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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaaattttgctgcaccttttagtcttgtattgtggatctctttcttgattctattctaactgtttttatttactctgtgtgtcttcttctgtgtatgcagGGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGCTTATTGGATCTGTTTTTCAGTGTCTGGATCCTGCATTAACAATCGCTGC

Basic information

species Oryza sativa
transcript LOC_Os10g33275.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 14
gtttgaaattttgctgcaccttttagtcttgtattgtggatctctttcttgattctattctaactgtttttatttactctgtgtgtcttcttctgtgt-atgcagGGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGCTTATTGGATCTGTTTTTCAGTGTCTGGATCCTGCATTAACAATCGCTGC
|| ||||||||| | ||      ||  ||     | |   | | |||    ||| ||||| |  |||||  ||  ||        ||| |||  || |  ||||||||||||||| ||||| || || || || |||||||| || |||||||||||||| |||||||| || ||||| |||||||| | ||| ||||| |||||
gtgtgaaattttccagc------taacctcca--tataagtttttttgcacatt-tattccagttgtttgcataaacctctcaaatctactttggttttgtgcagGGCGACATCTCTGTACTCTCCCACTGGACCCAAACATCGGGAAAATGCTGCTTATGGGATCTGTATTCCAGTGCCTGGATCCAGTATTGACAATTGCTGC
















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|33381742|gb|CF197085.1|CF197085
EST:     TTTGAAAACCGTTGGAGCATTGGATGACGTGGAGGAGCTGACTTCTTTAG                         GGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
genomic: TTTGAAAACCGTTGGAGCATTGGATGACGTGGAGGAGCTGACTTCTTTAGgtttgaaatt ... gtgtatgcagGGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
EST: gi|29681906|gb|CB678181.1|CB678181
EST:     TTTGAAAACCGTTGGAGCATTGGATGACGTGGAGGAGCTGACTTCTTTAG                         GGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
genomic: TTTGAAAACCGTTGGAGCATTGGATGACGTGGAGGAGCTGACTTCTTTAGgtttgaaatt ... gtgtatgcagGGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
EST: gi|58600773|gb|CK011301.1|CK011301
EST:     TTTGAAAACCGTTGGAGCATTGGATGACGTGGAGGAGCTGACTTCTTTAG                         GGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
genomic: TTTGAAAACCGTTGGAGCATTGGATGACGTGGAGGAGCTGACTTCTTTAGgtttgaaatt ... gtgtatgcagGGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
EST: gi|218492590|gb|FG952568.1|FG952568
EST:     TTTGAAAACCGTTGGAGCATTGGATGACGTGGAGGAGCTGACTTCTTTAG                         GGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
genomic: TTTGAAAACCGTTGGAGCATTGGATGACGTGGAGGAGCTGACTTCTTTAGgtttgaaatt ... gtgtatgcagGGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
EST: gi|29675438|gb|CB671713.1|CB671713
EST:     CTGACTTCTTTAG                         GGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC
genomic: CTGACTTCTTTAGgtttgaaatt ... gtgtatgcagGGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattctattctaactgtttttatttactctgtgtgtcttcttctgtgtatgcagGGCGACATCTTTGTACACTTCCGCTAGATCCAAACATTGGAAAAATGCTGCTTATTGGATCTGTTTTTCAGTGTCTGGATCCTGCATTAACAATCGCTGC
        ttctaac  putative branch site (score: 1)
                                    tcttcttctgt  putative PPT
      tattctaactgttttt  TA-rich tract