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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttatttgtgtaattggtgcattggaatgattttaagttgaatccatattattgttccagtttgttcttcatatggcaatttattgtcttgattttcagGAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACG

Basic information

species Oryza sativa
transcript LOC_Os12g40830.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 10
ttttatttgtgtaatt-ggtgcattgga-atgattttaagttgaatccatattattgttccagtttgttcttcatatg-gcaattta--ttgtcttgattttcagGAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACG
     |  |||||||| | | ||      ||| ||||   |||  |   |||  |  |   |  |   | |  || |  |  |||||  || || |  | ||||||||||||  |||||||||||||||||||||||||| |||||||||||||||||||||
-----tgggtgtaatttgattcagaacttatgctttttttttgttttggtatggtaatattatatgtatatgtatgtttgagatttactttatcattttcttcagGAACAACAGCCAGAACAATTTAAGATTGAGATACCAAAGATACCTGCATATTTCACG
















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|568331|gb|D39176.1|D39176
EST:     CACTTATTGAAGATAAGCTGCTCCTCATTGGAAGCCACAAAAAAGCAAAG                         GAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATAT
genomic: CACTTATTGAAGATAAGCTGCTCCTCATTGGAAGCCACAAAAAAGCAAAGgtaaactttt ... tgattttcagGAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATAT
EST: gi|427643|gb|D23776.1|D23776
EST:     CACTTATTGAAGATAAGCTGCTCCTCATTGGAAGCCACAAAAAAGCAAAG                         GAACAACCACCAGAACAATTTAAGATTGNGATACCCAAGATACCTGCATAT
genomic: CACTTATTGAAGATAAGCTGCTCCTCATTGGAAGCCACAAAAAAGCAAAGgtaaactttt ... tgattttcagGAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATAT
EST: gi|13165352|gb|AU174149.1|AU174149
EST:     CACTTATTGAAGATAAGCTGCTCCTCATTGGAAGCCACAAAAAAGCAAAG                         GAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATAT
genomic: CACTTATTGAAGATAAGCTGCTCCTCATTGGAAGCCACAAAAAAGCAAAGgtaaactttt ... tgattttcagGAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATAT
EST: gi|89185094|gb|CI049640.1|CI049640
EST:     CACAAAAAAGCAAAG                         GAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATAT
genomic: CACAAAAAAGCAAAGgtaaactttt ... tgattttcagGAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catattattgttccagtttgttcttcatatggcaatttattgtcttgattttcagGAACAACCACCAGAACAATTTAAGATTGAGATACCCAAGATACCTGCATATTTCACG
                                          tcttgat  putative branch site (score: 4)
                                       ttgtctt  CT-rich tract
                                 aatttattgt  TA-rich tract