 3
gtaagcagaacttctttggtttttcttttgaat-ttactttctaaaccttttgcagttattttacagtgagatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACC
|| ||     ||| | |        | |||  | |    ||  | || |  ||  | ||  ||          | ||| | | ||||||  |||||| ||||||||||| || ||||| ||||| ||||||||||| |||||||| |||||||||||||||||||| |||||||| |||||||||||| |||| |
gtgagtttt-cttttgtaaaccccatcttgtttatcgtatttcagacatgctgatgataccttctt------cattttattaatgcttttatcagGCCAAATGTAGAGAAACGGGAGAAATTGTGGCCATCAAGAAAGTTCTCCAGGACAAGCGCTACAAGAATAGAGAGTTACAAATTATGCAAATGCTGGATC

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 4
gtaagcagaacttctttggtttttcttttgaatttactttctaaaccttttgcagttattttacagtgagatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACC
|| ||      ||   |   | ||||    |   | || |  |    |     | | ||  |||  |       ||| | | ||||||  | |||||||||||||||| || ||||| ||||| ||||||||||| |||||||| ||||| || ||||||||||| |||||||| |||||||||||| |||| |
gtgagtttgcttttcatatctcttctaaacaccatgctgttgatgtatgacatactgatgataccttctt-cgttttatcaatgcttttattagGCAAAATGTAGAGAAACAGGAGAAATTGTGGCCATCAAGAAAGTTCTCCAGGACAAACGATACAAGAATAGAGAGTTACAAATTATGCAAATGCTGGATC

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcagaacttctttggtttttcttttgaatttactttctaaaccttttgcagttattttacagtgagatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACC
|| |||  |  |    |        |  ||  ||   | | |  |  |    |  ||    | ||         ||| |   | ||||    |||| |||||||| || ||||| ||| |||| ||||||||||||||||| |||||||| ||||||||||| |||||| |||| || ||||| ||| | ||||
gtgagctaatttaacataagacccatgatg--ttcgttctattgatttggctccattcccctgcac-------atttatgtttccttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGTTGCCATCAAGAAGGTTCTACAAGACAAACGCTACAAGAACAGGGAGCTACAAATAATGCAGATGCTAGACC

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaagcagaacttctttggtttttcttttgaatttactttctaaaccttttgcagttattttacagtg--agatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACC
                       |   |   |||  || |||     |||| |  ||  || | | |   | | | ||| |  || |||     |||| ||||| ||||| ||||| ||| |||| |||||||| || ||||| ||||||||||| |||||||| || || ||||| |||||||| ||| | ||||
----------------------gtgagtaagattgtctatcttgttgttttaccattggttaagattcccaaacattttatgtctccttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 4
gtaagcagaacttctttggtttttcttttgaatttactttctaaaccttttgcagttattttacagtgagatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACC
                       | ||   | |  |     |  | |    ||||   |||||  ||    |  || |     |   ||  ||||| || ||    || || ||||| |  || || ||||| ||||| |||||||||||||||||||||||  | ||| | ||||| ||||   |  | ||||
----------------------gtattgctagtccaaacagtgcaacaaaagcaggc-ttttatcgtttcttctttctctttgggaatg--cagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGCTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

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|156736132|gb|EV240253.1|EV240253
EST:     ACATAGCAGAACATGTGGTTGGAACTGGTTCTTTTGGTGTTGTTTTCCAA                         GCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAA
genomic: ACATAGCAGAACATGTGGTTGGAACTGGTTCTTTTGGTGTTGTTTTCCAAgtaagcagaa ... ctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAA
EST: gi|161706124|gb|FC057171.1|FC057171
EST:     ACATAGCAGAACATGTGGTTGGAACTGGTTCTTTTGGTGTTGTTTTCCAA                         GCAAAATGTACAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAA
genomic: ACATAGCAGAACATGTGGTTGGAACTGGTTCTTTTGGTGTTGTTTTCCAAgtaagcagaa ... ctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaaccttttgcagttattttacagtgagatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACC
                                    ttttaac  putative branch site (score: 2)
                                             ctttgttc  putative PPT
                               atagtttttaa  TA-rich tract