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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttacaaatctggcaatacttgctgctttatttatgtttcttccaaggtctaagtgaagattgttgggttttcctttaatttgttatatattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGGGAACCTTTGTATGCAAAATTCCGCCTCCGGGAACCTTTTCACAAGCCCA

Basic information

species Oryza sativa
transcript LOC_Os06g50380.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G151254_T02 (Zea mays), 3'ss of exon 3
agtttacaaatctggca-atacttgctgctttat--ttatgtttcttccaaggtctaagtgaagattgttgggttttcc-tttaatttgttatatattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGGGAACCTTTGTATGCAAAATTCCGCCTCCGGGAACCTTTTCACAAGCCCA
   | |||  ||| ||  |  |   ||   ||     ||    ||||    | | |   ||  |  | |    | ||   ||| || | |  |  |||  |||||| || ||||||||||||||||| ||||||||||    |||||||||| |||||||  | ||||||||||| |||||||| ||||||||||||||||| |
--gtcacatgtctagcctaccccaacttgcttgggactaaaagtctttgttgttattgttgttgtatatcaattattgagttttatctatcgtgcatt--gcagGTTTGTAGATCAATTGGTGATGCATATCTCAAAAAGCAAGAGTTCAACAGGGAACCCCTATATGCAAAATTTCGCCTCCGTGAACCTTTTCACAAGCCAA
















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|29646161|gb|CB651168.1|CB651168
EST:     ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAG                         GTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
genomic: ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAGgtgagttctc ... tattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
EST: gi|87023874|gb|CI288227.1|CI288227
EST:     ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAG                         GTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
genomic: ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAGgtgagttctc ... tattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
EST: gi|87023875|gb|CI288228.1|CI288228
EST:     ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAG                         GTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
genomic: ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAGgtgagttctc ... tattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
EST: gi|33793893|gb|CF322835.1|CF322835
EST:     ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAG                         GTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
genomic: ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAGgtgagttctc ... tattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
EST: gi|58679941|gb|CK068628.1|CK068628
EST:     ATA-TGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAG                         GTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
genomic: ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAGgtgagttctc ... tattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
EST: gi|29677203|gb|CB673478.1|CB673478
EST:     ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAG                         GTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
genomic: ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAGgtgagttctc ... tattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
EST: gi|87024482|gb|CI290012.1|CI290012
EST:     ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAG                         GTCTGCAGATCACGTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG
genomic: ATATTGTTGTTCTCAAGCACAACGTTTGGCGTGTAAAAGGTCTAATTCAGgtgagttctc ... tattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaggtctaagtgaagattgttgggttttcctttaatttgttatatattttgcagGTCTGCAGATCAATTGGTGATGCCTATCTCAAAAGATCAGAGTTCAACCGGGAACCTTTGTATGCAAAATTCCGCCTCCGGGAACCTTTTCACAAGCCCA
                              ctttaat  putative branch site (score: 4)
                         ttttcctttaatttgt  TA-rich tract