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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcatctacattaggcaatactgaactcctgtttctacattaccgaaagttagaagcaaacatgtcccatttatgttggcagttactttaaccaaaattttgtttgcatggatcaacagGCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTG

Basic information

species Oryza sativa
transcript LOC_Os02g57180.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143651_T01 (Zea mays), 3'ss of exon 7
------------------------gtgatcatctacatta-ggcaatactgaactcctgtttctacattaccgaaagttagaagcaaacatgtcccatttatgttggcagttactttaaccaaaattttgtttgcatggatcaacagGCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTG
                        || ||   | |   || |  |||  |    |        | ||    | |||   || || | | |  |  | ||| | |  ||||| | ||||||  |||  |  |||  ||   ||||||||||||||| ||||||||||| || |||||||||||||||||||| ||  |||| ||||||||||| ||||| || ||||||||||||||||| |||||||
gtgatcatcatttttttagctttagtaatgcgccaagctatgataattattgcttgagaaccatccaaaggccaaaaccagcagtagata-atatcctttttctaagcagtcagtttaactgaaaact-atttctatccgtcaacagGCTACAATCATGAGGCCTGCTACCATGATTGGCACAGAAGATCGAATCCTGAACAGATGGGCACAATTTGCAAAGAATTGGGGTTTCCTCCCGCTTGTTG

upper sequence: LOC_Os02g57180.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G18950.1 (Glycine max), 3'ss of exon 7
gtgatcatctacattaggcaatactgaactcctgtttcta-cattaccgaaagttagaagcaaacatgtcccatttatgttggcagttactttaaccaaaattttgtttgcatggatcaacagGCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTG
             |  ||  ||  || |||    | |    ||||  |     ||         |||||  ||     |||   |||   |   | || |||| |  | ||     || |||||| |||||  |||  |||||    |||||||| ||||| |||||||||||||||  |||||| || ||||| ||||| |  || || || ||  |  |||
-----------tgtgtggtcattttgcactggaatatggggcattttcatgctttg-------ccatgttgca--agagttaatagt--ataatatcagaattctaat-gctaacctctacagGCCACAATCTTGAAACCTGCTGTAATGATTGGTACAGAGGATCGGATTTTGAATCCATGGGCTCATTTTGCTAAAAAGTATGGCTTTCTTCCGTTGTTTG
















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|11442907|gb|BF430806.1|BF430806
EST:     TGAGGGCCAAGGCTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAG                         GCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTG
genomic: TGAGGGCCAAGGCTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAGgtgatcatct ... ggatcaacagGCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTG
EST: gi|58690755|gb|CK079442.1|CK079442
EST:     TGAGGGCCAAGGCTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAG                         GCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTG
genomic: TGAGGGCCAAGGCTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAGgtgatcatct ... ggatcaacagGCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTG
EST: gi|29671359|gb|CB667634.1|CB667634
EST:     CTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAG                         GCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTG
genomic: CTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAGgtgatcatct ... ggatcaacagGCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTG
EST: gi|58597371|gb|CK007899.1|CK007899
EST:     TGAGGGCCAANGCTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAG                         GCTACAATTAT
genomic: TGAGGGCCAAGGCTGCTGGGGAGGAATCTGTGTTGAAAGAATTTCCTGAGgtgatcatct ... ggatcaacagGCTACAATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccatttatgttggcagttactttaaccaaaattttgtttgcatggatcaacagGCTACAATTATGAGGCCTGCAACTATGATTGGCACAGAAGATCGGATTTTGAATAGATGGGCACAGTTTGCCAAAAATTGGGGTTTCCTCCCTCTTGTTG
                     ctttaac  putative branch site (score: 3)
                      tttaaccaaaatttt  TA-rich tract