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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttttacaactgttaaagaaaaaaaaattgtggtactttcctgcatagtttatttccacatttccatcattgagttgaaatggttgataatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGACCCCTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g68710.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G153991_T01 (Zea mays), 3'ss of exon 3
ctcttttacaactgttaaagaaaaaaaaattgt-ggtacttt-cctgcatagtttatttccacatttcca---------tcattgagttgaaatggttgataatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGACCCCTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG
             | | || ||  |    | || | |||||| ||||||  || | ||||| | |||  |         | ||| || ||||| | |||||| ||||||||||| ||||||||||||||||||| || |||||||||||||||||||||||||| |||||||| ||||||||||| ||||||||||||||||
----------ttcgattaaaaagcactcctcgtcgatactttacctgcagtgtctctttcctctttttaactctctttgttatttagctgaaaggcttgata-tgctgcagGGGACACTCACTGATGGATCAGTTTTCGATTCTAGCTATGACAGAGGTGACCCGTTTGAATTCACTCTTGGAAATGGCCAAGTGATAAAAG

upper sequence: LOC_Os01g68710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G031204_T01 (Zea mays), 3'ss of exon 3
ctcttttacaactgttaaagaaaaaaaaattgtggtactttcc----tgcatagttta-------tttccacatttccatcattgagttgaaatggttgataatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGACCCCTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG
            ||||  |  |||  |     || |||||| |    ||| | | ||        ||||    | ||  | |||  | ||||| | |||||| ||||||||||| |||||||||| |||||||| ||||||||| ||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
----------cgtgtttgattaaagcactccttgatactttacccgctgcgtcgctttcctctcttttctctctctcatttatttggctgaaaggcttgata-tgctgcagGGGGCACTCACTGACGGATCAGTTTTTGATTCTGGCTATGACAGAGGTGACCCGTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG
















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|86824178|gb|CI260793.1|CI260793
EST:     AGATGTCACGGAGCTTCAGATCGGTGTGAAG                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: AGATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
EST: gi|86824137|gb|CI260768.1|CI260768
EST:     GATGTCACGGAGCTTCAGATCGGTGTGAAG                         GGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC
genomic: GATGTCACGGAGCTTCAGATCGGTGTGAAGgtaaccggtt ... aatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagtttatttccacatttccatcattgagttgaaatggttgataatgctgcagGGGTCACTCACTGATGGATCAGTGTTTGATTCTAGCTATGACAGAGGTGACCCCTTTGAATTTACTCTTGGAAACGGCCAAGTGATAAAAG
                                      ggttgat  putative branch site (score: 5)
     tttattt  TA-rich tract