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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatagttacttattttattgttactatggtttgtttcttgtttaagacaataaatttattcgactcaaattataagaaactaatactctggtgcttacagTTGCTGGTAACCTAGTGAATGCATTGCTGGATGCTATATTTATTTTTCCACTTGGTCTAGGAGTAAGTGGCGCTGCATTGGCAACAGTGACTTCTGA

Basic information

species Oryza sativa
transcript LOC_Os12g01580.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G150557_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------tatagttac-ttattttattgttactatggtttgtttcttgtttaagacaataaatttattcgactcaaatta------taagaaactaatactctggtgcttacagTTGCTGGTAACCTAGTGAATGCATTGCTGGATGCTATATTTATTTTTCCACTTGGTCTAGGAGTAAGTGGCGCTGCATTGGCAACAGTGACTTCTGA
                                                                                 || |   || || |||| |||| |||||  ||| |||||| ||  ||  | |  || || | || ||||| |        ||| |||| ||  |  | ||||||||| |||||| |||||| | |||||| | || |||||  || ||||||||||| |||||||||||||||| || |||||| |||| || ||||| || ||
gtaagactttgccaattcattttgacaaaataatgtaacactagttttttgtccatctagaattggtttgaccttgctatttaaatgcacattcttttgttgtaactattttttatttcttattctagctactctatgtaattgattcaaaatgatcaagcaaggaactgatggtacgatgcttacagGTGCTGGCAACCTATTAAATGCAGTACTTGATGCATTACTTATTTTTCCAATTGGTCTAGGAGTAAGCGGTGCTGCACTGGCCACTGTGACCTCGGA

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G890665_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------tatagttacttattttattgttacta-tggtttgt-ttcttgtttaagacaataaatttattcgactcaaatta------taagaaactaatactctggtgcttacagTTGCTGGTAACCTAGTGAATGCATTGCTGGATGCTATATTTATTTTTCCACTTGGTCTAGGAGTAAGTGGCGCTGCATTGGCAACAGTGACTTCTGA
                                                                                        | ||  | | |||| | |||||   | |  ||| | ||  |  | | |  |||  || || | || ||||| |       |||| | || ||| |||| ||||||||| |||||| |||||| | |||||||| || ||||   || ||||||||||||||||||||||||||||||| |||||| |||| || ||||| |||||
gtatgtctttgcttgttcattttgacaaaatattgtaacacataacattgtcttttttttttcatctctaattgctttcaccttgctatttaaatgcatattcttttgttgtaactaatttttatttctaatcaggctaatctatgtaattgattcaaaatgatcaagtaaggatctgatagtctgatgcttacagGTGCTGGCAACCTATTAAATGCATTACTTGATGTGGTACTTATTTTTCCACTTGGTCTAGGAGTAAGTGGTGCTGCACTGGCCACCGTGACCTCTGA
















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|570085|gb|D40934.1|D40934
EST:     AGGTGCTTTTCGTGGATTCATGGATACAAAGACACCGTTGTTTGCTGTGG                         TTGCTGGTAACCTAGTGAATGCATTGCTGGATGCTATATTTATTTTTCCAC
genomic: AGGTGCTTTTCGTGGATTCATGGATACAAAGACACCGTTGTTTGCTGTGGgtaagacaat ... gtgcttacagTTGCTGGTAACCTAGTGAATGCATTGCTGGATGCTATATTTATTTTTCCAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaataaatttattcgactcaaattataagaaactaatactctggtgcttacagTTGCTGGTAACCTAGTGAATGCATTGCTGGATGCTATATTTATTTTTCCACTTGGTCTAGGAGTAAGTGGCGCTGCATTGGCAACAGTGACTTCTGA
                                aactaat  putative branch site (score: 2)
                   tcaaattataagaaac  TA-rich tract