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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatttttgtgttggggttggggttggactagtccgcgccccgttcgttccgcgggtgttgggagtctagggttgacgtgtgtttgtggtggtgcgcagGGTAGCAGCAGGAAGAGGGAGGAAGGGGGGGCATGGCGCTACGGAGGCTGCTCCAGGGGAGCGTCCTGCCGCGGATGGCGGGCAGAGCCGCCGCGGCGCC

Basic information

species Oryza sativa
transcript LOC_Os01g16900.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 1
-----------------------------------------------atgatt-tttgtgttggggttggggttggactagtccgcgccccgttcgttccgc--gggtgttgggagt---ctagggttgacgtgtgtttgtggtggtgcgcagGGTAGC----AGCAGGAAGAGGGAGGAAGGGGGGGCATGGCGCTACGGAGGCTGCT--CCAGGGGAGCGTCCTGCCGCGGATGGCGGGCAGAGCCGCCGCGGCGCC-------------------------------
                                               |||||    |    |    | || |  || |   ||  | ||       ||||||  |  | | | | ||   || || |  |     | | |||| |  | |  |  | |     ||   ||   |  ||| |    |     | |  | ||      |     ||||   |  | ||| ||| |  |  | |  | || | |  |||||                                
gtacattccctcctccgatcttgctacccaccgctccctgcctttttatgatcacctcccgttcaatcggaggcgggcctctctcccccgatcggattccgctcgaatctagagggtttcctcggatcaaatcccgctcgtggggacgggtggtttcgtgtatagtttgagttgttaggcaccatgcagGCGTCTTTCCGTCCCGCGACGATCAGGTCTGTTTGCTGTCGCAGG-GCTGTGTGGGGCAGGCATGGCGCTCCGGAGGCTGCTGCAGGGGAGCGTCCTGCCG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G120857_T01 (Zea mays), 3'ss of exon 1
atgatttttgtgttggggttggggttggactagtccgcgccccgttcgttccgcgggtgttgggagtctagggttgacgtgtgtttgtg--gtggtgcgcagGGTAGCA-GCAGGAAGAGGGAGGAAGGGGG--GGCATGGCGCTACGGAGGCTGCTCCAGGGGAGCGTCCTGCCGCGGATGGCGGGCAGAG---------CCGCCGCGGCGCC------
              |    |||||  ||     | || |    ||| |       | |||| ||   |    |  | ||| | |  ||   | |  |  ||||   |   || |    ||||  |   ||||  ||||||||||| ||||||||||| |||||||||||||||||||||||    ||||| |         | |||| ||||||      
------------ccgctcgtggggacgggtggtttcgtgtatagtttg------agttgttaggcacc--atgcaggcgtctttccgtcccgcgacgatcaggtctgtttgctgtcgcagGGCTGTGTGGGGCAGGCATGGCGCTCCGGAGGCTGCTGCAGGGGAGCGTCCTGCCGCGGATAATCGGCAGGGATTTGGCACCGGCCGTGGCGCCGTTTTC

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G018566_T02 (Zea mays), 3'ss of exon 1
atgatttttgtgttggggttggggttggactagtccgcgccccgtt--cgttccgcgggtgttgggagtctagggttgacgtgtgtttgtggtggtgcgcagGGTAGCAGCAGGAAGAGGGAGGAAGGGGGGGCATGGCGCTACGGAGGCTGCTCCAGGGGAGCGTCCTGCCGCGGATGGCGGGCAGAGCCGCCGCGGCGCC---------------
   |    ||  || | ||     | |   |  |  || |   |    ||| |  | | | |  |  |   ||| || ||||| |    || || |      ||  |  |||||    |    |  |||  | ||||||||| ||||||||||| |||||||| |||||||||||| |  | ||||| |   | ||  || |               
---acgggtggtttcgtgtacctttcgagttgttaggcactatgcaggcgtcctcccgttctgcgacgatcaggtttaacgtgcg----tgctgtt------ggctgtcgcagG----GCTGTGGGGGGCAGACATGGCGCTCCGGAGGCTGCTGCAGGGGAGTGTCCTGCCGCGGGTAACCGGCAGGGTTTCGGCACCGGCCGTGGCGCCGTTTTC

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|58666245|gb|CK054931.1|CK054931
EST:     TTCGCCGTCCG                         GGTAGCAGCAGGAAGAGGGAGGAANNNNNNNCATGGCGCTACGGAGGCTGC
genomic: TTCGCCGTCCGgtacattccc ... tggtgcgcagGGTAGCAGCAGGAAGAGGGAGGAAGGGGGGGCATGGCGCTACGGAGGCTGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttccgcgggtgttgggagtctagggttgacgtgtgtttgtggtggtgcgcagGGTAGCAGCAGGAAGAGGGAGGAAGGGGGGGCATGGCGCTACGGAGGCTGCTCCAGGGGAGCGTCCTGCCGCGGATGGCGGGCAGAGCCGCCGCGGCGCC
                          ggttgac  putative branch site (score: 4)