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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctaatatgagcagaggaatgacctatattgttcattctggtttgaatgtttgattcgtattttgagcaagttttcatctttcatgtttcatgtttgcagTTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCGCGAAATGGGGGATGAG

Basic information

species Oryza sativa
transcript LOC_Os01g04920.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G477503_T01 (Zea mays), 3'ss of exon 1
------------cctaatatgagcagaggaatgacctatattgttcattctggtttgaatgtttgattcgtattttgagcaagttttcatctttcatgtttcatgtttgcagTTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCGCGAAATGGGGGATGAG
             ||   | ||  ||| | ||  |||| | ||||  || |  |  ||||| |   |   ||||   |  || | | | ||||          ||| ||||| |||||||||||||| ||||||||||| |||||||||||||| || ||||| ||||||||||| |||
taacttgtaaggtctgcca-gaaaagaagcatatcctagactgttt-ttttcatgagaatgctc--tcactattgcaactaactctgcgtcttg--------gtgtctgcagATACATCTCTGGGTATAAGAACCGGTTCCAGAACTTCATCAAACATTTGCGAGAAATGGGGGACGAG
















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|58684663|gb|CK073350.1|CK073350
EST:     GCCGCGCGCCCTCGCCGCGTCGCGCTCTTCGTCGAGCCGTCTCCGTTCGC                         TTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCG
genomic: GCCGCGCGCCCTCGCCGCGTCGCGCTCTTCGTCGAGCCGTCTCCGTTCGCgtaaggatta ... atgtttgcagTTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCG
EST: gi|58668243|gb|CK056929.1|CK056929
EST:     GCCGCGCGCCCTCGCCGCGTCGCGCTCTTCGTCGAGCCGTCTCCGTTCGC                         TTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCG
genomic: GCCGCGCGCCCTCGCCGCGTCGCGCTCTTCGTCGAGCCGTCTCCGTTCGCgtaaggatta ... atgtttgcagTTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCG
EST: gi|4715717|gb|AU056833.1|AU056833
EST:     GCCGCGCGCCCTCGCCGCGTCGCGCTCTTCGTCGAGCCGTCTCCGTTCGC                         TTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCG
genomic: GCCGCGCGCCCTCGCCGCGTCGCGCTCTTCGTCGAGCCGTCTCCGTTCGCgtaaggatta ... atgtttgcagTTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtttgattcgtattttgagcaagttttcatctttcatgtttcatgtttgcagTTACATCTCTGGGTACAAGAACCGGTTTCAGAACTTCATCAAGCACTTGCGCGAAATGGGGGATGAG
   gtttgat  putative branch site (score: 5)
             tattttga  TA-rich tract