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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcattcatgtccatcttgtccataccccccatacttgggaactgctacaagcggcctccacgattggctcgccaattggagccgttttttctctatgggcgcggtttcgattcctcacaatggctgcctttgtgacgactgaatttgcagGCGGATTTGACACTGCTCATGCGGCGGCTCG

Basic information

species Oryza sativa
transcript LOC_Os04g55560.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G076602_T01 (Zea mays), 3'ss of exon 1
gtaagtttcattcatgtccatcttgtccataccccccatacttgggaactgctacaagcggcctccacgattggctcgccaattggagccgttttttctctatgggcgcggtttcgattcctcacaatggctgcctttgtgacgactgaatttgcagGCGGATTTGACACTGCTCATGCGGCGGCTCG
||||||||| | || ||||||   |||||| |   ||||||      |    |  |||      | |    |  | | |||||  ||| |||||||  | |  || | |||    || |||||||||     ||  ||||| |||||     |||||||||||||||||| || |||||||| |||||
gtaagtttcttgcacgtccatga-gtccatccattccatacgcatccatgcttggaaga-----cgatagataccgc-ccaatccgaggcgtttttggt-tccggactcgg----gactcctcacaaaaatggc--ttgtggcgact-----tgcagGCGGATTTGACACCGCCCATGCGGCTGCTCG

upper sequence: LOC_Os04g55560.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G174784_T01 (Zea mays), 3'ss of exon 2
gtaagtttcattcatgtccatcttgtccataccccccatacttgggaactgctacaagcggcctccacgattggctcgccaattggagccgttttttctctatgggcgcggtttcgattcctcacaa-tggctgcctttgtgacgactgaatttgcagGCGGATTTGACACTGCTCATGCGGCGGCTCG
||||||||| |||||||||||    | || |    || |||||||||      | | | ||       || ||   | |||||  ||| ||||||   |            | | ||| |||||||| |||||    |||||  |||   | |||||||||| |||||||| |||||||||||||||||
gtaagtttcgttcatgtccatgc-atacacat---ccgtacttgggag-----agaggtgg-----gtgactg---ccccaatccgaggcgttttcggt------------tctggatccctcacaaatggcttggcttgtg--gac--gacttgcagGCGGGTTTGACACCGCTCATGCGGCGGCTCG
















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|29644662|gb|CB649669.1|CB649669
EST:     GGATTGTGGCAAGCAGGTCTATTTGG                         GCGGATTTGACACTGCTCATGCGGCGGCTCG
genomic: GGATTGTGGCAAGCAGGTCTATTTGGgtaagtttca ... gaatttgcagGCGGATTTGACACTGCTCATGCGGCGGCTCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggcgcggtttcgattcctcacaatggctgcctttgtgacgactgaatttgcagGCGGATTTGACACTGCTCATGCGGCGGCTCG
                tcctcac  putative branch site (score: 2)
                                            tgaattt  TA-rich tract