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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggttgttaccagcacatttctttattcacaagctttaatattgctggatatatttcgttctgacatatcaattttttttgcctgctttgctgccaaagGCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAACACCACCCTTTGACACATTTATCAGAAATCCTAATGATCGAG

Basic information

species Oryza sativa
transcript LOC_Os03g22870.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22870.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G150834_T01 (Zea mays), 3'ss of exon 6
---gtggttgttaccagcacatttctttattcacaagctttaat---attgctggatatatttcgttctgacatatcaattttttttgcctgctttgctgccaaagGCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAACACCACCCTTTGACACATTTATCAGAAATCCTAATGATCGAG
   | ||  || | ||  | |||  | |   |    ||   |     | ||    ||||  || ||  ||   |||||| |  ||     ||     ||||  ||||  || | |||||| ||||||||||||||  |||||||||||||||| ||||| |||||||||  |||| |||||| |||||| |||||||||
tgggggggggtaaacaaaatattattcttgccttgtgcacaagctgaactgtaacatatcatttgtattg--gtatcaactccttccatttgt----ctgctgaagGTCCGAGCTAGAGCCTTAATGTACTTCAACTATAGTGGCTACAAACTCCAACATCACCCTTTGGAACATCTATCAGGAATCCTGATGATCGAG
















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|88249568|gb|CI249417.1|CI249417
EST:     CTGAAGGAACCGATCTTCAGCTGCGTCTGTTAGAACCTTTTCTCAATGAG                         GCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAA
genomic: CTGAAGGAACCGATCTTCAGCTGCGTCTGTTAGAACCTTTTCTCAATGAGgtaagccgaa ... gctgccaaagGCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAA
EST: gi|88225145|gb|CI225061.1|CI225061
EST:     CTGAAGGAACCGATCTTCAGCTGCGTCTGTTAGAACCTTTTCTCAATGAG                         GCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAA
genomic: CTGAAGGAACCGATCTTCAGCTGCGTCTGTTAGAACCTTTTCTCAATGAGgtaagccgaa ... gctgccaaagGCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAA
EST: gi|86497041|gb|CI139674.1|CI139674
EST:     CTGAAGGAACCGATCTTCAGCTGCGTCTGTTAGAACCTTTTCTCAATGAG                         GCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAA
genomic: CTGAAGGAACCGATCTTCAGCTGCGTCTGTTAGAACCTTTTCTCAATGAGgtaagccgaa ... gctgccaaagGCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAA
EST: gi|88964282|gb|CI045475.1|CI045475
EST:     CTGAAGGAACCGATCTTCAGCTGCGTCTGTTAGAACCTTTTCTCAATGAG                         GCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAA
genomic: CTGAAGGAACCGATCTTCAGCTGCGTCTGTTAGAACCTTTTCTCAATGAGgtaagccgaa ... gctgccaaagGCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggatatatttcgttctgacatatcaattttttttgcctgctttgctgccaaagGCTCGTGTTAGAGCATTAATGTACTTCAATCATAGTGGCTACAAACTTCAACACCACCCTTTGACACATTTATCAGAAATCCTAATGATCGAG
              ttctgac  putative branch site (score: 2)
                                         ctttgct  putative PPT
                   acatatcaattttttt  TA-rich tract