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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtctcctggataatgcatacctaatcgtgttggtctgatgagtgtctatatgccattgtgatgaaatttctgttcttttatcttgtcag

Basic information

species Oryza sativa
transcript LOC_Os04g41100.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G179097_T05 (Zea mays), 5'ss of exon 4
ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtctcctggataatgcatacctaatcgtgttggtctgatgagtgtctatatgccattgtgatgaaatttctgttcttttatcttgtcag------------
|| ||||||||||| ||||||||||| |||||||| |||||||||||||| ||||| || ||||| ||||| |||||||| |||||||||||||||||||    |  ||  |||| | |   ||||| | |    ||||||   ||     |||||    || ||| || |||  |||| |               
ATTTTTAGAACACTCGGCACACCTAATGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGTGTGAAAGTAAATTTTGTTAAACAACCgtaagtgtctct---accatttatacttcagt-tgttgttttacaaagtgtc---atttttgtgtgacaggatatcttttttttgttcttattgttaggtataatag

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G179097_T08 (Zea mays), 5'ss of exon 4
ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtctcctggataatgcatacctaatcgtgttggtctgatgagtgtctatatgccattgtgatgaaatttctgttcttttatcttgtcag---
|| ||||||||||| ||||||||||| |||||||| |||||||||||||| ||||| || ||||| ||||| |||||||| |||||||||||||||||||    |  ||  |||| | |   ||||| | |    ||||||   ||     |||||    || ||| || |||  |||| |      
ATTTTTAGAACACTCGGCACACCTAATGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGTGTGAAAGTAAATTTTGTTAAACAACCgtaagtgtctct---accatttatacttcagt-tgttgttttacaaagtgtc---atttttgtgtgacaggatatcttttttttgttcttattgttag

upper sequence: LOC_Os04g41100.6 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 4
ATATTTAGAACACTTGGCACACCTAACGAGAAGATATGGCCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtctcctggataatgc-atacctaatcgtgttggtctgatgagtgtctatatgccattgtgatgaaatttctgttcttttatcttgtcag
|| |||||||||||||||||||||| ||||||||| |||||||||||||| ||||| || || || ||||| ||||||||||||||||||||||||||||    ||| | | ||   || |  | ||| | |  |||||||| ||      ||||  ||| | || | ||  ||| | |||||||
ATTTTTAGAACACTTGGCACACCTAGCGAGAAGATTTGGCCTGGCTATGCTAAATTACCAGGCGTGAAAGTAAATTTTGTCAAACAACCgtaagtgtctctaccatagtactatttatacttttcttgttttactgagtgtcaat-----tttgtc-tgacagttttttttgtttttattgtcag

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|218494622|gb|FG958132.1|FG958132
EST:     CCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC                         GTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
genomic: CCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtct ... atcttgtcagGTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
EST: gi|44675738|gb|CR289172.1|CR289172
EST:     GCCGGGTGTAAAAGTCAATTTTGTCAAACAACC                         GTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
genomic: GCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtct ... atcttgtcagGTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
EST: gi|29631235|gb|CB636244.1|CB636244
EST:     TGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC                         GTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
genomic: TGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtct ... atcttgtcagGTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
EST: gi|86910572|gb|CI294713.1|CI294713
EST:     CCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC                         GTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
genomic: CCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtct ... atcttgtcagGTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
EST: gi|58687429|gb|CK076116.1|CK076116
EST:     CCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC                         GTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
genomic: CCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtct ... atcttgtcagGTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
EST: gi|29679248|gb|CB675523.1|CB675523
EST:     CCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACC                         GTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC
genomic: CCTGGCTATGCCAAATTGCCGGGTGTAAAAGTCAATTTTGTCAAACAACCgtaagtgtct ... atcttgtcagGTACAACCGATTAAGAGATAAGTTCCCAGCTGCATCTTTTTCTGGTCGTCC