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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctaaatcctaatccatcaatctctggtcatacaactcacgttgatgtatcgagactagtggcttttatgtttcttcatattaatttatttggttgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACA

Basic information

species Oryza sativa
transcript LOC_Os09g29404.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G150796_T03 (Zea mays), 3'ss of exon 12
atctaaatcctaatccatcaatctctggtcataca-actcacgttgatgtatcga---gactagtggcttttatgtttcttcata----ttaatttatttggttgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACA
          | | |||||| |||| |  |  | | | |||   | || | |  |     |   ||   || ||| || |   |     || ||||||||||||| ||||||||||||||||  ||||||| |||||||||||||||||||||||||||||||| || || ||||||||||| |||||| | |||||||| |||||||
--------tatgacccatcattctccgacccaatagattcattcttatttgtaaatttatcagatgttcttaatgattttatctgattctttatttatttggttgaagGAAATTGCCAAAGACTCTGTATTGTCTAGATGTAAGATCATTGCTGAACCTTGGGACTGTGGTGGCCTTTATCTAGTAGGGAGGTTCCCTAATTGGGACA

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 10
atctaaatcctaatccatcaatctctggtcatacaactcacgttgatgtatcgagactagtggctttta-tgtttcttcatattaatttatttggt----tgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACA
   | ||  | |   ||   |    | ||  |    ||||  | ||    |    | |  |   ||||| |||||      | |||||| | || |    || |||  ||||| |||||||| |||||||| |||||||| || ||||| || ||||||||||| || || || ||||| || ||| |||| ||||| |||||  
--ttgaagacaa---caatgagtagtagttttctccctcatctagaaaattgagaatttataaattttaatgttttagtcaactaatttttatgttcttttgcagGCTATTGCTAAAGATGCAGTATTATCAAGATGTAAAATTATTGCAGAGCCTTGGGATTGTGGAGGTCTCTATCTTGTTGGGAGTTTTCCTAATTGGGATC
















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|218500325|gb|FG953825.1|FG953825
EST:     TTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG                         GAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCT
genomic: TTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgtataatgta ... ttggttgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCT
EST: gi|58587143|gb|CF985451.1|CF985451
EST:     GGGTGCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG                         GAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCT
genomic: TTGT-CGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgtataatgta ... ttggttgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatcgagactagtggcttttatgtttcttcatattaatttatttggttgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCTTGGGATTGCGGCGGCCTTTATCTCGTAGGGCGTTTCCCTAACTGGGACA
                                  tattaat  putative branch site (score: 2)
                                        tttattt  CT-rich tract
                   ttttatgtttcttcat  TA-rich tract