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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgataccattacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatgcggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAGGCGAATCTGCGGCTGCGCGACCCCGTGTACGGCTGCATGGGCGCCATCT

Basic information

species Oryza sativa
transcript LOC_Os01g60960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G092517_T01 (Zea mays), 3'ss of exon 2
gtacgatacca--ttacaggtcaaagcattccttaaattgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatg-cggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAGGCGAATCTGCGGCTGCGCGACCCCGTGTACGGCTGCATGGGCGCCATCT
|||      ||  ||  ||   ||| | | | ||   |     || | | ||     |       | |  | ||    |    |   ||  |||||||| |  |||| |||||| || ||| | |||||||||||||||||||| ||||| || ||| |||| || || |||||||| ||||||||||||||||
gtaaagcctcaacttgaagaaaaaatcgtgcttt---tctagtctatagttaaaagatttcagtgtagacttgtaaacgtgtcgattgtcacagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT
















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|88226735|gb|CI224720.1|CI224720
EST:     CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTG                         GAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
genomic: CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgatacc ... gcggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
EST: gi|117249598|gb|CT863295.1|CT863295
EST:     CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTG                         GAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
genomic: CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgatacc ... gcggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
EST: gi|88385675|gb|CI566537.1|CI566537
EST:     CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTG                         GAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG
genomic: CCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtacgatacc ... gcggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacctttcgctagcttgtgcattaatggcttcgtcggtgcaatgcggtttcagGAGGTCGGCGAGGCGGAGAGAGCCGACGCGGCGAGCAGCCTGGTGTACGAGGCGAATCTGCGGCTGCGCGACCCCGTGTACGGCTGCATGGGCGCCATCT
                     cattaat  putative branch site (score: 3)
                      attaat  TA-rich tract