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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgtgaatatataaatgtgttacaaaataatgttatatattggataggtggctttatgtgtgaactatttattgtgttgattatcttgcattgctgtactacttcctaatccacttcattattcctactcaagcagGAATCTCTTGACAACATTAATCTTTTCTCAATCATAACTGTGATGTCATTTTTCCTTTTGGCCCCTGTTGCCTTCCTAACAGAAGGCATCAAAATCACTC

Basic information

species Oryza sativa
transcript LOC_Os08g25624.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25624.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G174107_T01 (Zea mays), 3'ss of exon 5
gtaattgtgaatatataaatgtgttacaaaataatgttatatattggatagg---tggctttatgtgtgaactatttattgtgttgattatcttgcattgctgta-ctacttcctaatccacttcattattcctactcaagcagGAATCTCTTGACAACATTAATCTTTTCTCAATCATAACTGTGATGTCATTTTTCCTTTTGGCCCCTGTTGCCTTCCTAACAGAAGGCATCAAAATCACTC
|||| |   ||||| |   ||  |   |||   |  || | ||| | | | |   ||||||  | | ||   | |  || |||   ||| ||   || | |  |  ||| |||||||| ||||||||     ||  |    ||||||||  | |||||| ||||||| ||||| ||||| || |||||||||||||||||||||||||||||| ||||| | ||||||||  ||||||| ||||
gtaacta-aaatatct---tgcatcttaaagatagtttgtttat-gaacatgcattggcttcttttctgtcatgtccat-gtgc-aattgtc---cacttccatctctaattcctaatgcacttcatatgctctctttccacagGAATCCTTGGACAACCTTAATCTCTTCTCTATCATTACAGTGATGTCATTTTTCCTTTTGGCCCCTGTTACCTTCTTTACAGAAGGTGTCAAAATTACTC
















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|58610772|gb|CK038484.1|CK038484
EST:     CCTTCCAGTCAAGGAATGTGCTGAGCAAGAAACTCATGGTTAAAAAGGAG                         GAATCTCTTGACAACATTAATCTTTTCTCAATCATAACTGTGATGTCATTT
genomic: CCTTCCAGTCAAGGAATGTGCTGAGCAAGAAACTCATGGTTAAAAAGGAGgtaattgtga ... actcaagcagGAATCTCTTGACAACATTAATCTTTTCTCAATCATAACTGTGATGTCATTT
EST: gi|58688340|gb|CK077027.1|CK077027
EST:     CCTTCCAGTCAAGGAATGTGCTGAGCAAGAAACTCATGGTTAAAAAGGAG                         GAATCTCTTGACAACATTAATCTTTTCTCAATCATAACTGTGATGTCATTT
genomic: CCTTCCAGTCAAGGAATGTGCTGAGCAAGAAACTCATGGTTAAAAAGGAGgtaattgtga ... actcaagcagGAATCTCTTGACAACATTAATCTTTTCTCAATCATAACTGTGATGTCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttgcattgctgtactacttcctaatccacttcattattcctactcaagcagGAATCTCTTGACAACATTAATCTTTTCTCAATCATAACTGTGATGTCATTTTTCCTTTTGGCCCCTGTTGCCTTCCTAACAGAAGGCATCAAAATCACTC
                      tcctaat  putative branch site (score: 2)
                                        ttcctactc  putative PPT
                                 ttcattatt  TA-rich tract