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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagattcacaacaatccacatgccattatttttcacagttcttatacatcaattagtttgattcaaactcaacaatgataaacttgatgaacaaaaagGGAATCATGGACGAAAGGGAGAGAGATTTGCAGCTCTCCTACGGGCTAGGATACCCTGAACCCAACGTCGTGTTCGCTCTGTGCAGAGGCAGCCGCTCCT

Basic information

species Oryza sativa
transcript LOC_Os01g05480.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05480.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G030712_T04 (Zea mays), 3'ss of exon 3
gtaagcagattcacaacaatccacatgccattatttttcacagttcttatacatcaattagtttgattcaaactcaacaatgataaacttgatga--acaaaaagGGAATCATGG---ACGAAAGGGAGAGAGATTTGCAGCTCTCCTACGGGCTAGGATACCCTGAACCCAACGTCGTGTTCGCTCTGTGCAGAGGCAGCCGCTCCT
||| ||| |   |  || | |   | || |  ||   |||  ||| |      |  |||| | |  || || || ||||| | ||    || |||  |  | ||||| || ||||   ||||  |  |||  ||| ||| || ||| ||||||||||| || || || ||||||||||| ||||| |||||||||||||||||||   
gtatgcaaa---aagactagcagaacgc-agaatgcatcatcgttttccctttttcattaatgtt-tttaatctgaacaagggtatgtatgttgatgatgataagGGCATTATGGGCGACGACGGACAGACGGATCTGCTGCACTCGTACGGGCTAGGGTATCCCGAGCCCAACGTCGTCTTCGCGCTGTGCAGAGGCAGCCGCT---
















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|86501668|gb|CI144301.1|CI144301
EST:     TTCTGTCGATCGAGCATCTCATCCTGAGACACTCCCCTGAAGGCAACCAA                         GGAATCATGGACGAAAGGGAGAGAGATTTGCAGCTCTCCTACGGGCTAGGA
genomic: TTCTGTCGATCGAGCATCTCATCCTGAGACACTCCCCTGAAGGCAAGCAAgtaagcagat ... gaacaaaaagGGAATCATGGACGAAAGGGAGAGAGATTTGCAGCTCTCCTACGGGCTAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatcaattagtttgattcaaactcaacaatgataaacttgatgaacaaaaagGGAATCATGGACGAAAGGGAGAGAGATTTGCAGCTCTCCTACGGGCTAGGATACCCTGAACCCAACGTCGTGTTCGCTCTGTGCAGAGGCAGCCGCTCCT
                                      acttgat  putative branch site (score: 5)
       aattagttt  TA-rich tract