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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagagtaactcatattttaactgatgttctcgtttgggttttgaggtttgatcggtaggttctttacttatttatgccatttatcggtattgtctttcagGGCTATTGACAAAAAAGTTCCTAAACTTGCTAAAGGGTGCACCTGGCGGCATAGTTGATTTGAATAATGCCGCAGAAACACTGGAG

Basic information

species Oryza sativa
transcript LOC_Os12g06200.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G333591_T01 (Zea mays), 3'ss of exon 5
gtaagaagagtaactcatattttaactgatgttctcgtttgggttttgaggtttgatcggtaggttctttacttatttat-gccatttatcggtattgtctttcagGGCTATTGACAAAAAAGTTCCTAAACTTGCTAAAGGGTGCACCTGGCGGCATAGTTGATTTGAATAATGCCGCAGAAACACTGGAG
|| |||||| | |   ||  |||  ||| | || | |||   || |  | |     | | |  ||| |    || || || || |  |||   | ||| |||| |||||| ||||||   |||||||| ||||||||||| ||||||||||| ||||| |||||| |||||||||| |||||||| || |||
gtgagaagaatcaactatggttttcctgttctttt-gttcacgtctccatggcatcttgatgagttttcctttttttaattgcgaggtat---tgttgccttttagGGCTCTTGACA---AAGTTCCTGAACTTGCTAAAAGGTGCACCTGGTGGCATTGTTGATCTGAATAATGCTGCAGAAACTCTAGAG

upper sequence: LOC_Os12g06200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 2
gtaagaagagtaactcatattttaactgatgttctcgtttgggttttgaggtttgatcggtaggttctttacttatttat-gccatttatcggtattgtctttcagGGCTATTGACAAAAAAGTTCCTAAACTTGCTAAAGGGTGCACCTGGCGGCATAGTTGATTTGAATAATGCCGCAGAAACACTGGAG
|| |||||| | |   ||  |||  ||| | || | |||    | |  | |     | | |  ||| |    || || || ||||  |||   | ||| |||| |||||| ||||||   ||| |||| || |||||||| ||||||||||| ||||| |||||| |||||||||| |||||||| || |||
gtgagaagaatcagctatggttttcctgttctttt-gttcacatctccatggcatcttgatgagttttcctttttttaattgccaggtat---tgttgccttttagGGCTCTTGACA---AAGGTCCTGAATTTGCTAAAAGGTGCACCTGGTGGCATTGTTGATCTGAATAATGCTGCAGAAACTCTAGAG

upper sequence: LOC_Os12g06200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G829408_T01 (Zea mays), 3'ss of exon 5
gtaagaagagtaactcatattttaactgatgttctcgtttgggttttgaggtttgatcggtaggttctttacttatttat-gccatttatcggtattgtctttcagGGCTATTGACAAAAAAGTTCCTAAACTTGCTAAAGGGTGCACCTGGCGGCATAGTTGATTTGAATAATGCCGCAGAAACACTGGAG
|| |||||| | |   ||  |||  ||| | || | |||   || |  | |     | | |  ||| |    || || || || |  |||   | ||| |||| |||||| ||||||   |||||||| ||||||||||| ||||||||||| ||||| |||||| |||||||||| |||||||| || |||
gtgagaagaatcagctatggttttcctgttctttt-gttcacgtctccatggcatcttgatgagttttcctttttttaattgcgaggtat---tgttgccttttagGGCTCTTGACA---AAGTTCCTGAACTTGCTAAAAGGTGCACCTGGTGGCATTGTTGATCTGAATAATGCTGCAGAAACTCTAGAG

upper sequence: LOC_Os12g06200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G086401_T01 (Zea mays), 3'ss of exon 5
gtaagaagagtaactcatattttaactgatgttctcgtttgggttttgaggtttgatcggtaggttctttacttatttat-gccatttatcggtattgtctttcagGGCTATTGACAAAAAAGTTCCTAAACTTGCTAAAGGGTGCACCTGGCGGCATAGTTGATTTGAATAATGCCGCAGAAACACTGGAG
   |||||| | |   ||  |||  ||| | || | |||    | |  | |     | | |  ||| |    || || || ||||  |||   | ||| |||| |||||| ||||||   |||||||| || |||||||| ||||||||||| ||||| |||||| |||||||||| |||||||| || |||
--gagaagaatcagctatggttttcctgttctttt-gttcacatctccatggcatcttgatgagttttcctttttttaattgccaggtat---tgttgccttttagGGCTCTTGACA---AAGTTCCTGAATTTGCTAAAAGGTGCACCTGGTGGCATTGTTGATCTGAATAATGCTGCAGAAACTCTAGAG

upper sequence: LOC_Os12g06200.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G052515_T01 (Zea mays), 3'ss of exon 3
gtaagaagagtaactcatattttaactgatgttctcgtttgggttttgaggtttgatcggtaggttctttacttatttatgccatttatcggtattgtctttcagGGCTATTGACAAAAAAGTTCCTAAACTTGCTAAAGGGTGCACCTGGCGGCATAGTTGATTTGAATAATGCCGCAGAAACACTGGAG
|| |||||| | |   ||   ||  |   |  | | |||    | |  | |     | | |  ||| |    || ||||             | ||| |||| |||||| |||||||| |||||||| ||||||||||| ||||||||||| ||||| |||||| |||||||||| |||||||| || |||
gtgagaagaatcagctattggttttcctgttcttttgttcacatctccatggcatcttgatgagttttcctttttttta-attgcggggtattgttgccttttagGGCTCTTGACAAAGAAGTTCCTGAACTTGCTAAAAGGTGCACCTGGTGGCATTGTTGATCTGAATAATGCTGCAGAAACTCTAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgatcggtaggttctttacttatttatgccatttatcggtattgtctttcagGGCTATTGACAAAAAAGTTCCTAAACTTGCTAAAGGGTGCACCTGGCGGCATAGTTGATTTGAATAATGCCGCAGAAACACTGGAG
 gtttgat  putative branch site (score: 5)
                                            ttgtctttc  putative PPT
              ttctttacttatttat  TA-rich tract