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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTCCTTCCACAACTACCGCATCTGGTCCTTCCTTGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctcgatcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcag

Basic information

species Oryza sativa
transcript LOC_Os05g37470.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G067022_T02 (Zea mays), 5'ss of exon 4
CCCCTCCTTCCACAACTACCGCATCTGGTCCTTCCTTGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctcgatcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcag
|||||| | ||||||||||||| ||||||||||||| |||||||||||||||||||||||||||||||||||| |||||||||| |||||||||||||||||||| || |      || || ||||||        || |||      | ||   || |   || ||    ||  |   |    |  | |  ||   |   |                                                                                   
CCCCTCGTACCACAACTACCGCGTCTGGTCCTTCCTCGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCACCATCGCCGCGGCCGTCCACGGCCAGgtgagccccc-----ccggcccccgtcgctcatt-caattcatggcggcgtc--tcgaccagtg-ttactgactgtccctccgcgtgtcggcgcgccggacag----------------------------------------------------------------------------------

upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G01240.2 (Arabidopsis thaliana), 5'ss of exon 3
CCCCTCCTTCCACAACTACCGCATCTGGTCCTTCCTTGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctcg--atcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcag
 || || |||||||| ||||| || ||||| ||||| ||||| |||||||||||||||||||| ||||||||| |||||||| |     |||| || |||||  ||||||   |  |||    |   |    |   | ||| ||||    | | | ||||    |   | ||      |||| ||                                                                                                      
ACCATCTTTCCACAATTACCGTATTTGGTCTTTCCTCGGCCTTGGCATGACCACCTACACCGCTTGGTACCTCACCATCGCCTCTTTTCTCCATGGTCAGgtatgtcctcatcaaaatcaaatgatttaaatgaagaaaaaacaatgtgacttaaaccggt-tgtaacttactg----gtttgtag-----------------------------------------------------------------------------------------------------

upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ21839 (Selaginella moellendorffii), 5'ss of exon 4
CCCCTCCTTCCACAACTACCGCATCTGGTCCTTCCTTGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctcgatcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcag
||| || || |||||||| ||  | ||||||||||| ||| | || |||||||| ||||| ||||||||| |  ||||||| ||   |||||||||||||||         |  |   |         ||   |  ||||    |  |  ||    | |     ||    | | || ||  |   |    ||      |  |                                                                                   
CCCGTCTTTTCACAACTATCGAGTGTGGTCCTTCCTCGGCTTGGGGATGACCACTTACACGGCCTGGTACATGACCATCGCTGCGATCGTCCACGGCCAGgtagag----aagaagaacaaagaaaaatc--tcccaaattcccactttgtc--ttgtcttcctctctctcgcgctattcgttctctcctttctccccacaacacgga-----------------------------------------------------------------------------

upper sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ34222 (Selaginella moellendorffii), 5'ss of exon 4
CCCCTCCTTCCACAACTACCGCATCTGGTCCTTCCTTGGCCTCGGCATGACCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctcgatcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcag
||| || || |||||||| ||  | ||||||||||| ||| | || |||||||| ||||| ||||||||| |  ||||||| ||   |||||||||||||||         |  |   |         ||   |  ||||    |  |  ||        |   ||    | | || ||  |   |    ||      |  |                                                                                   
CCCGTCTTTTCACAACTATCGAGTGTGGTCCTTCCTCGGCTTGGGGATGACCACTTACACGGCCTGGTACATGACCATCGCTGCGATCGTCCACGGCCAGgtagag----aagaagaacaaagaaaaatc--tcccaaattcccactttgtcttgtcttcctctctctctcgcgctattcgttctctcctttctccccacaacacg-------------------------------------------------------------------------------

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|29638464|gb|CB643473.1|CB643473
EST:     CCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAG                         GTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACT
genomic: CCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctc ... gatgtcgcagGTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACT
EST: gi|86891273|gb|CI307993.1|CI307993
EST:     CCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAG                         GTCAACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACT
genomic: CCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctc ... gatgtcgcagGTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACT