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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGAGTCTCCGTCAAATCCAGGAGCTGGTGACATCCTCATGGGATTTCTTGGGTCTGTCATCATATCGTTTGCATTTTCAATGTTCAATCAGAGAAAGgtaggtacccttctctcagttagtagtattactagtagttagcatatggttatatatgttgtgacatgatcatattcgaagctctctgtttaatttgttgcgagacgagtgtgcctagctgttggctagctaattaaccatgcatccaaccaaggagtaattaattaatgtttttgtgttggataatataatatttcag

Basic information

species Oryza sativa
transcript LOC_Os10g42780.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G873519_T01 (Zea mays), 5'ss of exon 4
CACAGAGTCTCCGTCAAATCCAGGAGCTGGTGACATCCTCATGGGATTTCTTGGGTCTGTCATCATATCGTTTGCATTTTCAATGTTCAATCAGAGAAAGgtaggtacccttctctcagttagtagtattactagtagttagcatatggttatatatgttgtgac-atgatcatattcgaagctctctgtttaatttgttgcgagacgagtgtgcctagctgttggctagctaattaaccatgcatccaaccaaggagtaattaattaatgtttttgtgttggataatataatatttcag
|||| ||   || || ||||| ||||| |||||| | || |||   || ||||||||||| |||||||| |||||||| || || ||||| ||||||||||||  |||    |    | |  ||     | ||  |    ||||  || || | | |  | ||||  | | | | | |   || ||   || |                                                                                                           
CACAAAGGTGCCCTCTAATCCTGGAGCCGGTGACGTACTAATGACTTTCCTTGGGTCTGTGATCATATCATTTGCATTCTCGATCTTCAAGCAGAGAAAGgtac-tactgcgcatcaattcggttaagct-ctgttccgcagcaagtgctttttttttatctgaccgtcaacttgtccatggccctgatttcag----------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os10g42780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G478212_T01 (Zea mays), 5'ss of exon 5
CACAGAGTCTCCGTCAAATCCAGGAGCTGGTGACATCCTCATGGGATTTCTTGGGTCTGTCATCATATCGTTTGCATTTTCAATGTTCAATCAGAGAAAGgtaggtacccttctctcagttagtagtattactagtagttagcatatggttatatatgttgtgacatgatcatattcgaagctctctgtttaatttgttgcgagacgagtgtgcctagctgttggctagctaattaaccatgcatccaaccaaggagtaattaattaatgtttttgtgttggataatataatatttcag
|||| || | || || ||||| |||||||||||| | || ||||| || ||||||||||| |||||||| |||||||| ||||||||||| ||||||||||||      || | |   |||| |  | | || |  | || |  || | |      || |  |     |     ||  | |   |||||  || ||||       |  |    |||   |   |                                                                           
CACAAAGGCGCCCTCTAATCCTGGAGCTGGTGACGTACTAATGGGTTTCCTTGGGTCTGTGATCATATCATTTGCATTCTCAATGTTCAAACAGAGAAAGgta---ctactgcacatggtta-tcttgtgac-atcatttcggttaagctc-----tgctccgctgcaagtgccttttatgtgatctgtc-aacttgtccatgctcttgaacccctgatttcag---------------------------------------------------------------------------

upper sequence: LOC_Os10g42780.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0056g01690.t01 (Vitis vinifera), 5'ss of exon 5
CACAGAGTCTCCGTCAAATCCAGGAGCTGGTGACATCCTCATGGGATTTCTTGGGTCTGTCATCATATCGTTTGCATTTTCAATGTTCAATCAGAGAAAGgtaggt-acccttctctcagttagtagtattactagtagttagcatatggttatatatgttgtgacatgatcatattcgaagctctctgtttaatttgttgcgagacgagtgtgcctagctgttggctagctaattaaccatgcatccaaccaaggagtaattaattaatgtttttgtgttggataatataatatttcag
 ||  || |  | || ||||| |||||||||||||| || ||||||||| | || ||||| ||  | || ||||| || || |||||||| |||||||||||| || |||  | | |||     |   || |  | |    |   |||||||    |  || |    | ||  |   | | | |    ||  |||||  | |                                                                                                  
TACGAAGGCATCTTCTAATCCTGGAGCTGGTGACATTCTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTGCTTTCTCCATGTTCAAACAGAGAAAGgtaagtgaccactttttcaaactctgacatgaa-attgaccattttatggttgctaaaattatttactaattctcagc-aggtttaaagtagaatttagtcc--------------------------------------------------------------------------------------------------

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|8858775|gb|AU096093.1|AU096093
EST:     TTGGGTCTGTCATCATATCGTTTGCATTTTCAATGTTCAATCAGAGAAAG                         CTTGTAAGGAGGCATGCAGCGGAAATTTTCACATCAATCGCTGTGGCATCA
genomic: TTGGGTCTGTCATCATATCGTTTGCATTTTCAATGTTCAATCAGAGAAAGgtaggtaccc ... aatatttcagCTTGTAAGGAGGCATGCAGCGGAAATTTTCACATCAATCGCTGTGGCATCA
EST: gi|29676079|gb|CB672354.1|CB672354
EST:     TTGGGTCTGTCATCATATCGTTTGCATTTTCAATGTTCAATCAGAGAAAG                         CTTGTAAGGAGGCATGCAGCGGAAATTTTCACATCAATCGCTGTGGCATCA
genomic: TTGGGTCTGTCATCATATCGTTTGCATTTTCAATGTTCAATCAGAGAAAGgtaggtaccc ... aatatttcagCTTGTAAGGAGGCATGCAGCGGAAATTTTCACATCAATCGCTGTGGCATCA