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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgttatacttattttatgtgtctaagtaccaagtgttttatccatgacatgcaagatatttatgtttccctatttggcttttttgatgcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATACCTGAACTAGCTAGAATGCCGACAGAATGGATTCATCATCCATGGGATG

Basic information

species Oryza sativa
transcript LOC_Os02g41550.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G172152_T01 (Zea mays), 3'ss of exon 4
-ttgtgttatacttattttatgtg---tctaagtaccaagtgttttatccatgacatgcaagatatttatgtttccctatttggcttttttgatgcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATACCTGAACTAGCTAGAATGCCGACAGAATGGATTCATCATCCATGGGATG
   |||  |   ||||| |  ||    |||  || |     |    ||  ||   ||  || |     | |||      |     || ||  |||  ||| |||||||| ||||||||||| || || || |||| |||||||||||||||||| |||||||| ||||||||||| ||||||||||| |||  |||||||| ||
ggagtgccagttttattattggtaaactctttgttctggaggaccaatttatt-tataaaaaaag---aggttctgacttgcattttgttgtatgtgaaagtagGTTCAGGGTCAAAAGTACGATCCGGACGGTGAATATGTAAGAACTTGGATTCCTGAACTTGCTAGAATGCCAACAGAATGGATCCATAGTCCATGGGCTG
















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|29674880|gb|CB671155.1|CB671155
EST:     CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAG                         GTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
genomic: CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAGgtatgcagtc ... gcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
EST: gi|29681035|gb|CB677310.1|CB677310
EST:     CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAG                         GTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
genomic: CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAGgtatgcagtc ... gcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
EST: gi|29668437|gb|CB664712.1|CB664712
EST:     CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAG                         GTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
genomic: CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAGgtatgcagtc ... gcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
EST: gi|27547709|gb|CA765778.2|CA765778
EST:     CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAG                         GTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
genomic: CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAGgtatgcagtc ... gcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
EST: gi|163922706|gb|EG714182.1|EG714182
EST:     CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAG                         GTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
genomic: CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAGgtatgcagtc ... gcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
EST: gi|33681243|gb|CF309482.1|CF309482
EST:     CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAG                         GTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
genomic: CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAGgtatgcagtc ... gcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
EST: gi|29674792|gb|CB671067.1|CB671067
EST:     CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAG                         GTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA
genomic: CTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAGgtatgcagtc ... gcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgacatgcaagatatttatgtttccctatttggcttttttgatgcaaaactagGTTCAAGGTCAAAAGTATGACCCAGATGGTGTATATGTAAGAACTTGGATACCTGAACTAGCTAGAATGCCGACAGAATGGATTCATCATCCATGGGATG
                                      ttttgat  putative branch site (score: 4)
          aagatatttatgttt  TA-rich tract