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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgatgcacagaaaaagcattagcatttaatgaattatcatttgttttgaggaaacatgtaataccagatttttgttctttccctaaaaataaatactatttgctccagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAG

Basic information

species Oryza sativa
transcript LOC_Os04g02050.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 3
gtatttgatgcacagaaaaagcattagcatttaatgaattatcatttgttttgaggaaacatgtaataccagatttttgttctttccctaaaaataaatactatttgctc-cagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAG
        |||||  |  |  || |    |||  |  |  |  |  |  |||||     ||| |  |   |   | |||     || ||     |     ||||   ||  ||||||||||| ||||||||||| || ||| ||||||| || |||||||||||||| ||| ||||||||||||||||||| |||||||||
------tgtgcactaatgattcaatt-tgtttgttttaccaaaaacttgtttgatttttcatctcctgtta---tcttgaatgctctcttgttttg----ctatcctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG

upper sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 3
gtatttgatgcacagaaaaagcattagcatttaatgaattatcatttgttttgaggaaacatgtaataccagatttttgttctttccctaaaaataaatactatttgctccagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAG
      | | |     |  |   ||| | |  |       ||||||| | ||    |  | | |  | | |    |   ||  |   ||||       || |||    | ||||| ||||||||||| |||||||  ||||||||||| || ||||||||||||||   ||| |||||||| ||||| ||||||||||||
----aaggttccttccattattgttaacttgaagacgcacatcatttttatt----atgcttttcctgcaatgaatccattaatcttctaact-----tattatactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG
















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|33796395|gb|CF324064.1|CF324064
EST:     TCCTTAGCATGGCTCCAGGTTTAGAGAAACTCAACATATTGCCCTTCAAG                         GTAGCAGCATATGATACAGTGGCGAAGAAGATGGCCTTCTTTGATCCTTCA
genomic: TCCTTAGCATGGCCCCAGGTTTAGAGAAACTCAACATATTGCCCTTCAAGgtatttgatg ... tttgctccagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtaataccagatttttgttctttccctaaaaataaatactatttgctccagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAG
                           ccctaaa  putative branch site (score: 3)
                                             tttgctcc  putative PPT
                              taaaaataaatactat  TA-rich tract