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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttttcataagatctatagaaatgtatgcgatctgaagagcatcgtttctataactataactgttctgtgattctattatacatttctacctgtctagGCCTGCTAAACTTGTTGAGATCATGAAAGAACGCTTCGTTTCTTCAGGAGGAGCCATATTTGAGGGGAAAAGTTTGTCAAGCATTTCTGTTCATGATGAC

Basic information

species Oryza sativa
transcript LOC_Os08g32630.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32630.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G851815_T01 (Zea mays), 3'ss of exon 5
-atcttttcataagatctatagaaatgtatgcgatctgaagagcatcgtttctataactataactgttctgtgattctattatacatttctacctgtctagGCCTGCTAAACTTGTTGAGATCATGAAAGAACGCTTCGTTTCTTCAGGAGGAGCCATATTTGAGGGGAAAAGTTTGTCAAGCATTTCTGTTCATGATGAC
 || |  |    | ||||      | | | |    || || |  |      | |||| | || ||  |   | | | |||  |    || ||||| || |||||||||||||||||||||| |||||||||||||||| ||||||| |||||||| |||||||||| ||||||| | |||||||||| |||  ||||||| 
catgtcctatgtatatcttgcagcaagaaagatcccttaacataaataaaacaataattttagctcatgcatcagtttat-gtttgattttacctttccagGCCTGCTAAACTTGTTGAGAACATGAAAGAACGCTTCATTTCTTCGGGAGGAGCAATATTTGAGGAGAAAAGTCTATCAAGCATTTATGTCTATGATGAT
















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|29676352|gb|CB672627.1|CB672627
EST:     GAGAGTAAAGGTGAAATTTGGGTGGAGAACATCCTTAATCTTGGAATTTC                         GCCTGCTAAACTTGTTGAGATCATGAAAGAACGCTTCGTTTCTTCAGGAGG
genomic: GAGAGTAAAGGTGAAATTTGGGTGGAGAACATCCTTAATCTTGGAATTTCgtaagttatc ... acctgtctagGCCTGCTAAACTTGTTGAGATCATGAAAGAACGCTTCGTTTCTTCAGGAGG
EST: gi|300215548|gb|HO088174.1|HO088174
EST:     GAGAGTAAAGGTGAAATTTGGGTGGAGAACATCCTTAATCTTGGAATTTC                         GCCTGCTAAACTTGTTGAGATCATGAAAGAACGCTTCGTTTCTTCAGGAGG
genomic: GAGAGTAAAGGTGAAATTTGGGTGGAGAACATCCTTAATCTTGGAATTTCgtaagttatc ... acctgtctagGCCTGCTAAACTTGTTGAGATCATGAAAGAACGCTTCGTTTCTTCAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtttctataactataactgttctgtgattctattatacatttctacctgtctagGCCTGCTAAACTTGTTGAGATCATGAAAGAACGCTTCGTTTCTTCAGGAGGAGCCATATTTGAGGGGAAAAGTTTGTCAAGCATTTCTGTTCATGATGAC
           ctataac  putative branch site (score: 3)
                                        tttctacct  putative PPT
                           attctattatacattt  TA-rich tract