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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgctcctgtcatttgcaaggaattaactgcacctgtcgtacaaagaaactgcagtactcgtatagatcactaacaaacataaatgaactatgctgcagATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCAC

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 6
gtaagatgctcctgtcatttgcaaggaattaactgcacctgtcgtacaaagaaactgcagtactcgtatagatcactaacaa--acataaatgaactatgctgcagATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCAC
                            | |  ||   | ||  || | |||||| |  | |||  |||||||| |||| ||  ||| ||||||| |||  ||||||||||||||||||||||||||||||||||||| || | |  |||||||||||||||||||||||| | ||||| ||| |||| | 
---------------------------gtaagatgtgacagtactatagagaaaccgttgcactaatatagatctctaataattacagaaatgaattattttgcagATGATCGTGCTGATGTTGAAGGAAATGCTCAAGATCGACCTGTTGTCAGGTTGTCTTTTGCATCGTTGTTTGATGCTTTTGGAAG

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G078576_T03 (Zea mays), 3'ss of exon 5
gtaagatgctcctgtcatttgcaaggaattaactgcacctgtcgtacaaagaaactgcagtactcgtatagatcactaacaa--acataaatgaactatgctgcagATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCAC
                            | |  | || |  |  |  | | | ||||  | |||  ||||| || |||| |   ||| ||| |||  ||  || ||||||||||||||||||||||||||||||||||||||| |  |||||||||||||||||||||| | | ||||| |||||||| | 
---------------------------gtaagattcagcaatact--agatagactgtggcactaatatagctctctaatagttacagaaacgaatcattatgtagATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGACCTGTTGTCAGGTTGTCTTTTGCATTGTTGTTTGATGCTCTTGGAAG
















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|29628456|gb|CB633467.1|CB633467
EST:     TCATGATAATCCATATTACAAGGCCTTAAGCAATGCCAAAGACAGTCAAT                         ATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGT
genomic: TCATGATAATCCATATTACAAGGCCTTAAGCAATGCCAAAGACAGTCAATgtaagatgct ... tatgctgcagATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGT
EST: gi|58693104|gb|CK081791.1|CK081791
EST:     TCATGATAATCCATATTACAAGGCCTTAAGCAATGCCAAAGACAGTCAAT                         ATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGT
genomic: TCATGATAATCCATATTACAAGGCCTTAAGCAATGCCAAAGACAGTCAATgtaagatgct ... tatgctgcagATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGT
EST: gi|58659682|gb|CK048362.1|CK048362
EST:     TCATGATAATCCATATTACAAGGCCTTAAGCAATGCCAAAGACAGTCAAT                         ATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGT
genomic: TCATGATAATCCATATTACAAGGCCTTAAGCAATGCCAAAGACAGTCAATgtaagatgct ... tatgctgcagATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaactgcagtactcgtatagatcactaacaaacataaatgaactatgctgcagATGATCGTGCTGATGTTGAAGGAAATGCTCAAAATGGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCAC
                        cactaac  putative branch site (score: 1)
                           taacaaacataaat  TA-rich tract