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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcttcaatatttatctctgttcatttattttgatgatctcttgtatatacatgctgcaacttattcatcaatcagcagcattatatgtttttttgggttcaattcaaggatttcattataagaatttcttctaaacagaattgagtttgggatgaccaagatttatcctctggcttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGCCCCAAGTCTGTGCGAGAAAAATTTACTGGAATAATTAG

Basic information

species Vitis vinifera
transcript Vv04s0043g00400.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0043g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G841900_T04 (Zea mays), 3'ss of exon 2
gtaagtttcttcaatatttatctctgttcatttattttgatgatctcttgtatatacatgctgcaacttattcatcaatcagcagcattatatgtttttttgggttcaattcaaggatttcattataagaatttcttctaaacagaattgagtttgggatgaccaagatttatcctctggc-ttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGCCCCAAGTCTGTGCGAGAAAAATTTACTGGAATAATTAG
                                                                                           ||  |||  ||     | |    | |  |  | | ||    || || |||| || |     ||    |   |  |    |     ||| |  | |   |||| || || |||||||||||||||||||| || ||||| |||||||||| | | ||| || |  ||||||| || ||||| || || ||
----------------------------------------------------------------------------------------ggcat-ctttgctgcaggaagtcgtcgaacatagtcacaatg--tttttttaaaaagcagaagtttctaaaccgctgattcctgaaagctgtcacttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGACTCAAAGGCTATCAGAGAAAAGTTCACTGGCATGATAAG

upper sequence: Vv04s0043g00400.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G36410.1 (Glycine max), 3'ss of exon 3
gtaagtttcttcaatatttatctctgttcatttattttgatgatctcttgtatatacatgctgcaacttattcatcaatcagcagcattatatgtttttttgggttcaattcaaggatttcattataagaatttcttctaaacagaattgagtttgggatgaccaagatttatcctctggcttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGCCCCAAGTCTGTGCGAGAAAAATTTACTGGAATAATTAG
                                                                                                                                   | | |||   ||    |    |||||  ||| | | || | |  |    ||| || ||||| || ||||| |||||| |    || ||||||||||| ||||||||||| || |||||||| ||||||||||| ||||| || |||||
-------------------------------------------------------------------------------------------------------------------------------gtgctcttttccttactctttc---tttggcttgaaccacatgttttttgcttctt-tgttagGTCACCAAAGTGATGGCTCGGTCCGCTTCAGCTGATATTATGTGTGTTGGACCAAAGTCTGTTCGAGAAAAATTCACTGGCATCATTAG
















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|351017981|gb|FQ439147.1|FQ439147
EST:     ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGG                         GTTACTAAAGCTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGC
genomic: ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGGgtaagtttct ... cttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGC
EST: gi|349828307|gb|FQ416260.1|FQ416260
EST:     ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGG                         GTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGC
genomic: ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGGgtaagtttct ... cttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGC
EST: gi|349821758|gb|FQ408196.1|FQ408196
EST:     ATAGTGCCCATGGTGCCATTCCTGACCCTGGTTCCATTGTCATTGCCGGG                         GTTACTAACGTTATGGCTAGAATGGCCTCACCTGATATAATGTGTGTTGGC
genomic: ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGGgtaagtttct ... cttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGC
EST: gi|349827092|gb|FQ421365.1|FQ421365
EST:     ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGG                         GTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGTTATAATGTGTGTTGGC
genomic: ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGGgtaagtttct ... cttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGC
EST: gi|110419251|gb|EC985464.1|EC985464
EST:     ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGG                         GTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGC
genomic: ATAGTGCCCATGGTGCCATTCCTGAGCCTGGTTCCATTGTCATTGCCAGGgtaagtttct ... cttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaaacagaattgagtttgggatgaccaagatttatcctctggcttatgatagGTTACTAAAGTTATGGCTAGAATGGCCTCAGCTGATATAATGTGTGTTGGCCCCAAGTCTGTGCGAGAAAAATTTACTGGAATAATTAG
 ttctaaa  putative branch site (score: 2)
                             aagatttat  TA-rich tract