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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcaatgcagcctcacatgttaacttgttccccttttttgtattaaaattccagaaatgttaaagaaaattttccattttgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGATGGCCATAGACAACACTGTTGGACTCCAAGGTGGTTTTATATGGGACTGG

Basic information

species Oryza sativa
transcript LOC_Os01g72340.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 3
gtatgttcaatgcagcctcacatgttaacttgttccccttttttgtattaaaattccagaaatgttaaagaaaattttccattttgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGATGGCCATAGACAACACTGTTGGACTCCAAGGTGGTTTTATATGGGACTGG
||||| | |      |||||||| ||||      ||| || |  ||||| | ||    ||  || | ||  || |||| | ||||| ||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||| ||||||||||||| ||||||||||||||||||
gtatgctaagcatgacctcacatattaata---accctttatccgtattcatat----gatttgatgaaagaactttttccttttgctttcaagATATTCACATGCTATGGGAAACAGTAATGGGAATATTGATGCGTATTGGATGGCCATAGACAACACTTTTGGACTCCAAGGAGGTTTTATATGGGACTGG

upper sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G26700.1 (Glycine max), 3'ss of exon 10
----------gtatgttcaatgcagcctcacatgttaacttgttccccttttttgtattaaaattccagaaatgttaaagaaaattttccattt--tgttttcaa-----------gATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGATGGCCATAGACAACACTGTTGGACTCCAAGGTGGTTTTATATGGGACTGG
          |||  || |   || |  || |   | |||| | |   |   |  | || | | |  | | ||  | |   || ||||  ||||  | | | |||           | ||||||||||| ||||||||||||||||| ||| |  ||  |||||||   || || ||||||||| ||||||||||||| || ||||| ||||| |||
gtatgattttgtagttttacatcaacaacataatatgacttctactgttccctgttgtttacagtg-atagataattatataatttttttatttgttatgtccaacccaaatggcagGTATTCACATGCAATGGGAAACAGTAATGGGAATCTACATATATATTGGGAAGCAATTGACAACACTTTTGGACTCCAAGGAGGCTTTATTTGGGATTGG

upper sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G37670.1 (Glycine max), 3'ss of exon 5
---------gtatgttcaatgcagcctcacatgttaacttgttccccttttttgtattaaaattccagaaatgttaaagaaaattttccattttgtt---ttcaa-----------gATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGATGGCCATAGACAACACTGTTGGACTCCAAGGTGGTTTTATATGGGACTGG
         |||  || |   || |  || |   | |||| | ||  |   |  | ||| | |   ||| |  ||| | ||  ||||    |||||    | |||           | ||||||||||| ||||||||||||||||| ||| |  ||  |||||||   || || ||||||||  ||||||||||||| || ||||| ||||| |||
gtatgatttgtagttttacatcaacaacataatatgacttctaccgttccctgattttacagtgatagata-attatataatttttttttatttgtgatgtccaacccaaatggcagGTATTCACATGCAATGGGAAACAGTAATGGGAATCTACATATATATTGGGAAGCAATTGACAACACATTTGGACTCCAAGGAGGCTTTATTTGGGATTGG

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|58688410|gb|CK077097.1|CK077097
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|58692909|gb|CK081596.1|CK081596
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|14571259|gb|BI118627.1|BI118627
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|58687216|gb|CK075903.1|CK075903
EST:     CTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|58663708|gb|CK052394.1|CK052394
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|38568808|gb|CD671023.1|CD671023
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|29657376|gb|CB653651.1|CB653651
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|58670588|gb|CK059274.1|CK059274
EST:     GAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: GAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtattaaaattccagaaatgttaaagaaaattttccattttgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGATGGCCATAGACAACACTGTTGGACTCCAAGGTGGTTTTATATGGGACTGG
                                   ttttccattttgtttt  CT-rich tract
                  agaaatgttaaagaaa  TA-rich tract