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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatgtagtttgttattgggtttacagtgatttcgaaagttgaactgttatttggatttcaggaattcatgtattaacaccattagtgttttgaacaattttatttactgctgtctgtctggagttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG

Basic information

species Oryza sativa
transcript LOC_Os07g47290.3
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 13
gtacatatgtagtttgttattgggtttacagtgatttcgaaagttgaactgttatttggatttcaggaattcatgtattaacaccattagtgttttg--aacaattttattt-actgctgtctgtctggagttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG
                                                         | | |  | |  ||||| | ||   |   | | |   |||  | ||| ||| | | | ||  |  ||| ||   ||||| || | || | |||  |    |  |   | || | ||||   | | |||||| |||||||| |||||||| |||||||| ||||||||||||||||| ||
---------------------------------------------------------gtaatataagttttcatatttttggaatgtgaatacattgtcagcaagtttctgtgagtgaagcttgtgtgagtttaactgtttgttctaaaagtac---acctttttactgtctcacatgacatagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACACAG

upper sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 13
gtacatatgtagtttgttattgggtttacagtgatttcgaaagttgaactgttatttggatttcaggaattcatgtattaacaccattagtgttttgaacaattttatttac-tgctgtctgtctggagttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG
                                                  || || |  |||||   | ||   | ||   ||      |  || | | ||||||| |  |  ||  |  ||| ||   ||| |  | | || ||||   |    |  |   |||| | ||||     |||||||| |||||||| |||||||| |||||||| ||||||||||||||||||||
--------------------------------------------------gtaatataaatttccatattttcaggatgtccat-----gcattgttaccaattttctacaagtgaagcttgtgtgagtttagctttctgttctgaatgtac---actttttttctgtatcacatggcacagGAGAGTTCAAGATTAATGTTGAGTGCAACCATGCTACTCTATCTGGACATAG
















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|29637953|gb|CB642962.1|CB642962
EST:     TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
genomic: TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATA
EST: gi|88306647|gb|CI671406.1|CI671406
EST:     TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAG                         GAGAATTCAAGATAAATGTTGAATGCAACCACGCCTACTCTATCTGGACAT
genomic: TTGGGATGTTGCAACCACATTCTCTTTCCTACAGAAATATGGTCTAACAGgtacatatgt ... ccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGC-TACTCTATCTGGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaaccgtgtattgtgaaataatctaaagtacattctttttcaccatatacagGAGAATTCAAGATAAATGTTGAATGCAACCACGCTACTCTATCTGGACATAG
                       atctaaa  putative branch site (score: 3)
                                 cattctttttcacc  putative PPT
                  aaataatctaaagta  TA-rich tract