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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctctgtagctctaagctgttcagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA

Basic information

species Oryza sativa
transcript LOC_Os02g39570.6
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G407044_T02 (Zea mays), 3'ss of exon 8
gtctctgtagctctaagctgtt----cagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
     | | ||| ||||   |      | || |  |  | |||||| ||| ||||     | |   ||||| | |||| | |    ||||||| | | || ||| | | ||||||||| || |||||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| |||||||||||||| ||||||||||
----atatggctttaagaaatggtaataatgcttgacctgcatgtttatgcatactgttgttatcttgcagctgctaatccagtattgattttgtgttgtacagGCGACTGGACTTCGCTCGCATACTCTCTCCATCCTTGTGAATGACTGTCCTGGTGTCCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G007647_T01 (Zea mays), 3'ss of exon 7
gtctctgtagctctaagctgtt--cagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
     |  |  |  ||  || |   | || | ||  | |||||| ||| ||||     | |   ||||| | |||| | |    ||||||| | |||| ||| ||| ||||||| | || ||||| || ||||||||||| |||||||| |||||||||||||||||||| ||||| |||||||||||||| ||||||||||
--acatagatttaaaaaatggtaataatgcttaacctgcatgtttatgaatactgttgttatcttgcagctgctaatccagtattgattttgtgtggtacagGCAACTGGACTTTGCTCGCATACCCTCTCCATCCTTGTGAATGATTGTCCTGGTGTTCTCAACATTGTAACAGGAGTCTTTGCTCGCAGGGGCTACAATA

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 7
gtctctgtagct---ctaagctgttcagtgttaaatatacatgttaatgtata-caaaattaaggatg-caggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
    ||||  ||   |||   |||| | ||| | ||   ||||| ||| |  | |||  ||  | ||| || ||| ||   |   |  |||  |   |    ||| | |||||| |||||||||| ||| ||||||| ||||| || |||   ||||| ||||| |||||||||||||| || |||||| | |||||||| || |
tctcctgtgccttcactactatgtttattgt-acattagcatgt-aatattcatcaattttctgaatgacatgtcttactgttggtgggataatgcct---tcagACTAGTGGAATTCGATCACACACTTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA

upper sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 7
----gtctctgtagctctaagctgttcagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
        || |   | |     ||| ||  |  ||||| ||  | ||| |    ||    | |  ||    |      ||     ||   | |||   | ||| | |||||| |||||||||| ||  ||||||| ||||| || |||   ||||| ||||| |||||||||||||| || |||||| | |||||||| || |
cttcactactatgtttattgtacgtt-agcatgtaatattca--tcaattttatgaatgacatgcttgtgactgtcttactgttggtggaataattcctt-cagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA

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|32948291|gb|BP184863.1|BP184863
EST:     GCTCACTGGGGCGTCCTTGATGATGAAGAT                         TCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
genomic: GCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
EST: gi|32948361|gb|BP184933.1|BP184933
EST:     CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT                         TCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
genomic: CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
EST: gi|33682200|gb|CF310439.1|CF310439
EST:     CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGAT                         TCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT
genomic: CCATGAACCAAGTACTTGATGCTCACTGGGGCGTCCTTGATGATGAAGATgtaagtttca ... tttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA
                            agctaaa  putative branch site (score: 3)
                                        ttttattt  putative PPT
                          taagctaaatatgatt  TA-rich tract