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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtccagttctattaaatctgtttatcctgatgaagcttttgctcattctgaattcatgatggtctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g60120.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60120.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G021589_T05 (Zea mays), 3'ss of exon 6
gtaatgtccagttctattaaatctgtttatcctga---------tgaagcttttgctcattctgaattca-------tgatggtctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG
||||| |||  |     ||| |||| |||    ||         || ||||     ||||| | | || |         ||| ||  || |||||||||||| ||||||||| |||||||    || |||||||||||||||||  ||||||| ||||| |||||||||
gtaatatcctttgtcgctaa-tctgcttagtaagaagtaagagctggagctacgattcattttaattttaaagtttgcaatgatcc-ctacagGTATTTGGACGTTGCTGGTCAGAAGACTTGCAATCTTTACTTATACAATGGTGTGGCTCTATTTGTTGGATGGCTG

upper sequence: LOC_Os01g60120.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G021589_T02 (Zea mays), 3'ss of exon 6
gtaatgtccagttctattaaatctgtttatcctga---------tgaagcttttgctcattctgaattca-------tgatggtctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG------------------------
||||| |||  |     ||| |||| |||    ||         || ||||     ||||| | | || |         ||| ||  || |||||||||||| ||||||||| |||||||    || |||||||||||||||||  ||||||| ||||| |||||||||                        
gtaatatcctttgtcgctaa-tctgcttagtaagaagtaagagctggagctacgattcattttaattttaaagtttgcaatgatcc-ctacagGTATTTGGACGTTGCTGGTCAGAAGACTTGCAATCTTTACTTATACAATGGTGTGGCTCTATTTGTTGGATGGCTGGTACAACAACTGCTCTCACGAGTC
















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|86261222|gb|CI004787.1|CI004787
EST:     ACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: ACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|8859152|gb|AU096470.1|AU096470
EST:     TCATGGTTCTCTTTTACTGAAGCCACCA-TCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: TCATGGTTCTC-TTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|29669062|gb|CB665337.1|CB665337
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|29664738|gb|CB661013.1|CB661013
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|8527754|gb|AU092569.1|AU092569
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
EST: gi|29669064|gb|CB665339.1|CB665339
EST:     CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATG                         GTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG
genomic: CTCATGGTTCTCTTTACTGAAGCCACCACTCCCTTTGTGAACCTTAGATGgtaatgtcca ... tctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttatcctgatgaagcttttgctcattctgaattcatgatggtctgctgcagGTATTTGGAGGTTGCTGGTAAGAAGACGCATAACCTTTACTTATACAATGGATTGGCTCTGTTTGTCGGATGGCTG
       tcctgat  putative branch site (score: 3)
                                 aattcat  TA-rich tract