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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcttgatatagtttgtttcagtattgctaaatcatgaacaattattttttatgccaattgatttttccttgtaaaagatatcttattttactcatttgccaatgatccagTGTGGTGTTGAGTTTGCTGCGGAGTACGTGATTCCTCTCGTCTTCCCACTGCTCACAGCACATCAACTGAATGTACAGCAATTTGCTAAGTACATACTAT

Basic information

species Oryza sativa
transcript LOC_Os01g42950.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42950.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G061681_T01 (Zea mays), 3'ss of exon 12
gtttgttcttgatatagtttgtttcagtattgctaaatcatgaacaattattttttatgccaattgatttttccttgtaaaagatatcttattttactcatttgccaatgatccagTGTGGTGTTGAGTTTGCTGCGGAGTACGTGATTCCTCTCGTCTTCCCACTGCTCACAGCACATCAACTGAATGTACAGCAATTTGCTAAGTACATACTAT
   | | |||   | | ||   |   ||       |  | |   || ||  | |    ||| || |||||  |   |||| |     || | |||||||  ||| |  |||||||||| ||||| |||||||||||||| || |||||||||||| |||||||| | |||||||||||||||||||||||||| |||||||| ||||| || ||||
--atttccttcccagatttcactcatgtg----ggagccttcggcacttggtct----gcccat-gatttagctcagtaata-----ctcaatttactctcttgtctctgatccagTGCGGTGTGGAGTTTGCTGCGGAATATGTGATTCCTCTCATCTTCCCATTACTCACAGCACATCAACTGAATGTACAACAATTTGCCAAGTATATGCTAT
















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|66918018|gb|CX104866.1|CX104866
EST:     CACCAACACTTATGTGCACCCTTGGAGTGGCTAATGCA-TTTTTAACCCG                         -GTGGTGTTGA-TTTGC
genomic: CACCAACACTTATGTGCACCCTTGGAGTGGCTAATGCAATTTTTAAACAGgtttgttctt ... aatgatccagTGTGGTGTTGAGTTTGC
EST: gi|58688741|gb|CK077428.1|CK077428
EST:     CACCAACACTTATGTGCACCCTTGGAGTGGCTAATGCAATTTTTAAACAG                         TGTGGTGTTGAGTTTGCTGCGGAGTACGTGATTCCTCTCGTCTTCCCACTG
genomic: CACCAACACTTATGTGCACCCTTGGAGTGGCTAATGCAATTTTTAAACAGgtttgttctt ... aatgatccagTGTGGTGTTGAGTTTGCTGCGGAGTACGTGATTCCTCTCGTCTTCCCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgatttttccttgtaaaagatatcttattttactcatttgccaatgatccagTGTGGTGTTGAGTTTGCTGCGGAGTACGTGATTCCTCTCGTCTTCCCACTGCTCACAGCACATCAACTGAATGTACAGCAATTTGCTAAGTACATACTAT
 aattgat  putative branch site (score: 4)
             ttgtaaaagatatctt  TA-rich tract