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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattatcacttatcatttctttatcttgggcataagatcttccagaatggagtttttggatgttctatttgattggagatcaccaggttacctatacttacatgaaattcttttgaaatgttgcaccttctgtctgatagGCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTT

Basic information

species Oryza sativa
transcript LOC_Os01g42950.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42950.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 5
gtaaattatcacttatcatttctttatcttgggcataagatcttccagaatggagtttttggatgttctatttgattggagatcaccag-gttacctatacttacatgaaatt-cttttgaaatgttgcaccttctgtctgatagGCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTT
||   | | ||| |  | || | | || |  || | ||       || |   || |||||       ||   ||   | | ||||  |     ||  ||  || ||||||||   |||| ||||| |  |  || |||     ||| ||||| ||||||||| |||||||| ||||||| |||||||||||||||||||||||||||
gtgtgt-aacaccttcctttccctcatttaagggaaaa------tcaaaggagattttttca-----ctcactgggggtaaatcatgaccaccactgattatttcatgaaatgatttttaaaatgcta-aatttttgt---gcagGTTCTTCTTTCTTCCGGGATGATACGAGGTTGCGCGCTCTTCGTTTCCTTGACCATTTGCTT
















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|58665583|gb|CK054269.1|CK054269
EST:     GATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAG                         GCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTG
genomic: GATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAGgtaaattatc ... tgtctgatagGCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTG
EST: gi|58653744|gb|CK042424.1|CK042424
EST:     GATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAG                         GCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTG
genomic: GATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAGgtaaattatc ... tgtctgatagGCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTG
EST: gi|29622819|gb|CB627830.1|CB627830
EST:     GATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAG                         GCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTG
genomic: GATGCTATCAGTTGATGTAGCATCACGCCCTAGTGCTATGGCGTTCACAGgtaaattatc ... tgtctgatagGCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttacctatacttacatgaaattcttttgaaatgttgcaccttctgtctgatagGCTCTTCCTTCTTCCGGAATGATACGCGGTTGCGTGCTCTTCGTTTCCTTGACCATTTGCTT
         tacttac  putative branch site (score: 1)
                                        ccttctgtct  putative PPT
                   aaattcttttgaaat  TA-rich tract