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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcccgagcccgactcttctgtggatctcgccctcctcctgcttggttggtgttcgttactggtgtgagctttagatttgatctggttgtggtggtggtggtgtgcagGTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGCTGGTGCCGTCGCCGGAGCCGGCGTCCACCAGGCCGCTCAAGGTCGGCGT

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 1
gtcagtcccgagcccgactcttctgtggatctcgccctcc--tcctgcttggttggtgttcgttactggtgtgagct--ttagatttgatctggttgtggtggt-ggtggtgtgcagGTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGCTGGTGCCGTCGCCGGAGCCGGCGTCCACCAGGCCGCTCAAGGTCGGCGT
|| |||  |  | || ||  | ||||   |   |  |||   || ||| ||     ||||   || |     |||||  | ||||| |   ||| ||    | | | |     |||| ||||||||| ||||| ||||||||||||||||||||||| || | |||||||||||||||| | ||||| ||| | ||||||||||||||| |||||||
gtgagtgacc-gtccaacgttgctgtaacttaggatctcgggtcatgcatgtggtttgttacgtattccatcgagctcatcagattcg---tggctggctcgatcgatctctcgcagATGAGATCGCCAAGCTCTTCCCCAACCTGTTCGGCCAGCCCTCGGCGTCGCTGGTGCCGTCGGCCGAGCCCGCGGCGACCAGGCCGCTCAAGATCGGCGT

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 1
gtcagtcccgagcccgactcttctgtggatctcgccctcctcc---tgcttggttggtgttc-gttactggtgtgagctttagatttgatctggttgtggtggtggtggtgtgcagGTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGCTGGTGCCGTCGCCGGAGCCGGCGTCCACCAGGCCGCTCA-AGGTCGGCGT-
                             ||||||   |  ||   |||||  |   | ||| ||||    |   ||  ||  || | || | |  ||  |     |    |||||  |||||||||||||||||||| || |||||||| || ||||| | | |  ||||||||     |   ||  ||  |  || ||   ||  | |  |  |  
----------------------------gtctcgcttcctcccatttgcttcttcaattttccgttaacaattccag--ttgtatgtaattttgaagtcctctctctctcttgcagAGGAGATCGCGAAGCTGTTCCCGAAACTGTTCGGGCAACCGTCGGCGGCTTTGGTGCCG--AGTGATTCCCACGCGCCGCATGCAAATCGGAAGCTGAAGAT
















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|58611734|gb|CK039446.1|CK039446
EST:     CGCCCTCGCCGACGGCCCCGCCAGCTCCGCCGCCGGCAACCCCG                         GTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGC
genomic: CGCCCTCGCCGACGGCCCCGCCAGCTCCGCCGCCGGCAACCCCGgtcagtcccg ... tggtgtgcagGTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGC
EST: gi|58598594|gb|CK009122.1|CK009122
EST:     TCGCCGACGGCCCCGCCAGCTCCGCCGCCGGCAACCCCG                         GTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGC
genomic: TCGCCGACGGCCCCGCCAGCTCCGCCGCCGGCAACCCCGgtcagtcccg ... tggtgtgcagGTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttactggtgtgagctttagatttgatctggttgtggtggtggtggtgtgcagGTGAGATCGCGAAGCTGTTCCCCAACCTGTTCGGCCAGCCGTCCGTGTCGCTGGTGCCGTCGCCGGAGCCGGCGTCCACCAGGCCGCTCAAGGTCGGCGT
                      atttgat  putative branch site (score: 5)
                 tttagattt  TA-rich tract