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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactgttactattatcatggcactgatacatcaaaaaaatttgggatggtacttttacagtatgctgagagtttgaaactttgcatggcag

Basic information

species Oryza sativa
transcript LOC_Os07g39010.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g39010.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G060762_T01 (Zea mays), 5'ss of exon 12
GGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactgttactattatcatggcactgatacatcaaaa--aaatttgggatggtacttttacagta----tgctga-gagtttgaaactttgcatggcag
|| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||| ||| ||||||||||||||||||||||||||||||| ||||  |||||    ||          ||||| ||  ||| ||||  | ||| | || | ||     |  ||| ||| |||  | ||||||||||||
GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAGTAGTTCTGTATATTCTTGAGTCCTATCAAGgtaattactgccactatctgaatacttgcacatcatcataagcaaaattggctttgtaatcttccggtgaaagttttgatgaggttggtattttgcatggcag

upper sequence: LOC_Os07g39010.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G121458_T01 (Zea mays), 5'ss of exon 12
GGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactgttactattatcatggcactgatacatca-----aaaaaatttgggatggtacttttacagta-----tgctga-gagtttgaaactt----tgcatggcag
|| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||| ||||||| ||| |||| |||||||||||||||||||||||| |    |||| | | ||||  ||||||     |  ||| ||    | ||| | || | |||     |  ||| ||| |||  |  |    ||||||||||
GGAGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTTTCATGTGGAATAGCTCTCTATGTTCTCGAGTCCTATCAAGgtaatgactgtca--gctatcttagtactggcacatcatcataagcaaaattaaccttgtaatcttccggtaaaaagttttgatgagattgggatctgacatgcatggcag
















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|55827807|gb|AU056171.2|AU056171
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
EST: gi|29630209|gb|CB635218.1|CB635218
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
EST: gi|29638656|gb|CB643665.1|CB643665
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
EST: gi|29666892|gb|CB663167.1|CB663167
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
EST: gi|4715053|gb|AU056170.1|AU056170
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
EST: gi|29655797|gb|CB652072.1|CB652072
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
EST: gi|29630236|gb|CB635245.1|CB635245
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
EST: gi|29666893|gb|CB663168.1|CB663168
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTTCCAATCCCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
EST: gi|29630208|gb|CB635217.1|CB635217
EST:     TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAG                         GAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA
genomic: TGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 66 (upstream exon), 73 (downstream exon)
Score: 20

GGTGAAGATCTAAATGGTTGTGCTTTTGTGTATGGCTCATTAAGTTTTGTTGACAAAGTGTCATGCGGACTAGCTCTGTATATTCTTGAGTCCTATCAAGgtaatgactg ... tgcatggcagGAAGTACCAATACCAGACAGAACCTAGAGTTGGCATTTGGTTATTCAGTTACAAGACTTGGTTTGGGGTTAGTCCCAGCTGCCTGTTCACTGCTCTCAGC




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