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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctcctacaaacacccttgcttcatttgacactgtaaaaccgcaaagaagttactgaaaaagtttggtttaattttgcagGAATCGATCATTTCCTTGGTAAGGTGGAGAGCCCCGGGAGCTTCCCCCACATGCGATCCGGTGAAAGCTTTGATATGTATTGATGACGCGGCAATTCTGG

Basic information

species Oryza sativa
transcript LOC_Os01g60270.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G805026_T01 (Zea mays), 3'ss of exon 2
-----gtacctcctacaaacacccttgcttcatttgac-----actgtaaaaccgcaaagaagtt-actgaaaaagtttggtttaattttgcagGAATCGATCATTTCCTTGGTAAGGTGGAGAGCCCCGGGAGCTTCCCCCACAT---GCGATCCGGTGAAAGCTTTGATATGTATTGATGACGCGGCAATTCTGG
      |  || | || | | || ||||||| ||         | |||      || || |||||    |   | | ||||||   |  |||||||||||||| |||||  |  |||||||||||| || |||||||||||||  |    | |  ||| ||| ||||||  |||| | ||||||  |   || ||| 
gtatgttctctgcgaccagcgccgttgcttcgttaaggttccgaatgtgtgttagctaaaaagtttggcgtgcatggttggtt-gttggtgcagGAATCGATCGTTTCCCGGCGAAGGTGGAGAGCTCCCGGAGCTTCCCCCATCTCCAACAACACGGGGAAGGCTTTGGCATGTTTGGATGACATGC--ATGCTG-

upper sequence: LOC_Os01g60270.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069274_T01 (Zea mays), 3'ss of exon 3
gtacctcct-----acaaacacccttgcttcatttgacactgtaaaaccgcaaagaagttactgaaaaagtttggt------ttaattt-tgcagGAATCGATCATTTCCTTGGTAAGGTGGAGAGCCCCGGGAGCTTCCCCCACATGCGATCCGGTGAAAGCTTTGATATGTATTGATGACGCG--GCAATTCTGG
||| || ||     || | | || || ||||||| | ||  ||||||   | ||  |||      ||||||||||       ||  ||| ||||||||||||||||||||  || |||||||||||| || |||||||| ||||  | | |  ||| ||| ||||||| |||| | ||||||  |  ||    ||  
gtatcttctccgcaaccagcgccattacttcattaggcaacgtaaaattccgaaagagtgttactaaaagtttggcgtggtgttggtttgtgcagGAATCGATCATTTCCCGGGGAAGGTGGAGAGCTCCCGGAGCTTCTCCCATCTCCAACACGGGGAAGGCTTTGACATGTTTGGATGACATGATGCGGCGCT--
















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|86502978|gb|CI145611.1|CI145611
EST:     AGGCAGTTTGGGCCAGATGTCCTTCTACGACAATGTTATGTCAAATCCAA                         GAATCGATCATTTCCTTGGTAAGGTGGAGAGCCCCGGGAGCTTCCCCCACA
genomic: AGGCAGTTTGGGCCAGATGTCCTTCTACGACAATGTTATGTCAAATCCAAgtacctccta ... aattttgcagGAATCGATCATTTCCTTGGTAAGGTGGAGAGCCCCGGGAGCTTCCCCCACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacactgtaaaaccgcaaagaagttactgaaaaagtttggtttaattttgcagGAATCGATCATTTCCTTGGTAAGGTGGAGAGCCCCGGGAGCTTCCCCCACATGCGATCCGGTGAAAGCTTTGATATGTATTGATGACGCGGCAATTCTGG
                                         gtttaat  putative branch site (score: 4)
                                     tttggtttaatttt  TA-rich tract