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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaccaagctgtatcgcggttcaatataattaccatgaacttgtgcttatttaatttagtttttcatggggtagcttttgtacttatattcttctttcagCTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCCAGCCAATGTGCTCCTTGGTAATGGATTCTCAGTACGTGTCGCTGAATGT

Basic information

species Oryza sativa
transcript LOC_Os02g07960.4
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07960.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G335638_T01 (Zea mays), 3'ss of exon 13
gtaagttaccaagctgtatcgcggttcaatataattaccatgaacttgtgcttatttaatttagtttttcatggggtagcttttg----------------tacttatattcttctttcagCTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCCAGCCAATGTGCTCCTTGGTAATGGATTCTCAGTACGTGTCGCTGAATGT
          |||||||||     ||  |||| ||  |||||| |||||   | || || |||| || ||| | | |  || |                  || | |   | ||||| ||| ||||| ||||| | |||||||||||| ||||| |||||||||||||| |||||||| |||||||| |  ||| ||| |||||| ||||| |||||||||
--------gtaagctgtattcaacttagatattatatccatgaccttgtttgtgttaaacttagcttgtcaagagatgactatcacaatcttaatatttactattcacgcttttcttccagGTATCTCCATGACACCTGTGAACCTCCTGTAGTACACCAGAATTTTGAACCAGCCAACGTGCTCCTCGACAATAGATGCTCAGTGCGTGTTGCTGAATGT
















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|58669825|gb|CK058511.1|CK058511
EST:     TCATGGAATGCTCGCCTCCAAGTTGCTCTTGGTGCAGCAAAGGCCTTAGA                         CTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
genomic: TCATGGAATGCTCGCCTCCAAGTTGCTCTTGGTGCAGCAAAGGCCTTAGAgtaagttacc ... cttctttcagCTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
EST: gi|29656568|gb|CB652843.1|CB652843
EST:     TCATGGAATGCTCGCCTCCAAGTTGCTCTTGGTGCAGCAAAGGCCTTAGA                         CTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
genomic: TCATGGAATGCTCGCCTCCAAGTTGCTCTTGGTGCAGCAAAGGCCTTAGAgtaagttacc ... cttctttcagCTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
EST: gi|58611356|gb|CK039068.1|CK039068
EST:     CATGGAATGCTCGCCTCCAAGTTGCTCTTGTGTGCAGCAAAGGCGTNA-A                         CTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
genomic: CATGGAATGCTCGCCTCCAAGTTGCTCTTG-GTGCAGCAAAGGCCTTAGAgtaagttacc ... cttctttcagCTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
EST: gi|29674397|gb|CB670672.1|CB670672
EST:     AAGGCCTTAGA                         CTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
genomic: AAGGCCTTAGAgtaagttacc ... cttctttcagCTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
EST: gi|29671438|gb|CB667713.1|CB667713
EST:     TCATGGAATGCTCGCCTCCAAGTTGCTCTTGGTGCAGCAAAGGCCTTAGA                         CTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
genomic: TCATGGAATGCTCGCCTCCAAGTTGCTCTTGGTGCAGCAAAGGCCTTAGAgtaagttacc ... cttctttcagCTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCC
EST: gi|8860079|gb|AU097397.1|AU097397
EST:     TCATGGAATGCTCGCCTCCAAGTTGCTCTTGGTGCAGCAAAGGCCTTAGA                         CTATCTACATGAGAGCTGTGA
genomic: TCATGGAATGCTCGCCTCCAAGTTGCTCTTGGTGCAGCAAAGGCCTTAGAgtaagttacc ... cttctttcagCTATCTACATGAGAGCTGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatttaatttagtttttcatggggtagcttttgtacttatattcttctttcagCTATCTACATGAGAGCTGTGAACCTCCAGTAGTGCACCAGAATTTTGAGCCAGCCAATGTGCTCCTTGGTAATGGATTCTCAGTACGTGTCGCTGAATGT
   atttaat  putative branch site (score: 4)
                                     cttatattcttctttc  putative PPT
     ttaatttagtttttca  TA-rich tract