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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacttcatccgtcaactggtcgatggctaagtttcttgtttttctgggcttccttccatatcttttgtgctttttttgggttatatttaacaagtatttcttgatatgttctactcaactgtctttgtgattgcttctggtgctaaattatatcacttctctgtcatcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTATGTGCTTTGGGATTGGGTTCTTGTTGAATACAATTGCTATATTCTATGG

Basic information

species Vitis vinifera
transcript Vv12s0035g00280.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 9
gtatgtacttcatccgtcaactggtcgatggctaagtttcttgtttttctgggcttccttccatatcttttgtgctttttttgggttatatttaacaagtatttcttgatatgttctactcaactgtctttgtgattgcttctggtgctaaatt-atatcacttctctgtcatcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTATGTGCTTTGGGATTGGGTTCTTGTTGAATACAATTGCTATATTCTATGG
                                                                                        |||  |   ||| || ||| | || ||  ||           | |  |    |  | |||| |  | || | | | ||  ||   ||   |||| |||| |||||| ||| | |||||| | || |||||||| ||||| |||||||||||||| |||||  |  || | || ||||| |||||||||||| |
---------------------------------------------------------------------------------------gtatgaactcagt-ttactttacatcttgaacaggcacacacctattttactataagatgctcacctcatttaaatccttggtttgctgagcagGGAAAAACTGGATCAAGGCAATGATTATGACAGCATCACTATTTCCGTTTATGTGCTTTGGAATTGGCCTAGTGCTTAACACAATCGCTATATTCTATCG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 8
gtatgtacttcatccgtcaactggtcgatggctaagtttcttgtttttctgggcttccttccatatcttttgtgctttttttgggttatatttaacaagtatttcttgat-atgttctactcaactgtct--ttgtgattgcttctggtgctaaattatatcacttc--tctgtcatcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTATGTGCTTTGGGATTGGGTTCTTGTTGAATACAATTGCTATATTCTATGG
                                                                                                | |   || || || ||||   | | |||||| |   | |  ||   |  |||||| | || | | |  ||  | ||         |||| |||| |||||| ||| | |||    | || ||||||||||| ||||||||||||||||| |||||  |  || | || || ||||||||         
----------------------------------------------------------------------------------------------gtatgggcttatttatcatgtaaaattgaactgtatacctatagttctataaggtgctcagttgttttaaatccttttggagGAGGAGCAGGGAAAAACTGGATCAAGGCAATGGCCATGACAGCATCACTTTTCCCATTTATGTGCTTTGGAATTGGCCTGGTGCTTAACACTATTGCTAT---------

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 9
gtatgtacttcatccgtcaactggtcgatggctaagtttcttgtttttctgggcttccttccatatcttttgtgctttttttgggttatatttaacaagtatttc--ttgatatgttctactcaactgtctttgtgattgcttctggtgctaaattat-atcacttctctgtcatcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTATGTGCTTTGGGATTGGGTTCTTGTTGAATACAATTGCTATATTCTATGG
                                                                                                ||| ||||   ||||| | | ||||     ||| |  ||| ||   |||    || ||| || || ||    ||   |  || ||||||||||  |||||||| || ||||| || || |||||||| || ||||| ||||||||||| ||||| ||  | || || ||||||||||||||||||||
----------------------------------------------------------------------------------------------gtaagaatttgcattgatctttgctacatgtttgtttgggtgcttctctctccctctgaatgattataaccgtgcttataattt-tcagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCATTCATGTGCTTTGGAATTGGTTTTATTTTAAACACAATTGCTATATTCTATGG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 9
gtatgtacttcatccgtcaactggtcgatggctaagtttcttgtttttctgggcttccttccatatcttttgtgctttttttgggttatatttaacaagtatttcttgatatgttctactcaactgtctttgtgattgcttctggtgctaaattatatcacttctctgtcatcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTATGTGCTTTGGGATTGGGTTCTTGTTGAATACAATTGCTATATTCTATGG
                                                           |    ||||| | |  |||| |    ||    |   | ||||| | | | |   ||   ||||    |||   |  | | ||    || | |  | || |  || | | ||   |||| |||||||  ||||||||| || |||||||| ||||| || || || ||||| ||||||||||| ||||| ||  | || || ||||| ||||||||||||||
----------------------------------------------------------gtaagaatcttctttaattttctgtattttcgctc--ctagtatgtttgggtggctttgtctcagtcttctccttt-tggttttgaatgatta--tgtaactattttttatctgtttgttagGTAAACACTGGATTAAATCCATGATTCTTACTGCTTCTCTGTTCCCATTCATGTGCTTTGGAATTGGATTTATCTTAAACACAATCGCTATATTCTATGG

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 9
gtatgtacttcatccgtcaactggtcgatggctaagtttcttgtttttctgggcttccttccatatcttttgtgctttttttgggttatatttaacaagtatttcttgatatgt-tctactcaactgtctttgtgattgcttctggtgctaaattat-atcact-tctctgtcatcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTATGTGCTTTGGGATTGGGTTCTTGTTGAATACAATTGCTATATTCTATGG
                                                                     |     |    |||   |||  |  ||| || | ||||||| | | | ||     || ||| | |   |   |||    || ||| || || ||| |   | |||| ||  |||||||||  |||||||| || ||||| || || |||||||| || || || ||||||||||| ||||| ||  | || || || |||||||||||||||||
--------------------------------------------------------------------gtaagattcgcattgatctatgct--acatgt-tctcttgatgtttgtttaggtgcctctctctctctctctctct--ctctgaatgattatgactgtgcttatcatttt--cagGTAAAAATTGGATTAAATCCATGATCCTTACAGCATCACTGTTCCCTTTCATGTGCTTTGGAATTGGTTTTATTTTAAACACTATTGCTATATTCTATGG

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|33407406|gb|CF213033.1|CF213033
EST:     ATCATTCATTTCGGGTTATGTGAGTGGTGGGATGTACTCACGCAATGGTG                         GTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTA
genomic: ATCATTCATTTCGGGTTATGTGAGTGGTGGGATGTACTCACGCAATGGTGgtatgtactt ... atcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTA
EST: gi|28959529|gb|CB339765.1|CB339765
EST:     ATCATTCATTTCGAGTTATGTGAGTGGTGGGATGTACTCACGCAATGGTG                         GTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTA
genomic: ATCATTCATTTCGGGTTATGTGAGTGGTGGGATGTACTCACGCAATGGTGgtatgtactt ... atcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTA
EST: gi|161713978|gb|FC063163.1|FC063163
EST:     GTGAGTGGTGGGATGTACTCACGCAATGGTG                         GTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTA
genomic: GTGAGTGGTGGGATGTACTCACGCAATGGTGgtatgtactt ... atcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctttgtgattgcttctggtgctaaattatatcacttctctgtcatcttgtcagGTAAAACCTGGATTAAGTCGATGATTCTCACTGCATCACTTTTTCCATTTATGTGCTTTGGGATTGGGTTCTTGTTGAATACAATTGCTATATTCTATGG
                    tgctaaa  putative branch site (score: 2)
                                   cttctctgtcatctt  putative PPT
                       taaattatatcactt  TA-rich tract