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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaacaaccacatctcgtgagattcttggaagacatggtagaattgggaattcatcgatcatatatgattacccatttcttgatttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGCTGCTCCACAATTTCTGCATATACCACATAAATCCTCAGGGGCACGAGGT

Basic information

species Oryza sativa
transcript LOC_Os05g10740.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g10740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G100102_T01 (Zea mays), 3'ss of exon 3
gtgagtaacaaccacatctcgtgagattcttggaagacatggtagaattgggaattcatcgatcatatatgattacccatttcttgatttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGCTGCTCCACAATTTCTGCATATACCACATAAATCCTCAGGGGCACGAGGT
    ||||          |||     || ||   |  ||  |   |      |   ||| | | |||| |   | |     | |||  |||   |||||||||||||  |||||||||||  | || ||||| || ||||||||  ||||||| ||||| |||||| | |||||||| ||||| |||||||| |||  
----gtaagtgttgtcgatcgaagattttttctgattcactgccaagacttaa---cattgtttatatctcgctgctt-cctattggcttgg--gcagACATGTCCTATTTCCAAGGATTTTTCTTCTGCCCAGAAGTGGCGTCTTTGCTGCTACACAACTTCTGCGTCTACCACATCAATCCCCAGGGGCATGAG--

upper sequence: LOC_Os05g10740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G100102_T02 (Zea mays), 3'ss of exon 3
gtgagtaacaaccacatctcgtgagattcttggaagacatggtagaattgggaattcatcgatcatatatgattacccatttcttgatttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGCTGCTCCACAATTTCTGCATATACCACATAAATCCTCAGGGGCACGAGGT
    ||||          |||     || ||   |  ||  |   |      |   ||| | | |||| |   | |     | |||  |||   |||||||||||||  |||||||||||  | || ||||| || ||||||||  ||||||| ||||| |||||| | |||||||| ||||| |||||||| |||||
----gtaagtgttgtcgatcgaagattttttctgattcactgccaagacttaa---cattgtttatatctcgctgctt-cctattggcttgg--gcagACATGTCCTATTTCCAAGGATTTTTCTTCTGCCCAGAAGTGGCGTCTTTGCTGCTACACAACTTCTGCGTCTACCACATCAATCCCCAGGGGCATGAGGT

upper sequence: LOC_Os05g10740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G084011_T01 (Zea mays), 3'ss of exon 1
gtgagtaacaaccacatctcgtgagattcttggaagacatggtagaattgggaattcatcgatcatatatgattacccatttcttgatttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGCTGCTCCACAATTTCTGCATATACCACATAAATCCTCAGGGGCACGAGGT
    ||||   |      |||     || ||   |  ||  |   |      |   ||| | | |||| |   | |     | |||  ||| |  ||||||||||||| |||||||||||  | || ||| | || ||||||||  ||||||| ||||| |||||| | |||||||  ||||| ||||||||||||  
----gtaagtgctgtcgatcgaagattttttctgattcactgccaagacttaa---cattgtttatatctcgctgctt-cctattggcttgga--cagACATGTCCTGTTTCCAAGGATTTTTCTTCTGCTCGGAAGTGGCGTCTTTGCTGCTACACAACTTCTGCGTCTACCACACCAATCCCCAGGGGCACGAG--

upper sequence: LOC_Os05g10740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G096996_T01 (Zea mays), 3'ss of exon 3
gtgagtaacaaccacatctcgtgagattcttggaagacatggtagaattgggaatt--catcgatcatatatgattacccatttcttgatttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGCTGCTCCACAATTTCTGCATATACCACATAAATCCTCAGGGGCACGAGGT
    ||||   |      |||  ||||| ||            |    |  || ||  ||| | | |||| |   | |    || |||  |||   |||||||||||||| |||||||||||  | || | ||| || |||||| |  || |||| ||||| |||||| | |||||||| ||||| |||||||| ||| |
----gtaagtgctgtcgatcg-aagattttttttttctgattcactgctaagacttaacattgtttatatgtcgctgctt-cttattggcttgg--gcagACATGTCCTGTTTCCAAGGATTTTTCTTCTACCCGGAAGTGGCGACTTTGTTGCTACACAACTTCTGCGTCTACCACATCAATCCCCAGGGGCATGAGAT

upper sequence: LOC_Os05g10740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G023818_T01 (Zea mays), 3'ss of exon 1
gtgagtaacaaccacatctcgtgagattcttggaagacatggtagaattgggaattcatcgatcatatatgattacccatttcttgatttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGCTGCTCCACAATTTCTGCATATACCACATAAATCCTCAGGGGCACGAGGT
    ||||   |      ||      || ||   |  ||  |   |      |   ||| | | |||| |   | |     | |||  ||| |  ||||||||||||| |||||||||||  | || ||| | || ||||||||  ||||||| ||||| |||||| | |||||||  ||||| ||||||||||||  
----gtaagtgctgtcgatcaaagattttttctgattcactgccaagacttaa---cattgtttatatctcgctgctt-cctattggcttgga--cagACATGTCCTGTTTCCAAGGATTTTTCTTCTGCTCGGAAGTGGCGTCTTTGCTGCTACACAACTTCTGCGTCTACCACACCAATCCCCAGGGGCACGAG--

upper sequence: LOC_Os05g10740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G083635_T01 (Zea mays), 3'ss of exon 1
gtgagtaacaaccacatctcgtgagattcttggaagacatggtagaattgggaatt--catcgatcatatatgattacccatttcttgatttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGCTGCTCCACAATTTCTGCATATACCACATAAATCCTCAGGGGCACGAGGT
    ||||   ||     ||      || ||    ||     |        || ||  ||| | | |||| | | | |     | |||  |||   |||||||||||||| |||||||||||  | || | ||| || ||||||||  ||| ||| || || |||||| | |||||||| ||||| ||||||||||||  
----gtaagtgccgtcgatcaaagtttttttttctgattcactg---ccaagacttaacattgtttatatctcactgctt-cctattggcttg---gcagACATGTCCTGTTTCCAAGGATTTTTCTTCTACCCGGAAGTGGCGTCTTTGCCGCTACAAAACTTCTGCGTCTACCACATCAATCCCCAGGGGCACGAG--

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|29643622|gb|CB648629.1|CB648629
EST:     AGACGAGGACAAGCCGGCGCTCATCACGTACCCGGACATCGCGTTGAACC                         ACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGC
genomic: AGACGAGGACAAGCCGGCGCTCATCACGTACCCGGACATCGCGTTGAACCgtgagtaaca ... ttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaattgggaattcatcgatcatatatgattacccatttcttgatttgcatgcagACATGTCCTGCTTCCAAGGATTGCTGTTTTGCCCCGAGGTGGCGTCGCTGCTGCTCCACAATTTCTGCATATACCACATAAATCCTCAGGGGCACGAGGT
                                      tcttgat  putative branch site (score: 4)
                  atcatatatgatta  TA-rich tract