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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttttaacctccacttttatatttgtttttcctagtatatgtataccttggggtttcaataaatatttattggattagtgatgaaatcagtggatttaatatactgagggatgatcacataaattaaatatttaatatgaaccgcaatttaacttcacatgtgctgtccacatgcagGAGAAAGCTTTAGCAGAGGCAGAAAATAGGCCGCTGCCCCAATCATTTTCAAGTAACGATGTCCGTGCCTTACGACTAAGTGATTTCAAACATGCTCATG

Basic information

species Oryza sativa
transcript LOC_Os03g22420.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 5
gttagtttttaacctccacttttatatttgtttttcctagtatatgtataccttggggtttcaata--aatatttattggattagtgatgaaatcagtg-gatttaatatac-tgagggatgatcacataaattaaatatttaatatgaaccgcaatttaacttcacatgtgct-gtccacatgcagGAGAAAGCTTTAGCAGAGGCAGAAAATAGGCCGCTGCCCCAATCATTTTCAAGTAACGATGTCCGTGCCTTACGACTAAGTGATTTCAAACATGCTCATG
||| ||||| || |||        |   |||||  |||      ||||  ||||||||||  ||||  |  | || ||| |   |  |   ||| | |  |||      ||| |  |  ||      ||  |||   | ||||||| |||  |||||| |  ||||  ||   | |  ||||||||||||| ||||| |||||| |||||||||||  |  |||| |  |||    | || || ||||||||||| ||| ||  ||||||||||| |||||| ||||
gtttgtttt-aatctct-------tgagtgtttcccctgtgggctgtactccttggggttctaatatcatcagttcttgaaaatggaacagaattattttgatactggttacatttgatatacatggatgtattctttgtttaataggaattgcaattgagtttcaagtggatttgctcacatgcagGAGAGAGCTTCAGCAGAAGCAGAAAATAGATCATTGCCTCCGTCACACACTAGCAATGATGTCCGTGCATTAAGAACAAGTGATTTCATACATGCGCATG

upper sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 21
gttagtttttaacctccacttttatatttgtttttcctagtatatgtataccttggggtttcaataaatatttattggattagtg--atgaaatcagtggatttaatatactgagggatgatcac--ataaattaaatatttaatatgaaccgcaatttaacttcacatgtgctgtccacatgcagGAGAAAGCTTTAGCAGAGGCAGAAAATAGGCCGCTGCCCCAATCATTTTCAAGTAACGATGTCCGTGCCTTACGACTAAGTGATTTCAAACATGCTCATG
||| ||||  |||||| | || |   | |||  |   || |   ||     ||  |  | ||| |   |  |      |  | ||  |   ||| | |    |     | ||    |||   ||   ||  |||   | ||||||||  |  |||||| |  ||||  ||   ||||||| ||||||||| ||||| ||||||  |||||||||||||  |||| |  ||     | || || ||||||||||| ||| || |||||||||||| |||||| ||||
gtttgtttc-aacctcgagttcttcctgtgtgctg--tactccttggggttctaagaatatcagttggtgctagcaaaaccaatggaacagaattattttgatactggttctatttgatatacatggatggattctttgtttaatatttaatgcaattgattttcaagtgcattgtccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATG
















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|33680639|gb|CF308878.1|CF308878
EST:     TTACTGCTGCTCATCTCCCTATTAAAGATATCCTTGAAAAGGAGAAGAAG                         GAGAAAGCTTTAGCAGAGGCAGAAAATAGGCCGCTGCCCCAATCATTTTCA
genomic: TTACTGCTGCTCATCTCCCTATTAAAGATATCCTTGAAAAGGAGAAGAAGgttagttttt ... ccacatgcagGAGAAAGCTTTAGCAGAGGCAGAAAATAGGCCGCTGCCCCAATCATTTTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaatatttaatatgaaccgcaatttaacttcacatgtgctgtccacatgcagGAGAAAGCTTTAGCAGAGGCAGAAAATAGGCCGCTGCCCCAATCATTTTCAAGTAACGATGTCCGTGCCTTACGACTAAGTGATTTCAAACATGCTCATG
                        atttaac  putative branch site (score: 3)
     atatttaatatgaa  TA-rich tract