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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggatcatagttgtcgatgttctcatgtaatgcaatgtggttgccgtgtgatgatgaggagctgatgttttttttcctctcggcagGGGAAGAGGGAGAGGCGGCGACGACGACGCCAGTGTACGTGGCGGCAATCGACTTGTCCT

Basic information

species Oryza sativa
transcript LOC_Os04g33690.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g33690.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G095810_T01 (Zea mays), 3'ss of exon 1
----------------gtatggatcatagttgtcgat--gttctcatgtaatgcaatgtggt----tgccgtgtgatgatga---ggagctgatgttttttttcctctcggcagGG-GAAGAGGGAGAGGCGGCGACGACGACGCCAGTGTACGTGGCGGCAATCGACTTGTCCT
                 | |    |    | | || |  |||   ||| |  ||  ||||||    ||| || |   | | |   || | || ||   |||| |      | |||| || | || || ||||||| |  ||||||| |||||||||||||| |||||||||||||
gtacacgtctctatctatctctccctctctcggcgttcggtttggatgcagcgcgctgtggtacggtgcggtattgcggtaacctggtggtggtggaattttgcagTGGAGGAGGGCGAGGCGGCAGCGGCGGCGGCTCCGACGCCCGTGTACGTGGCGGCGATCGACTTGTCCT
















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|58665409|gb|CK054095.1|CK054095
EST:     CCAGGACCCGCCCGAGATGCGCTCCGCCTTCGTGGACCTCCTCCTCCCTG                         GGGAAGAGGGAGAGGCGGCGACGACGACGCCAGTGTACGTGGCGGCAATCG
genomic: CCAGGACCCGCCCGAGATGCGCTCCGCCTTCGTGGACCTCCTCCTCCCTGgtatggatca ... ctctcggcagGGGAAGAGGGAGAGGCGGCGACGACGACGCCAGTGTACGTGGCGGCAATCG
EST: gi|88728168|gb|CI751678.1|CI751678
EST:     CCAGGACCCGCCCGAGATGCGCTCCGCCTTCGTGGACCTCCTCCTCCCTG                         GGGAAGAGGGAGAG
genomic: CCAGGACCCGCCCGAGATGCGCTCCGCCTTCGTGGACCTCCTCCTCCCTGgtatggatca ... ctctcggcagGGGAAGAGGGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatgtggttgccgtgtgatgatgaggagctgatgttttttttcctctcggcagGGGAAGAGGGAGAGGCGGCGACGACGACGCCAGTGTACGTGGCGGCAATCGACTTGTCCT
                            agctgat  putative branch site (score: 4)
                                  tgttttttttcctctc  CT-rich tract
                                 atgtttttttt  TA-rich tract