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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaaatatgtcatttattttcatttgctaactctcttaaatacaagtttgatgtttcttttagttgatcatttgtgattgttcgtaatgtccaccttcttcttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGATATGCACAGTCACCATACAACCCATACAATCCTTACATACCTGGTGCCA

Basic information

species Vitis vinifera
transcript Vv05s0020g00460.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G36110.1 (Glycine max), 3'ss of exon 4
gtaagttaaatatgtcatttattttcatttgctaactctcttaaatacaagtttgatgtttcttttagttgatcatttgtgattgttcgtaatgtccaccttcttcttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGATATGCACAGTCACCATACAACCCATACAATCCTTACATACCTGGTGCCA
                        | | |  |||  |||| |  |     || | |||| || | |  | | |          || |   ||||    | |  |  ||||  |||||||| ||||  || ||||| || ||| |||||||||||||||||||||||| ||||||||| |||||||| |||||||||||||| || |||||||| |
-----------------------gtgagt--ctagttctcctctacttgtgtat-atgtgtcatatgctgggttg---aaagctgatttgaatg----cttgttctttgc--cagGGTGCACAAAACGAAAGTTTTCCATATATATATTATACACCTAGCTATGGATTTGCACAGTCTCCATACAATCCATACAATCCTTATATTCCTGGTGCAA

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G14490.1 (Glycine max), 3'ss of exon 4
gtaagttaaatatgtcatttattttcatttgctaactctcttaaatacaagtttgatgtttcttttagttgatcatttgt--gattgttcgtaatgtccaccttctt--cttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGATATGCACAGTCACCATACAACCCATACAATCCTTACATACCTGGTGCCA------
                                                |||||| |  | | ||| | |  ||| |  ||  | |  |   | || |  |  ||  |   ||  |||||||||| |||| ||| ||||| || |||||||||||||      ||||||||||||||||||| |||||||| ||||||||||||||||| |||||||| |      
----------------------------------------------gtaagtttaacctctgtttcactctatcctaagttgggtcatggctgatttttatgtttctgttttttttcagGGTGCACAAAATGAAAGTTTTCCGTATGTATATTATA------GCTATGGATATGCACAGTCTCCATACAATCCATACAATCCTTACATTCCTGGTGCTATGATTG

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 2
gtaagttaaatatgtcatttattttcatttgctaactctcttaaatacaagtttgatgtttc-ttttagttgatcatttgtgattgttcgtaatgtccaccttctt---cttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGATATGCACAGTCACCATACAACCCATACAATCCTTACATACCTGGTGCCA------
                                    |   || ||     || |  ||||||  | ||  |  | | ||| |   ||   | || |  |  ||  |    ||  |||||||||| |||| ||| |||||||| |||||||||||||       |||||||||||||||||| |||||||| ||||| ||||||||||| |||||||| |      
-----------------------------------gtaagtttaacttctgtgttctgtttcactctatatcctaagttggggcagtggctgatttttatgtttctggttttttttcagGGTGCACAAAATGAAAGTTTGCCGTATGTATATTATA------ACTATGGATATGCACAGTCTCCATACAATCCATATAATCCTTACATTCCTGGTGCTATGATTG

upper sequence: Vv05s0020g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttaaatatgtcatttattttcatttgctaactctcttaaatacaagtttgatgtttcttttagttgatcatttgtgattgtt--cgtaatgtccaccttcttcttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGATATGCACAGTCACCATACAACCCATACAATCCTTACATACCTGGTGCCA
                   || | ||       ||  ||  | | ||   |||   |  ||||| ||  |     |||||  |||||  | | || |||   || || || || ||||||| ||| | ||| | ||  || ||| |||  ||||||||||| ||||||||||||||||| || || || |||| |||||||||||||||||| ||  
---------------gtactaatctcggacataaagacttctcattaatcgttgatttgttcttatacat-----tttgtatttgttgacatgatatcc-tttttttgtttctccagGGTGGGCAGAATGAAAATTCTCCCTATATATGCTATACACCTAGTTATGGATATGCACAGTCTCCTTATAATCCATTCAATCCTTACATACCTGGCGCTT

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|161720955|gb|FC070341.1|FC070341
EST:     ATGACCACCATAGGATTTTTGGTCTGGATGGTCCAGATATCCAGTACTCG                         GGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGA
genomic: ATGACCACCATAGGATTTTTGGTCTGGATGGTCCAGATATCCAGTACTCGgtaagttaaa ... cttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttagttgatcatttgtgattgttcgtaatgtccaccttcttcttgcttcagGGTGCGCAAACTGATAGTTTGCCTTATGTATATTATACACCTAGCTATGGATATGCACAGTCACCATACAACCCATACAATCCTTACATACCTGGTGCCA
      agttgat  putative branch site (score: 5)
                                tgtccaccttcttctt  putative PPT
           atcattt  TA-rich tract