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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatgatgaattcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT

Basic information

species Oryza sativa
transcript LOC_Os11g06340.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G122039_T05 (Zea mays), 3'ss of exon 2
ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatg-atgaat-tcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT
   ||| |||||||| |  |||||      |   ||   |     ||||       |||| | |    | | |||   ||| ||||  ||| || ||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| || || || ||||||||||| |||||||||||||      
-tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg-ttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGTGTAA------

upper sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatg-atgaat-tcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT
   ||| |||||||| |  |||||      |   ||   |     ||||       |||| | |    | | |||   ||| ||||  ||| || ||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| || || || ||||||||||| |||||||||          
-tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg-ttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT----------

upper sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2
ccctttcaccctaggct--cataatatcgcgacgacttagcaatgat-atgcgctatgatgaattcaacgcttaaatcctaatggtgtttgtatggtttgc---agAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT
           ||   |  || | | | |    | ||||   ||  | ||    |   || || |    ||||       ||  ||  |||| |   ||||   ||  |||| | || ||  |  |    |||||  ||||||| |||||||||||||| |||||||| || |||||||| || ||||||||||||          
------agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----------

upper sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2
ccctttcaccctaggct--cataatatcgcgacgacttagcaatgatatgcgctatgatgaattcaacgcttaaatcctaatggtgtttgtatggtttgc---agAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT
    |      ||   |  || | | | |  | | ||||    |  |||    |   || || |    ||||       ||  ||  |||| ||  ||||   ||  |||| | || ||  |  |    |||||| ||||||| |||||||||||||| |||||||| || |||||||| || ||||||||||||          
----tgagtgataaattgtcaaatttttgttatgccttaattttt-tatttcttcaaattaagttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT----------

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|66919054|gb|CX105902.1|CX105902
EST:     TTGAGGAGCGCTGCAAGCCCCAGTGCGTAAAGCCACTCTATGAGTATGAG                         AAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACT
genomic: TTGAGGAGCGCTGCAAGCCCCAGTGCGTAAAGCCACTCTATGAGTATGAGgtgcgtctgt ... tggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACT
EST: gi|58671735|gb|CK060421.1|CK060421
EST:     TTGAGGAGCGCTGCAAGCCCCAGTGCGTAAAGCCACTCTATGAGTATGAG                         AAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAAC
genomic: TTGAGGAGCGCTGCAAGCCCCAGTGCGTAAAGCCACTCTATGAGTATGAGgtgcgtctgt ... tggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAAC
EST: gi|163928761|gb|EG711898.1|EG711898
EST:     TTGAGGAGCGCTGCAAGCCCCAGTGCGTAAAGCCACTCTATGAGTATGAG                         AAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACT
genomic: TTGAGGAGCGCTGCAAGCCCCAGTGCGTAAAGCCACTCTATGAGTATGAGgtgcgtctgt ... tggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcgctatgatgaattcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT
                            tcctaat  putative branch site (score: 2)
                       ttaaat  TA-rich tract