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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattgactgcccgtttttcagagtgtgcctgtctttattcctcattatatcatggcactatagatttgactgaactgctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g40140.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G124557_T02 (Zea mays), 3'ss of exon 7
gtgagattgact-----gcccgtttttcagagtgtgcctgtctttattcctcattatatcatggcactatagatttgactgaac--tgcta---cctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG
||||| || |||      |  ||  | |   || ||| |   |   | | |  ||  |  |   | |||| ||||| | |||||  | | |    ||| |||| |||||||| ||||||||||| || ||| |  | |||||||| |||||||| |||||||||||||| || ||  | ||||||||||| || || |||
gtgaggtttactctgtcacaagtcatgcgtggtctgcattcttcagtacatgtttccacgagcccgctatggatttaattgaaccctaccaaattctcaagGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAG

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 7
gtgagattgact-gcccgtttttcagagtgtgcctgtct-----ttattcctcattatatcatggcactatagatttg-actgaactgcta--------cctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG
||   ||    | |||  | ||||    | |  || ||        || | |    ||   ||||  ||     ||   |||||| |   |         ||  |||| || ||||| ||||||||||| ||||||||||| |||||||| ||||  || |||||||||||||| || ||    ||||| ||| || | || |||
gtacaatccctttgcctttctttccttttttctctttcaagggaccatactttcccatgcaatggttcttggtcttcacactgaagtttcaattgtatctcttcagGTCTGTTACTCATGGTGGGTGCTTTCAAGCTTGATCATGATTGACAGAGCTCATTGGATTGACAAGGATAAGCTCATTAAATTTATAATAGACTGTCAG

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv15s0024g00080.t01 (Vitis vinifera), 3'ss of exon 7
---------------------gtgagattgactgcccgtttttcagagtgtgcctgtctttattcctcattata-tcatggcactatagatttgactg--aactgctac-------ctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG
                      |    ||   |    ||| || |   |      | | | ||| |  || | | ||||     ||    | | |||   |  | |||        ||  |||| || ||||| ||||||||||| |||||| |||| |||||||| ||||  || |||||||||||||| || ||    ||||||||  || |||| |||
gtatgattctttttttcttccatatatttatttatttgttatttattttagagaagccataatttcctataaaaatcatttttatagttttcttactataagttcctattgtatcacttcagGTCTGTTACTCATGGTGGGTGCTATCAAGCCTGATCATGATTGACAGAGCTCATTGGATTGACAAGGAAAAGCTCATTAAATTCATCTTAGATTGTCAG

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|58681560|gb|CK070247.1|CK070247
EST:     GTCAGTGCAAAGAGGGAGGGCTCAATGGACGGCCTGAGAAACTTGCTGAT                         GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTG
genomic: GTCAGTGCAAAGAGGGAGGGCTCAATGGACGGCCTGAGAAACTTGCTGATgtgagattga ... ctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTG
EST: gi|33381466|gb|CF196809.1|CF196809
EST:     GTCAGTGCAAAGAGGGAGGGCTCAATGGACGGCCTGAGAAACTTGCTGAT                         GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTG
genomic: GTCAGTGCAAAGAGGGAGGGCTCAATGGACGGCCTGAGAAACTTGCTGATgtgagattga ... ctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttattcctcattatatcatggcactatagatttgactgaactgctacctctagGTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG
                               atttgac  putative branch site (score: 4)
                                             ctacctct  putative PPT
           attatatcat  TA-rich tract