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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctccttccaactttctcatatagttatatgactggtttatacataagctgtatgtattacgctaagttgtaattgatcaattcgtatttaatattttagGATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGATAAGGTCGCAACACAGAACTACGTTTCAACTCGACTCCGTTATTCTCTTA

Basic information

species Oryza sativa
transcript LOC_Os01g36840.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36840.3 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G030596_T02 (Zea mays), 3'ss of exon 9
---cctccttccaa----ctttctcatatagttatatgactggtttatacataagctgtatgtattacgctaagttgtaattgatcaattcgtatttaatattttagGATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGATAAGGTCGCAACACAGAACTACGTTTCAACTCGACTCCGTTATTCTCTTA
     || | ||||     |||     || ||||||||||  | | |  |||   |||||  | ||         | | |    |  ||   |   || ||| |||||||||||||||||||||||| |||| ||||||||| || ||||     || ||| | ||  ||||||||||||| |||||||| || || ||||||||||
attggtcttgccaaaatgtttttgggaattgttatatgaccagatgaaccatggcctgtacat-ttgta------tctgaacagttgatctctgcctactatcttagGATATCCTCATTACTGGGGCCCACAAGAAGGTGAAAACAAACAGTTTGGACAAGATTGCTGCACAGAACTACGTCTCAACTCGGCTTCGCTATTCTCTTA
















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|86905480|gb|CI285443.1|CI285443
EST:     GGTTCAATGATGATGGGGATATGGAGCTTGATTTCAACTCCGATAAGAAG                         GATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGAT
genomic: GGTTCAATGATGATGGGGATATGGAGCTTGATTTCAACTCCGATAAGAAGgtaagtaatg ... aatattttagGATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGAT
EST: gi|88570562|gb|CI661935.1|CI661935
EST:     GGTTCAATGATGATGGGGATATGGAGCTTGATTTCAACTCCGATAAGAAG                         GATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGAT
genomic: GGTTCAATGATGATGGGGATATGGAGCTTGATTTCAACTCCGATAAGAAGgtaagtaatg ... aatattttagGATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGAT
EST: gi|58692285|gb|CK080972.1|CK080972
EST:     GGTTCAATGATGATGGGGATATGGAGCTTGATTTCAACTCCGATAAGAAG                         GATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCGAGA
genomic: GGTTCAATGATGATGGGGATATGGAGCTTGATTTCAACTCCGATAAGAAGgtaagtaatg ... aatattttagGATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGC-AGA
EST: gi|87023564|gb|CI286315.1|CI286315
EST:     GGTTCAATGATAATGGGGATATGGAGCTTGATTTCAACTCCGATAAGAAG                         GATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGAT
genomic: GGTTCAATGATGATGGGGATATGGAGCTTGATTTCAACTCCGATAAGAAGgtaagtaatg ... aatattttagGATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctgtatgtattacgctaagttgtaattgatcaattcgtatttaatattttagGATATCCTCATTACTGGGGCACACAGGAAGGTGAATACCAACAAGGCAGATAAGGTCGCAACACAGAACTACGTTTCAACTCGACTCCGTTATTCTCTTA
                                         atttaat  putative branch site (score: 4)
                         taattgatcaattcgt  TA-rich tract