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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcctcctcccccccaaccctaaccacccaccttccgccacggttgggatcgccgtcgtcgtcggttgcttgcttgtttcctctcgctttgccacggatatgtatatgcttgtgttggaagcaatcgccgggcttccattctgtggctggtgaattcttacgtgggaggtcgcgattgctgctgctgctgcagGGATGCCGATTTCCGATGCGTTCGCGCAGATAGAGGGCCAGCCAACACTCTACGACGTTGTCCACGTGAAGTACTTCGATGAG

Basic information

species Oryza sativa
transcript LOC_Os06g49990.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49990.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 1
gtgagctcctcctcccccccaaccctaaccacccaccttccgccacggttgggatcgccgtcgtcgtcggttgcttgcttgtttcctctcgctttgccacggatatgtatatgcttgtgttggaagcaatcgccgggcttccattctgtggctggtgaattcttacgtgggaggtcgcgattgctgctgctgctgcagGGATGCCGATTTCCGATGCGTTCGCGCAGATAGAGGGCCAGCCAACACTCTACGACGTTGTCCACGTGAAGTACTTCGATGAG
                                                                                          |  ||      ||| |  | |   |  | |   ||| |   |  ||  ||  |||    |  |    || | | ||        |  ||| |   ||    | |||||| |||||||| || ||||||||  | ||||||||| | ||||| |   |||||||||||||||||||||| |||||||| |||
-----------------------------------------------------------------------------------------ggagtttaattagatttacaaactttactctcttaagtaga-gtaggagtttaatt---agatttacaaactttgacccaa----ttccgact-tcgcaatcggtgcagGCATGCCGATATCGGATGCGTTTACACAGATAGAGCGGCAGCCGAATATCTACGACGTTGTCCACGTGAAATACTTCGACGAG
















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|11442702|gb|BF430605.1|BF430605
EST:     GCTCGACCTCCGCCCCGGCAACGGCGTCGGGCCCTTCACCCTCG                         GGATGCCGATTTCCGATGCGTTCGCGCAGATAGAGGGCCAGCCAACACTCT
genomic: GCTCGACCTCCGCCCCGGCAACGGCGTCGGGCCCTTCACCCTCGgtgagctcct ... gctgctgcagGGATGCCGATTTCCGATGCGTTCGCGCAGATAGAGGGCCAGCCAACACTCT
EST: gi|33675671|gb|CF303910.1|CF303910
EST:     CGGCAACGGCGTCGGGCCCTTCACCCTCG                         GGATGCCGATTTCCGATGCGTTCGCGCAGATAGAGGGCCAGCCAACACTCT
genomic: CGGCAACGGCGTCGGGCCCTTCACCCTCGgtgagctcct ... gctgctgcagGGATGCCGATTTCCGATGCGTTCGCGCAGATAGAGGGCCAGCCAACACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtggctggtgaattcttacgtgggaggtcgcgattgctgctgctgctgcagGGATGCCGATTTCCGATGCGTTCGCGCAGATAGAGGGCCAGCCAACACTCTACGACGTTGTCCACGTGAAGTACTTCGATGAG
                ttcttac  putative branch site (score: 2)
              aattctta  TA-rich tract