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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatctttcataaatatttaggatcattcttgattattttccagctcctagaattttgtgtttctttcaggttgatctttcatagacatttaggatcattcttgattattttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g12800.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G134582_T01 (Zea mays), 3'ss of exon 5
gtgagtgatctttcataaatatttaggatcattcttgattattttccagctcctagaattttgtgtttctttcaggttgatctttcatagacatttaggatcattcttgatta--ttttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG
                                                |    |    ||   | ||| | | |   | || |   ||   | |  | |    |  ||| |||  | || |   || ||||||  |   | || ||||||||||| |||||||| |||||||||||| | || |||||| ||||||| || | |||||| ||| | | ||||||  | || |||  |||  ||| || ||
------------------------------------------------gtgagtgatgttcaatatttttattaaaatcatttaatattttcttgcatgccattgtttgcttagatgtttctgtctgcttgaacctgc-gcttgtttcagGCCCATATTGAGCAATGGATTGACTTTGCTGCAACAGAGATTGATGCAAACATTGGAAAGTGGTTGTACCCACGGATGGGGTTTTATCCCCATGCTGGTG

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 5
gtgagtgatctttcataaatatttaggatcattcttgattattttccagctcctagaattttgtgtttctttcaggttgatctttcatagacatttaggatcattcttgattattttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG
                                                |    ||   ||   | |||| ||||  || || ||  ||     | | | ||  || |   |   | |  | |  | ||  |     || || ||||||||||| |||||||||||||| |||||| | || |||||||||||||| |  | |||||| ||| | | ||||||| | || |||  ||| |||| |||||
------------------------------------------------gtgagtaatgttcaatatttcattcaaattaattttatatt----tcttgaatttttttgcttagatgtttctgtccgtttgaacctgtgcttgtttcagGCCCATATTGAGCAGTGGATGGACTTTGCTGCGACAGAGGTTGATGCCAGCATTGGAAAGTGGTTGTACCCACGTATGGGGTTTTATCCCTATGCTGCTG
















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|88991494|gb|CI034829.1|CI034829
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58601569|gb|CK012097.1|CK012097
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58691659|gb|CK080346.1|CK080346
EST:     CCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
EST: gi|58663459|gb|CK052145.1|CK052145
EST:     CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATAT                         GCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT
genomic: CTCGCTCGAAGTCTGACAACCCACTCTATGGGTCTTCACTGATTGAATATgtgagtgatc ... tttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaggatcattcttgattattttaccagctccttgaatttcttgtttctttcagGCCCACATTGAGCAGTGGATTGACTTTTCAGCCACAGAGGTTGATGCTAATACTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTG
           tcttgat  putative branch site (score: 4)
                                      tttcttgtttctttc  putative PPT
         attcttgattatttta  TA-rich tract