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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcacttagctatagctagctccggccacatctccgtttccgcgccgccgccgccgccgccgccggcacaaactgaccgattcgatccatgtccatattgtgcagGGATATCGGCGACGGTGCCGTGGGGCACGCGTCTGAAGATCGCCATCGGCGCCGCCAAGGGCCTCGCCTTCCTCCACGGCGCCTCCACCCCCGTCATCTA

Basic information

species Oryza sativa
transcript LOC_Os03g24930.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24930.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AC234171.1_FGT001 (Zea mays), 3'ss of exon 1
gtacgca-cttagctatagctagctccggccac----atctccgtttccgcgc-cgccgccgccgccg-ccgccggcacaaactgaccgattcgatccat-gtccatat---tgtgcagGGATATCGGCGACGG---TGCCGTGGGGCACGCGTCTGAAGATCGCCATCGGCGCCGCCAAGGGCCTCGCCTTCCTCCACGGCGCCTCCACCCCCGTCATCTA
||| |   | ||||||   || ||||  ||       | |   |      ||  ||   | ||  |||  || | ||     |    |   |||||  || || | |       ||||||||| ||| |||||    ||||||||||||| || |||||| | |||||||||||||||||||| || || |||||||||| ||||  ||| ||||||||   
gtaggtgtcctagctagctcttgctcttgctcttgggagcaaggggagtacgtacgtatcagcaaccgatcgactgcttgctcctcacacctcgatggatcgttcgtgcgtgcctgcagGGATCTCGACGACGACGCTGCCGTGGGGCACCCGGCTGAAGGTGGCCATCGGCGCCGCCAAGGGGCTGGCTTTCCTCCACGCCGCCAACACGCCCGTCAT---
















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|88409616|gb|CI568906.1|CI568906
EST:     CGTCTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAAGA                         GGATATCGGCGACGGTGCCGTGGGGCACGCGTCTGAAGATCGCCATCGGCG
genomic: CGTCTACGAGTTCATGCCGCGCGGCAGCCTCGAGAACCACCTCTTCAAGAgtacgcactt ... tattgtgcagGGATATCGGCGACGGTGCCGTGGGGCACGCGTCTGAAGATCGCCATCGGCG
EST: gi|55827813|gb|AU057426.2|AU057426
EST:     AACCACCTCTTCAAGA                         GGATATCGGCGACGGTGCCGTGGGGCACGCGTCTGAAGATCGCCATCGGCG
genomic: AACCACCTCTTCAAGAgtacgcactt ... tattgtgcagGGATATCGGCGACGGTGCCGTGGGGCACGCGTCTGAAGATCGCCATCGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgccgccgccgccggcacaaactgaccgattcgatccatgtccatattgtgcagGGATATCGGCGACGGTGCCGTGGGGCACGCGTCTGAAGATCGCCATCGGCGCCGCCAAGGGCCTCGCCTTCCTCCACGGCGCCTCCACCCCCGTCATCTA
                    aactgac  putative branch site (score: 2)
                                            atattgt  TA-rich tract