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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcactcctcctctccaccaaccctctcgtcaaatcaacccctcaatccagccaaaaccgatgctgcgggtggtagctaactacggttttggcgttttttttcttggggggtagGCGGCGGAGGGTATGGGGGGCATGGGTACTCGGAGGAGCGGAGCAGCGCGCGGCGGGTGGCGGACCACTACAGCGCGAGGTCGAACCAGACGCTCGAGGA

Basic information

species Oryza sativa
transcript LOC_Os08g08200.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08200.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G042398_T01 (Zea mays), 3'ss of exon 2
gtaactcactcctcctctccaccaaccctctcgtcaaatcaacccctcaatccagccaaaaccgatgctgcgggtggtagctaactacggttttggcgtttttttt---cttgggg----ggtagGCGGCGGAGGGTATGG---GGGGCATGGGTACTCGGAGGAGCGGAGCAGCGCGCGGCGGGTGGCGGACCACTACAGCGCGAGGTCGAACCAGACGCTCGAGGA
||| ||| |   ||| |  ||||  || ||   ||      ||| ||    ||  ||   | || ||  | || | |  ||      ||| ||||| |  |   |     |||| |     || |  ||||||||||||||   |  ||| || |||||||| |||||||||||||||||||||||||| ||||||||||||||| |||| |||||||| ||||||||
gta-ctc-cctatccgcatcaccccccttcctctcttgctcaccact-gcccctcccggcatcg-tggcgaggctagctgccgcggtcggatttggtggctaactagggtttggtgcttgagtggcagGCGGAGGGTATGGCCCGCAGCAGGGTTACTCGGAAGAGCGGAGCAGCGCGCGGCGGGTGGCCGACCACTACAGCGCGCGGTCCAACCAGACACTCGAGGA
















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|88409979|gb|CI573218.1|CI573218
EST:     CGAGCCCTCCTCCTCCTTCGCCTCCGCCCCCAAGCGCCAGTACGGCGCAG                         GCGGCGGAGGGTATGGGGGGCATGGGTACTCGTGAGGAGCGGAGCAGCGCG
genomic: CGAGCCCTCCTCCTCCTTCGCCTCCGCCCCCAAGCGCCAGTACGGCGCAGgtaactcact ... tggggggtagGCGGCGGAGGGTATGGGGGGCATGGGTACTCG-GAGGAGCGGAGCAGCGCG
EST: gi|88350138|gb|CI622069.1|CI622069
EST:     CGAGCCCTCCTCCTCCTTCGCCTCCGCCCCCAAGCGCCAGTACGGCGCAG                         GCGGCGGAGGGTATGGGGGGCATGGGTACTCGGAGGAGCGGAGCAGCGCGC
genomic: CGAGCCCTCCTCCTCCTTCGCCTCCGCCCCCAAGCGCCAGTACGGCGCAGgtaactcact ... tggggggtagGCGGCGGAGGGTATGGGGGGCATGGGTACTCGGAGGAGCGGAGCAGCGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgctgcgggtggtagctaactacggttttggcgttttttttcttggggggtagGCGGCGGAGGGTATGGGGGGCATGGGTACTCGGAGGAGCGGAGCAGCGCGCGGCGGGTGGCGGACCACTACAGCGCGAGGTCGAACCAGACGCTCGAGGA
               agctaac  putative branch site (score: 2)
                                 cgttttttttctt  putative PPT
                                   ttttttttctt  TA-rich tract