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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttctgcttccattatcatccctttgtctcgatttgtgatgtcactacgaagaaactggagtttaagatgaaataactgttttatgcatgttcttcagTCAGTTAGATTGACAGATGAATTCATCGAACTTGCAAAGGAGAATACAGGCAACAATGTAGAGACTTGTGGAATCCTAGGTGCTTCATTT

Basic information

species Oryza sativa
transcript LOC_Os01g47262.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g47262.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G013625_T01 (Zea mays), 3'ss of exon 2
gtacgttctgcttccattatcatccctttgtctcga---tttgtgatgtcactacgaaga------aactggagtttaagatgaaataactgttttatgcatgttcttcagTCAGTTAGATTGACAGATGAATTCATCGAACTTGCAAAGGAGAATACAGGCAACAATGTAGAGACTTGTGGAATCCTAGGTGCTTCATTT
|||||||||  |||  |   ||||  ||| | |  |   | |    |||  ||  || ||       |||| || || ||||||||||||    |||  |||||| |||||||||| ||||||||||  |||||||| || |||||||||||||||||| |||| ||| |||||||||||||||| || ||||||||||||
gtacgttctctttcgttccccatcattttcttttaagaatatacagtgtttcttggaggatggtaagactgaagattgagatgaaataacatcctta--catgttattcagTCAGTGAGATTGACAGCCGAATTCATGGAGCTTGCAAAGGAGAATACAAGCAATAATCTAGAGACTTGTGGAATTCTTGGTGCTTCATTT
















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|44677600|gb|CR291034.1|CR291034
EST:     TTCACCATCGGTCAATTTGCATGACAACCAGATA                         TCAGTTAGA-TGCACAGATGAATTCATCGAAC-TGCCAAAGGAGAATACAG
genomic: TTCAGCATCTGTCAATTTGCATGACATGCAGATAgtacgttctg ... tgttcttcagTCAGTTAGATTG-ACAGATGAATTCATCGAACTTG-CAAAGGAGAATACAG
EST: gi|33658750|gb|CF281363.1|CF281363
EST:     CTTCAGTGGGGCAGTCTTCAGCATCTGTCAATTTGCATGACATGCAGATA                         TCAGTTGGATTGACAGATGAATTCATCGAACTTGCAAAGGAGAATACAGGC
genomic: CTTCAGTGGGGCAGTCTTCAGCATCTGTCAATTTGCATGACATGCAGATAgtacgttctg ... tgttcttcagTCAGTTAGATTGACAGATGAATTCATCGAACTTGCAAAGGAGAATACAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actacgaagaaactggagtttaagatgaaataactgttttatgcatgttcttcagTCAGTTAGATTGACAGATGAATTCATCGAACTTGCAAAGGAGAATACAGGCAACAATGTAGAGACTTGTGGAATCCTAGGTGCTTCATTT
                           aaataac  putative branch site (score: 2)
                                             tgttcttc  putative PPT
                  tttaagatgaaataa  TA-rich tract