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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagttatcatgatgataatatttgcatgtttttcatatgttgctgatccaagcttacttatcttaataccatgcagCTGAGACTAAAGTTGCACCTGTTACACCCCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTTCTG

Basic information

species Oryza sativa
transcript LOC_Os06g07090.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G030144_T02 (Zea mays), 3'ss of exon 14
gtaaaagttatcatgatgataatatttgcatgtttttcatatgttgctg--atccaagcttacttatcttaataccatgcagCTGAGACTAAAGTTGCACCTGTTACACCCCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTTCTG
            |||    ||         |||||||  || ||| |||  ||    ||||| ||||||  | ||||||| || |||||||||  ||   |||||||||| ||||||||||||||||||||||||||||||||| ||||||||||| |||
----------gtatgtctgtatagacaatctgtttttttta-gtttctgccatttctgcttatttatct-gacaccatgctgcagAGACTAAATCTGTCGCTGTTACACCTCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAGGCACATCTCTTCCTG

upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G017421_T01 (Zea mays), 3'ss of exon 15
gtaaaagttatcatgatgataatatttg-catgtttttcatatgttgc-tgatccaagcttacttatcttaataccatgcagCTGAGACTAAAGTTGCACCTGTTACACCCCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTTCTG
||||||   |   |   ||  |||       ||||| |    | ||   | |||   ||||| ||||||  | ||| | | || |||||||||  | | ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| |||
gtaaaaaaaagtctagagagtatagacaatctgtttcttgagttttttgtaatctgtgcttatttatct-gacaccgtactgcagAGACTAAACCTCCCCCTGTTACACCTCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTCCTG
















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|27546490|gb|CA764691.2|CA764691
EST:     AGTACAAAATGGCCCACCAACAGTATCAAACTTTAGCCTTCCTGGTCAAG                         CTGAGACTAAAGTTGCACCTGTTACACCCCAAGTTGTGGATCTTCTTGATG
genomic: AGTACAAAATGGCCCACCAACAGTATCAAACTTTAGCCTTCCTGGTCAAGgtaaaagtta ... taccatgcagCTGAGACTAAAGTTGCACCTGTTACACCCCAAGTTGTGGATCTTCTTGATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatgtttttcatatgttgctgatccaagcttacttatcttaataccatgcagCTGAGACTAAAGTTGCACCTGTTACACCCCAAGTTGTGGATCTTCTTGATGGTTTGTCCTCAAGCACATCTCTTTCTG
                                       tcttaat  putative branch site (score: 3)
                                ttacttatcttaata  TA-rich tract