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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcggtcactgccattctaatcatcctttatcatgcttgttgaatcaataccaaaattatggatgaaaacttgtaccaatgaactagattgatctgatgaacctctccgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC

Basic information

species Oryza sativa
transcript LOC_Os12g31850.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g31850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G025528_T02 (Zea mays), 3'ss of exon 5
gtaattcggtcactgccattctaatcatcctttatcatgcttgttgaatcaataccaaaattatggatgaaaacttgtaccaatgaactagat--tgatc-tgatgaacctctccgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC
                                              || ||  |     ||||||||| || |   |  |    |   | |||  |||    | | |   | |    ||| ||||| ||||| |||| ||||||||| ||||| ||||| || |||||| | || || |||||||| |||||||||||||| |||||||| ||||| || ||||
--------------------------------------------gtaaccaccatactcattatggatcaatagcagccctggggtttttgatcttgacgacggtaattgtatttcctgc-cagGTATTCGGTTCAAACACCTTCATCGGGCTGGGGATCGTCTTCTTCGCGGGCGTGTGCTTCTCGCTCTTCTCCCCGGCGTTCAACCTGGCCACTAACGACC

upper sequence: LOC_Os12g31850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G091891_T01 (Zea mays), 3'ss of exon 4
----------------------gtaattcggtcactgccattctaatcatcctttatcatgcttgttgaatcaataccaaaattatggatgaaaa-----------cttgtaccaatgaactagattgatctgatgaacctctccgttgcgc-------agGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC
                         | ||   ||    |||    || | |    |  |      || | | || ||  |  || || | |||||            ||    |    |||| ||  |     |||     | |     |||       |||| ||||| |||| ||| ||||| || || ||||| ||||||||| | || |  |||||||| |||||||||||||| |||||||| || ||||| ||||
gtatccgtccgtccatccatccaatactcatccatactcatggggataaacacagacgacctcatttaatttaacacttag-ttctgaaagaaaaaaaaacattttttttcttctcaaaactggaacgtaaaaatggcttgcacacccacgcgggcaccagGTATTCGGTTCAAACACGTTCATCGGTCTGGGGATCGTGTTCTTCGCGGGGGCGTGCTTCTCGCTCTTCTCCCCGGCGTTCAACCTGGCAACCAACGACC
















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|11025713|gb|AU162314.1|AU162314
EST:     AGGAACTNG-GNAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: AGGAACT-GCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|218501335|gb|FG958585.1|FG958585
EST:     CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|29644126|gb|CB649133.1|CB649133
EST:     CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|29614658|gb|CB619671.1|CB619671
EST:     CAGGAACTGCGGAATACTTGATCGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCANGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|29665274|gb|CB661549.1|CB661549
EST:     CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|218483875|gb|FG965316.1|FG965316
EST:     CAGGAACTGCGGAATACTTGATCGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaaacttgtaccaatgaactagattgatctgatgaacctctccgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC
                             atctgat  putative branch site (score: 4)
                                       cctctccgtt  putative PPT