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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGAAGCTCCAAGTACAGGGGCGTGACGCTCCACA

Basic information

species Oryza sativa
transcript LOC_Os04g55560.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G076602_T01 (Zea mays), 3'ss of exon 3
gtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgc-cacggtttcgttagatcatactactattactgtagctgcaagattaacg----ggatcatt-gcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGAAGCTCCAAGTACAGGGGCGTGACGCTCCACA
        | |||  |||  |||||    |      ||    | |  |  || ||  |  |   |  || || ||| || | ||       ||     ||  |||    ||   |   ||||||| || |||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||
--------gtgatttatt--tattatacaa------ctgcgctatactaggtagcatatagcaacaatatat-atagtaattttttctcgtctatctaatccacgtcttggtctaccagcagATGTGCCACCTGAGCAAGGAGGAGTTCGTTCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGCAGCTCCAAGTACAGGGGCGTGACGCTCCACA

upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G174784_T02 (Zea mays), 3'ss of exon 3
gtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGAAGCTCCAAGTACAGGGGCGTGACGCTCCACA
                              | ||    | || | |       |   ||     | ||   |||   | | || || |   |    |  || | |        |||||| || |||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||   
---------------------------gtgatttatactcctatacggagcatgtagcgagaaagata---catgtaattttttctttccttc---gtctaccag-

upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G174784_T03 (Zea mays), 3'ss of exon 3
gtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGAAGCTCCAAGTACAGGGGCGTGACGCTCCACA
                              | ||    | || | |       |   ||     | ||   |||   | | || || |   |    |  || | |        |||||| || |||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||
---------------------------gtgatttatactcctatacggagcatgtagcgagaaagata---catgtaattttttctttccttc---gtctaccag--------cagATGGGCCACCTGAGCAAGGAGGAGTTCGTTCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGCAGCTCCAAGTACAGAGGCGTGACGCTCCACA

upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G18640.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------gtgagagcgcgatcgattattattacctgaactttcctttcttttcatgagtcgccacggtttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGAAGCTCCAAGTACAGGGGCGTGACGCTCCACA
                                                          |   | |  || |  | ||   ||  |    |   | || | | |   |||        |||  |||  |   | || | | |   |        | | || |  ||  |   |||||||||| || |||||||| ||||||||||||||||| || || || ||||| || || ||  | ||||||||||| || || || || ||  | ||||
gtgatcaatttgtggattatgttttttttattcgatataaatgcatttatcgtatttatcttatcttgaacagtcatacgta--taggatgcaccttatctcctacagttagtgttttttttttatcttgaattattctcatgat-----tttgttaaatgcaatgttaatagATGAGCAATCTTACCAAGGAAGAGTTCGTCCACGTGCTTCGCCGACAAAGCACTGGATTTCCGAGAGGAAGCTCCAAATATAGAGGTGTCACTTTGCACA

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|29644662|gb|CB649669.1|CB649669
EST:     AGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAG                         ATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGC
genomic: AGGCCGACATCAATTTCAGCTTGGAGGATTACGAGGATGACCTGAAGCAGgtgagagcgc ... atcattgcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgttagatcatactactattactgtagctgcaagattaacgggatcattgcagATGAGCAACCTGACCAAGGAGGAGTTCGTCCACGTGCTCCGGCGGCAGAGCACGGGGTTCCCCCGGGGAAGCTCCAAGTACAGGGGCGTGACGCTCCACA
                                   gattaac  putative branch site (score: 2)
               tactatta  TA-rich tract