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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattaacatttttttctgggatttggaaataatcagtaattgattgaattacctttgattgctttaataagcacagTCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCACTTCCCTGTGAATCTTGACAAGTTAGCTGGGGTCCGTTGTCTTTTGTTG

Basic information

species Oryza sativa
transcript LOC_Os01g42850.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42850.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G005304_T01 (Zea mays), 3'ss of exon 7
-----gtagattaacatttttttctgggatttggaaataatcagtaattgattgaa--ttacctttgattgctt-taataagcacagTCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCACTTCCCTGTGAATCTTGACAAGTTAGCTGGGGTCCGTTGTCTTTTGTTG
      |  ||    |||||  | | |  ||| || |||||||  | |   | |||   || ||| ||||| || |   | ||||||||| ||||||||||||||  |||||||||| ||||||||||| ||||||||||| ||||||||| | |||| |||| |    || ||   |||| | |||
gtggttttaatatgtattttgctttcgagttttgatataatcaacagtgcgtagaaaactatctt-gattgtttatttcatgcacagTCAGGATGAAGAAAAACAATTGATGCACTTAAAGCTTATGGGGTGGCGCCACTTTCCTGTGAATATAGACAGGTTATCACATGTTCGAGTTCTTCTCTTG
















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|25798441|gb|CA754402.1|CA754402
EST:     AAAGAGATGAAACCGAAAGAAATTGATCTTTCTTCAATTAATCCAGCAAG                         TCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCA
genomic: AAAGAGATGAAACCGAAAGAAATTGATCTTTCTTCAATTAATCCAGCAAGgtagattaac ... ataagcacagTCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCA
EST: gi|29672224|gb|CB668499.1|CB668499
EST:     AAGAGATGAAACCGAAAGAAATTGATCATTTCTTCAATTAATCCAGCGAG                         TCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCA
genomic: AAGAGATGAAACCGAAAGAAATTGATC-TTTCTTCAATTAATCCAGCAAGgtagattaac ... ataagcacagTCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCA
EST: gi|29674599|gb|CB670874.1|CB670874
EST:     ATTAATCCAGCAAG                         TCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCA
genomic: ATTAATCCAGCAAGgtagattaac ... ataagcacagTCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCA
EST: gi|29674597|gb|CB670872.1|CB670872
EST:     ATTAATCCAGCAAG                         TCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCA
genomic: ATTAATCCAGCAAGgtagattaac ... ataagcacagTCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggaaataatcagtaattgattgaattacctttgattgctttaataagcacagTCAAGATGAAGAAAAACAGCTGATGCACTTGAAGCTTATGGGATGGCGCCACTTCCCTGTGAATCTTGACAAGTTAGCTGGGGTCCGTTGTCTTTTGTTG
                                        ctttaat  putative branch site (score: 4)
     aaataatcagtaatt  TA-rich tract