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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatcatgtatacatactggttaatttttcctcaatttccattgatatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT

Basic information

species Vitis vinifera
transcript Vv18s0001g03540.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatcatgtatacatactggttaatttttcctcaatttccattgatatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT
                           | |  |       | || |         |     | | |  ||| | ||||   |  | |    | | |  |   | | || ||      |||||||||||||||||||| || |||||  | |||||||| || ||||| |||||||||||||| ||||| || ||||| || ||||| || || ||||| || 
------------------------gtacgtacctgcagctactaaagccactgaagtctgaatgtactcatta-gtatctgttttagc--gtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC

upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatc---atgtatacatactggttaatttttcctcaatttccattgatatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT
                                                                   |     || ||     ||  | ||   ||||| || ||  | | || |     ||| |   |||     |||    |   || |||   || |    |   || || |  |   |||||  ||||||||||||||||||| || ||||| |  |||||| | || |||||||||||||||||||||||||| || || ||||| ||||| || || ||||| || 
gtaatcatccattcatgcctacattcgcatccatcgataaaactcatatacaattaacacaatcaaagcttttcctaattaataactgcaag--cattaaaa-gtgtagtgtaatcgatcttgtaattacgctctgatctagctacctatatatgagtgatccatggatcgatatatacatatatga-gcagCAACATCTACTACATCAACGACAAGTATGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACCACCGTGTTCATCCCCTCCTTCCACAAC

upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 3
gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatcatgtatacatactggttaatttttcctcaatttccattgatatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT
                                 || ||   ||   |    | | | |  |         | |    |   | | |  |||   | | |  ||  | |   |       |||||||||||||||||| || |||||  | |||||| | || |||||||||||||||||||||||||| || ||||| || ||||| || || ||||| || 
-------------------------------gtaaggttgcttgcttgctcgctcgcatggttcgccggctaac---tgtgtgccgcgtaagcgtacatatata-ctaccaa------acagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC

upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 4
gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatcatgtatacatactggttaatttttcctcaatttcca-ttgatat-gctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT
                             | | |  ||| || ||  || |  ||| | |          | || |||| |  |||  || ||  || | || |   | || |||| | | ||| ||||| |||||||||||||||||| | ||||| ||||||||||| |||||||| ||||| |||||||| || || || ||||| ||||| ||||| |||
----------------------------gtaagacagtagatcatgctttt--ttgaata----------ttatatatataatctgtatatttcatcataaactgagaatttatattgtttcagTAACATATACTACATAAATGACAATCTGGACAAAAGAACTTGGACTTACATCTTTGGCGCATGCTGTGCAACAACAGTCTTCATCCCTTCTTTCCACAAT

upper sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 4
gtaaacccaaaaggggaaaggaaaaatcattacaatgtacattatatttctgtttggacagacgaatacatcatgtatacatactggttaatttttcctcaatttccattgatat-gctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT
                                            ||   | ||      |||  |  |  |  |  |||     |  | || |     |  || | ||   |||| | | ||| ||||| ||||||||||| |||||| | ||||||||||||||||| |||||||| || || |||||||| || || || ||||| ||||| ||||| || 
-------------------------------------------gtaagacagt---agtagatcatgattttcttaatattgcattataaactaagtttatatatacaacaatattgtttcagTAACATATACTACATAAACGACAATCTGGACAAGAGAACTTGGACTTACATCTTTGGGGCATGCTGTGCAACAACGGTCTTCATCCCTTCTTTCCACAAC

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|294965879|gb|GW837362.1|GW837362
EST:     TGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGATTGCCTGTGCAAG                         CAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACAT
genomic: TGCACTTTCCTTCTCTTTGGCTCCGTGATACAGCTGATTGCCTGTGCAAGgtaaacccaa ... tatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatcatgtatacatactggttaatttttcctcaatttccattgatatgctgcagCAACATCTACTACATAAATGACAATTTCGACAAGAGAACTTGGACGTACATCTTCGGCGCCTGCTGTGCTACGACCGTTTTCATTCCTTCATTCCATAAT
                                       cattgat  putative branch site (score: 4)
                    ttaattttt  TA-rich tract