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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatttcaaactgtttttttagttcagatacaattgccgatgtctttctgtggatcaaaaagaatgacagatgtattgtaccaacctgctatggttttagGGGAGATATGGTTCAAGTTGACACATGGGTCGCTGCTGCTGGCAAAAATGGCATGCGTCGAGACTGGCATGTTCGTGACTACAACTCTGGCCGAACAATC

Basic information

species Oryza sativa
transcript LOC_Os02g43090.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43090.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 3
--caatttcaaactgtttttttagttcagatacaattgccgatgtctttctgtggatcaaaaag--aatgacagatgtattgtaccaacctgctatggttttagGGGAGATATGGTTCAAGTTGACACATGGGTCGCTGCTGCTGGCAAAAATGGCATGCGTCGAGACTGGCATGTTCGTGACTACAACTCTGGCCGAACAATC
  ||| || |   |   || || |   ||||| | |||  ||  | |   | |||    |||     |  | | || | ||| |  ||||||||||  ||| |||| ||| | ||||||||| ||||| ||||| ||||| ||||| ||||||||||||||||||||||||||||| |  |||| ||| |||||  | || |||
tacaacttgagtataccttgttgg---agatatatttgtggacatttgcttatgggctgaaagattgaccaaatatttgttgaaaaaacctgctataattt-agGGAAGACACGGTTCAAGTGGACACGTGGGTAGCTGCCGCTGGGAAAAATGGCATGCGTCGAGACTGGCATGTCCTCGACTGCAAGTCTGGATGTACGATC

upper sequence: LOC_Os02g43090.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G829544_T01 (Zea mays), 3'ss of exon 3
caatttcaaactgtttttttagttcagatacaatt-gccgatgtctttctgtggatcaaaaagaatgacagatgtattgt-accaacctgctatggttttagGGGAGATATGGTTCAAGTTGACACATGGGTCGCTGCTGCTGGCAAAAATGGCATGCGTCGAGACTGGCATGTTCGTGACTACAACTCTGGCCGAACAATC
    ||||     |   |  |  | |  ||| ||| |  ||  | |   | |||    ||||         || | |  | |  ||| ||||||  ||| ||||||||||  |||||||| ||||||||||| ||||||||||| |||||||||||||||||||| ||||||||||||||| | |||||||| || ||||||
-ggattcatcggctcactacatctaatttactatttgtggacatatgcttatgggatgaaaaactgactgaatatctgctgaaaaacttgctataattt-agGGGAGATACTGTTCAAGTGGACACATGGGTAGCTGCTGCTGGGAAAAATGGCATGCGTCGAGATTGGCATGTTCGTGACGAAAACTCTGGACGCACAATC
















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|58678184|gb|CK066871.1|CK066871
EST:     ATATGGGTTGTCAGCAAAATCCAGCTTCTTGTTGAGCAATACCCCGCATG                         GGGAGATATGGTTCAAGTTGACACATGGGTCGCTGCTGCTGGCAAAAATGG
genomic: ATATGGGTTGTCAGCAAAATCCAGCTTCTTGTTGAGCAATACCCCGCATGgtactttttt ... atggttttagGGGAGATATGGTTCAAGTTGACACATGGGTCGCTGCTGCTGGCAAAAATGG
EST: gi|29643342|gb|CB648349.1|CB648349
EST:     ATATGGGTTGTCAGCAAAATCCAGCTTCTTGTTGAGCAATACCCCGCATG                         GGGAGATATGGTTCAAGTTGACACATGGGTCGCTGCTGCTGGCAAAAATGG
genomic: ATATGGGTTGTCAGCAAAATCCAGCTTCTTGTTGAGCAATACCCCGCATGgtactttttt ... atggttttagGGGAGATATGGTTCAAGTTGACACATGGGTCGCTGCTGCTGGCAAAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtggatcaaaaagaatgacagatgtattgtaccaacctgctatggttttagGGGAGATATGGTTCAAGTTGACACATGGGTCGCTGCTGCTGGCAAAAATGGCATGCGTCGAGACTGGCATGTTCGTGACTACAACTCTGGCCGAACAATC
           aaaaagaat  TA-rich tract