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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacttggtgtctgttatagttatagttacattcactcattagaaattaaaataattgatattttttatcgtcctccagAATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACT

Basic information

species Oryza sativa
transcript LOC_Os05g01470.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G098039_T01 (Zea mays), 3'ss of exon 7
gtaagacttgg------tgtctgttatagttatagttacat-tcactcattagaaattaaaataattgatattttttatcgtcctccagAATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACT
|||||| |||       |||||   |   |    |||  || |  ||        ||| | || ||    ||||||   |   | | ||||||| ||||| |||||||| ||  ||||||||||||| |||||||||| ||| |||||||| |||||||| || |||||||||||| | ||||||||||
gtaagatttgtctaaattgtcttaaaatctacctgttctatgtttctttcctatgattcacatgatgctgatttttctcctatcactagAATGTCGTTGTGTTCCCTTCTCGCTCTGTGGCAATAGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACT

upper sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 8
-------gtaagacttggtgtctgtta-tagttatagttacattcactcattagaaattaaaat--------aattgatatttttta--tcgtcctccagAATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACT
         ||   |   | ||||||| || | ||  ||   ||||  |  |    |  ||  |         | |  | ||| | |  || | | | ||||||||||  | || |||||  | ||||||||||| || |||||||||||||||||||||||    ||||| || ||||||||| |||||||  ||||  
agttctaaaaatcttcattatctgttagtattgattttttttttcatactgtgttgagcaagttttatttctgacttgtttttctcaattcttgcgcaagAATGTTGTCATATTTCCTTCAAGGGCTGTGGCAATTGAGAATGCTCTTCGATTATTCTCACCCCGTCTTGCAATTGTTGATGAAGATCTGACTCGACATC
















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|58673143|gb|CK061829.1|CK061829
EST:     TTGTTGCTGGATTTATGAAGAGCTACCACCATATCCCATTAACTCCTGAT                         AATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGA
genomic: TTGTTGCTGGATTTATGAAGAGCTACCACCATATCCCATTAACTCCTGATgtaagacttg ... cgtcctccagAATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGA
EST: gi|33675151|gb|CF303390.1|CF303390
EST:     TTGTTGCTGGATTTATGAAGAGCTACCACCATATCCCATTAACTCCTGAT                         AATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGA
genomic: TTGTTGCTGGATTTATGAAGAGCTACCACCATATCCCATTAACTCCTGATgtaagacttg ... cgtcctccagAATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGA
EST: gi|4715491|gb|AU056608.1|AU056608
EST:     TTGTTGCTGGATTTATGAAGAGCTACCACCATATCCCATTAACTCCTGAT                         AATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGA
genomic: TTGTTGCTGGATTTATGAAGAGCTACCACCATATCCCATTAACTCCTGATgtaagacttg ... cgtcctccagAATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttacattcactcattagaaattaaaataattgatattttttatcgtcctccagAATGTTGTTGTTTTCCCTTCCCGTGCTGTGGCAATAGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACT
                             aattgat  putative branch site (score: 4)
                                     ttttttatcgtcctcc  CT-rich tract
      attcactcattagaaa  TA-rich tract