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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGACAAAAGCCAAGCTGAGAGGGATTGGGTTCTTTCTGAATTTAAATCAGGGAAAAGCCCTATCATGACAGCGACTGATGTGGCTGCTCGAGGCTTAGgtatacaaaaatcctcccagatcgatgaattatatttatttctgtaaactaatgccacttatatctggaaacag

Basic information

species Oryza sativa
transcript LOC_Os01g10050.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10050.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G143246_T01 (Zea mays), 5'ss of exon 8
GGTGACAAAAGCCAAGCTGAGAGGGATTGGGTTCTTTCTGAATTTAAATCAGGGAAAAGCCCTATCATGACAGCGACTGATGTGGCTGCTCGAGGCTTAGgtatacaaaaatcctcccagat-cgatgaattatat-ttatttctgtaaactaatgc-cacttatatct----ggaaacag
|||||||| |||||||| ||  |||||||||| |||||||||||||| ||||||||||| ||||| ||||| || |||||||| |||||||||||| ||||||| |  ||   ||   ||||  |||  ||  ||| ||   |  | ||| | || | |  || | ||     | ||||||
GGTGACAAGAGCCAAGCAGAACGGGATTGGGTCCTTTCTGAATTTAAGTCAGGGAAAAGTCCTATTATGACGGCCACTGATGTTGCTGCTCGAGGCCTAGgtatgcccaa---ctttgagatgtgatacatcttatatttcctgaggaaattgatacacgtttctttcccttggaaaacag

upper sequence: LOC_Os01g10050.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA08G20670.1 (Glycine max), 5'ss of exon 8
GGTGACAAAAGCCAAGCTGAGAGGGATTGGGTTCTTTCTGAATTTAAATCAGGGAAAAGCCCTATCATGACAGCGACTGATGTGGCTGCTCGAGGCTTAGgtatacaaaaatcctcccagatcgatgaatt---atatttat-ttctgtaaactaatgccacttat--atctggaaacag--------------------
|| || ||||| ||||| || || |||||||| || || |||||||||||||| ||||| ||||| ||||| || || ||||| || || || || ||||||  | ||  ||   |     |  || | ||   |||||  | ||| ||  |  ||    | |||   || |    | ||                    
GGAGATAAAAGTCAAGCAGAAAGAGATTGGGTGCTCTCAGAATTTAAATCAGGAAAAAGTCCTATTATGACGGCAACAGATGTTGCAGCCCGTGGTTTAGgtgcaaaagcatttgctttatttaattatttgtcatattgttattcagtggatgaaaatgaattagtgatataattatagttatggaaatactcggtact

upper sequence: LOC_Os01g10050.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA07G01260.1 (Glycine max), 5'ss of exon 8
GGTGACAAAAGCCAAGCTGAGAGGGATTGGGTTCTTTCTGAATTTAAATCAGGGAAAAGCCCTATCATGACAGCGACTGATGTGGCTGCTCGAGGCTTAGgtatacaaaaatcctcccagatcgatgaatt---atatttat-ttctgtaaactaatgccactta----tatctggaaacag------------------
|| || ||||| ||||| || || |||||||| || || |||||||||||||| ||||| ||||| ||||| || || ||||| || || || ||  |||||  | |||  |   |     |  ||   ||   |||||  | ||| ||  |  ||    | |||    ||| | |  |  |                  
GGAGATAAAAGTCAAGCAGAAAGAGATTGGGTGCTCTCAGAATTTAAATCAGGCAAAAGTCCTATTATGACGGCAACAGATGTTGCAGCCCGTGGTCTAGgtgcaaaaacttttgctttatttaattctttgtcatattgttattcagtggatgaaaatgatttagtgatatatagttatggaaatactcagtactttta

upper sequence: LOC_Os01g10050.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTGACAAAAGCCAAGCTGAGAGGGATTGGGTTCTTTCTGAATTTAAATCAGGGAAAAGCCCTATCATGACAGCGACTGATGTGGCTGCTCGAGGCTTAGgtatacaaaaatcctcccagatcgatg--------aattatatttatttctgt---aaactaatgccacttatatctgg---aaacag
|| || ||||| ||||| || || ||||||||||| || || |||| |||||| ||||||||||| ||||| || || || || || ||||| || |||||||   ||   |  || ||  |   ||        || | | || |     ||   || ||||   || || | | ||     |||||
GGAGATAAAAGTCAAGCGGAAAGAGATTGGGTTCTCTCGGAGTTTAGATCAGGCAAAAGCCCTATAATGACTGCTACAGACGTTGCAGCTCGTGGATTAGgtactaaatctttttctcatctgcgtgcaaacatcaactctcttaaccatggtgacaagctaacaacagttctttttgttttgaacag

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|66914774|gb|CX101622.1|CX101622
EST:     AGGGAAAAGCCCTATCATGACAGCGACTGATGTGGCTGCTCGAGGCTTAG                         ATGTTAAGGATGTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGG
genomic: AGGGAAAAGCCCTATCATGACAGCGACTGATGTGGCTGCTCGAGGCTTAGgtatacaaaa ... ctggaaacagATGTTAAGGATGTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGG
EST: gi|88504584|gb|CI432090.1|CI432090
EST:     CTGCTCGAGGCTTAG                         ATGTTAAGGATGTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGG
genomic: CTGCTCGAGGCTTAGgtatacaaaa ... ctggaaacagATGTTAAGGATGTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGG
EST: gi|88484026|gb|CI421297.1|CI421297
EST:     TGGCTGCTCGAGGCTTAG                         ATGTTAAGGATNTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGG
genomic: TGGCTGCTCGAGGCTTAGgtatacaaaa ... ctggaaacagATGTTAAGGATGTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGG
EST: gi|86259893|gb|CI065766.1|CI065766
EST:     GGCTGCTCGAGGCTTAG                         ATGTTAAGGATGTAAAATATGTCATTAACTATGACTTTCCGGGATCATTGG
genomic: GGCTGCTCGAGGCTTAGgtatacaaaa ... ctggaaacagATGTTAAGGATGTTAAATATGTCATTAACTATGACTTTCCGGGATCATTGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGACAAAAGCCAAGCTGAGAGGGATTGGGTTCTTTCTGAATTTAAATCAGGGAAAAGCCCTATCATGACAGCGACTGATGTGGCTGCTCGAGGCTTAGgtatacaaaaatcctcccagatcgatgaattatatttatttctgtaaactaatgccacttatatctggaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT