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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagaaaattctattcttatgcaattctagaaagatgatgcatgttctgaaaattgacattgctccatttctgtctagGTGAGACGTCTCTCATCCTGCGAAACAATGGGATCTGCAACTACAATATGCAGTGATAAAACAGGGACACTTACCTTGAATAAG

Basic information

species Oryza sativa
transcript LOC_Os08g40530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 17
gtaaaagaaaattctattcttatgca-attctagaaagatgatgcatgttctgaaaattgacattgctccatttctgtcta--------gGTGAGACGTCTCTCATCCTGCGAAACAATGGGATCTGCAACTACAATATGCAGTGATAAAACAGGGACACTTACCTTGAATAAG
|||||  ||||||  ||| ||||||| ||  |    | |  | | | |    || ||   | ||   |  |||| ||| ||        |||||| || ||||| || || |||||||||||||| || |||||||||||||||||||| ||||| || ||||| |||||||||
gtaaataaaaatt--atttttatgcatatatttattaaaaaaggtacgacaggagaaagaatatgatttgatttttgtttatttaaatagGTGAGGCGGCTCTCGTCATGTGAAACAATGGGATCAGCTACTACAATATGCAGTGATAAGACAGGAACCCTTACATTGAATAAG

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 13
gtaaaagaaaattctattcttatgcaattctagaaagatgatgcatgttctgaaaat-tgacattgctccatttctgtc-tagGTGAGACGTCTCTCATCCTGCGAAACAATGGGATCTGCAACTACAATATGCAGTGATAAAACAGGGACACTTACCTTGAATAAG
                                 ||          |||| || || |  |   ||| | ||| | |||   ||||  | | | |  |  ||||||||||||||||||||||||| || || || |||||||| || || || || ||||||||  ||
-------------------------------gtaagtcccccaagtgttttgtaagtacggttttgatgcatgtttgttacagGTCCGTCATTTGGCTGCCTGCGAAACAATGGGATCTGCAACGACTATCTGTAGTGATAAGACCGGAACCCTGACCTTGAACCAG

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 14
gtaaaagaaaattctattcttatgcaattctagaaagatgatgcatgttctgaaaat-tgacattgctccatttctgtc-tagGTGAGACGTCTCTCATCCTGCGAAACAATGGGATCTGCAACTACAATATGCAGTGATAAAACAGGGACACTTACCTTGAATAAG
                                 ||      |   |||| || || | ||   ||| | ||||| |||   ||||  | | | |  |  ||||||||||||||||||||||||| || || ||||||||||| || || || || ||||||||  ||
-------------------------------gtaagtcccctaagtgttttgtaagtatggttttgattcatttttgttacagGTCCGTCATTTGGCTGCCTGCGAAACAATGGGATCTGCAACGACTATCTGCAGTGATAAGACCGGAACCCTGACCTTGAACCAG

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|29636898|gb|CB641907.1|CB641907
EST:     GCGAGACAAGGCACTG                         GTGAGACGTCTCTCATCCTGCGAAACAATGGGATCTGCAACTACAATATGC
genomic: GCGAGACAAGGCACTGgtaaaagaaa ... ttctgtctagGTGAGACGTCTCTCATCCTGCGAAACAATGGGATCTGCAACTACAATATGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctagaaagatgatgcatgttctgaaaattgacattgctccatttctgtctagGTGAGACGTCTCTCATCCTGCGAAACAATGGGATCTGCAACTACAATATGCAGTGATAAAACAGGGACACTTACCTTGAATAAG
                            aattgac  putative branch site (score: 3)
                                       ctccatttctgtct  putative PPT
                        tgaaaatt  TA-rich tract