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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG

Basic information

species Oryza sativa
transcript LOC_Os01g64650.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 1
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgtt-gttaatgaacggtcatgtaa-acaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
 ||      | | ||  | | || | | | | |||  |||  |     |||| |||   ||   | | | |  | | | | |   | || |   |||| ||||||| ||||| ||||| |||||||| ||||| ||||| || || ||||||||||||||||||||||||||||||||||||||||||||||||||| ||
cataacatatggctgaccctgtttgctttggagatttggaatacatt-tttgttgtccatttccgcatgctgttttgacatacaatctcttcccattt-cagAATATAAGGTTCACTCCCACAACAGAAATGGGCTTTGTGCGGTGGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G446711_T01 (Zea mays), 3'ss of exon 1
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgtt-gttaatgaacggtcatgtaa-acaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
|        | | ||  | | || | | ||| |||   ||  | |   |||||| ||  ||      || |  ||| |   |   | || |   |||| ||||||||||||||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||||||||||  ||||||||||||||||||||| ||
ataacattatggctggccctgtttgctttagagatattgaatacttt-tttgctattcatttccactcgctgttgtgacgtacaatctcttttcattt-cagAATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCAGTTGCATTCATGGATGATCATTATCCTGTACAGAGTGCATTTTCTCTTCTGAATCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 2
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgtt-gttaatgaacggtcatgtaa-acaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
|        | | ||  | | || | | ||| |||  |||  |     |||||||||  ||      || |  ||| |   |   |||| |   |||| ||||||||||||||||||| ||||| || ||||| ||||| || |||||||| ||||||||||| ||||| ||||| ||||||||||||||||||||| ||
ataacattatggctgaccctgtttgctttagagatatggaatacatt-tttgctgttcatttccactcgctgttgtgacgtacaatgtcttttcattt-cagAATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
|   |    |   | || || |  |||    |  |        |  ||| | |  |   |  |         |||||     ||    |  | | |||||| |||||||| ||| || ||||||| ||||||||||||||  | | ||||||||||||||| || ||  | || ||||| ||||||||||| ||  ||
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctgtgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 1
aatctgcagtcgatgtt-cattttcggtctagtgatcaggagaattcagtttgc----tgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
       |  || | |   || || | | |   | |  |     ||    ||||    |  ||| | |       | | |  |    ||    | || |||||||| |||||||| ||| || ||||||||||||||||||||||  | | ||||||||||||||| || ||  | || ||||| ||||||||||| ||| ||
-----ataaccgttttgatatcttggttttgccggttcgatttctttttgttgcaaaattgtgtaagtttgaaaacttatttatttatttattttatgtttgcagAGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAG

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 1
----aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtca-tgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
      | | | || ||   || ||||   | |  ||||  |      | |   || | |  ||  | || | | | | |      || |   | ||||    |||||| || || || ||  ||||||| ||||||||||| ||| | |  ||||||||||| ||||||||||| ||||| ||||||||  | || ||  ||
gttttgtttcctgtggaaagtc-ttttgtatgttttgatatgttattgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatat----agAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG

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|218482998|gb|FG956126.1|FG956126
EST:     CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
EST: gi|88573365|gb|CI664936.1|CI664936
EST:     GTCGCCCAGCCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: GTCGCCCAGC-GCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
EST: gi|4879970|gb|AU064269.1|AU064269
EST:     CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTTGCGCATTTGCATTT
genomic: CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTT-GCGCAGTTGCATTT
EST: gi|27578119|gb|CB000814.1|CB000814
EST:     CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAG                         AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA
genomic: CGTCGCCCAGCGCACCCAGCCAGGCCAGCGCCAGTCCGTCCAGCACGAAGgtaaacaacc ... atatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttgctgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG
                                        tcctgat  putative branch site (score: 3)
          ttgttaat  TA-rich tract