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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaacagctcctgttgcactggtgtccaattggtagtttctaaaatcttgatcatatccctgatatacacagcataaagacattgttttcatactttcagGTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATGTAA

Basic information

species Oryza sativa
transcript LOC_Os02g42520.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G149272_T06 (Zea mays), 3'ss of exon 7
------------------------------------------------------------------------------------------tcaacagctcctgttgcactgg-tgtccaattggtagtttctaaaatcttgatcatatccctgatatacaca-gcataaagacat-tgttttcatactttcagGTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATGTAA
                                                                                          | |  | | |    || |   | || | | ||||     |  | ||  |  |    |||   | |    |   ||||  |   |  | ||||||| ||| |||||  | ||  || | ||  ||||||| |  |||||||| ||||| || ||||||||| | |||||||| || |||||||| |||||||||||||||||||
gtatttacaccatgcaattggtcatctgctcatcgctctcttttggtatcatgcaattctgcttgactgctacactaataaactgttgacttataatcacactatgtatgagatgactatttggggaaataaacaaaatacagtgcatcatcgttccctaagtgcatgtaagtagattttttcatgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGATGTAA

upper sequence: LOC_Os02g42520.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G149272_T02 (Zea mays), 3'ss of exon 7
------------------------------------------------------------------------------------------tcaacagctcctgttgcactgg-tgtccaattggtagtttctaaaatcttgatcatatccctgatatacaca-gcataaagacat-tgttttcatactttcagGTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATGTAA
                                                                                          | |  | | |    || |   | || | | ||||     |  | ||  |  |    |||   | |    |   ||||  |   |  | ||||||| ||| |||||  | ||  || | ||  ||||||| |  |||||||| ||||| || ||||||||| | |||||||| || |||||||| |||||||||||||||    
gtatttacaccatgcaattggtcatctgctcatcgctctcttttggtatcatgcaattctgcttgactgctacactaataaactgttgacttataatcacactatgtatgagatgactatttggggaaataaacaaaatacagtgcatcatcgttccctaagtgcatgtaagtagattttttcatgcttgcagGTAATCAAAAGGATTACTGATGGAGGGGTGGATTACTCATTTGAATGTGTGGGTGATTCTGGAGTAGTCTCCACTGCACTTCAATCATGTTCTGAT----
















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|27576860|gb|CA999554.1|CA999554
EST:     GTGTCACAGATTTTATTAATCCAGAAGAATTGAATGAACCTGTTCAGCAG                         GTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTG
genomic: GTGTCACAGATTTTATTAATCCAGAAGAATTGAATGAACCTGTTCAGCAGgtacatcatc ... atactttcagGTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTG
EST: gi|27577599|gb|CB000294.1|CB000294
EST:     GTGTCACAGATTTTATTAATCCAGAAGAATTGAATGAACCTGTTCAGCAG                         GTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTG
genomic: GTGTCACAGATTTTATTAATCCAGAAGAATTGAATGAACCTGTTCAGCAGgtacatcatc ... atactttcagGTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatcatatccctgatatacacagcataaagacattgttttcatactttcagGTGGTGAAGCGGCTGACCAATGGAGGTGCAGATTACTCTTTTGAGTGCGTGGGTGATACAGGAGTAGTGTCGACTGCACTGCAATCATGTTCTGATGTAA
            ccctgat  putative branch site (score: 4)
                                        ttttcat  putative PPT
                                    attgtttt  TA-rich tract