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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGGTGGTCGGCGGCATCACGCCGACGCCGCTCGGGGAGGGCAAGTCGACCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgagaggctttccatgccactttcgcttgttctataatcgacagggtatcttggttacttattggttatagataaagtttgtgattggtgttgaggtaa...

Basic information

species Oryza sativa
transcript LOC_Os09g27420.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g27420.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G824944_T01 (Zea mays), 5'ss of exon 2
CGTGGTGGTCGGCGGCATCACGCCGACGCCGCTCGGGGAGGGCAAGTCGACCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgagaggctttccatgccactttcgcttgttctataatcgacag---ggtatcttggttacttattggttat-agataaagtttgtgattggtgttgaggtaa
||| ||||| |||||||||||||| ||||| ||||||||||| ||||| ||||||||||| |||||||| ||||| || || || || |||||||||||||||||| ||||   |||| | ||| |||||    | | ||        | |     | |||    ||  ||||  ||  ||  |||| | | || ||||  |  
CGTCGTGGTGGGCGGCATCACGCCAACGCCCCTCGGGGAGGGGAAGTCAACCACCACCGTCGGGCTGTGTCAGGCTCTCGGCGCTTTCCTTGATAAAAAGgtgagatgctta--atgctaattttgcttgacacagagtccgttcaccgatgagaagattaacattttattatcggagcaaacttgttactagtattgaatt--

upper sequence: LOC_Os09g27420.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP08942 (Chlamydomonas reinhardtii), 5'ss of exon 3
CGTGGTGGTCGGCGGCATCACGCCGACGCCGCTCGGGGAGGGCAAGTCGACCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgag-----aggctt-----tccatgccactttcgcttgttctataatcgacagggtatcttggttacttattggttatagataaagtttgtgattggtgttgaggtaa
  |||| || | |||||||||||| ||||| || || ||||||||||| ||||||||| |||| ||||||||||||||||| || |  ||  | || |||||| |      ||| |     |   || ||| || || || |   |  |||   ||    | | || || | || ||  |   |   |   | ||   ||||        
--TGGTTGTTGCCGGCATCACGCCCACGCCCCTGGGTGAGGGCAAGTCCACCACCACCATTGGCCTGTGCCAGGCGCTGGGGGCCTACCTCAAGAAGAAGgtgggtgtgggggcgtgtgtgtgtttgacacgtttgcatgcttggt--tcgtgtggaggacatagtgacatgtttgtagtg--tcgggcgggagacgtgtgtac------

upper sequence: LOC_Os09g27420.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ27738 (Selaginella moellendorffii), 5'ss of exon 2
CGTGGTGGTCGGCGGCATCACGCCGACGCCGCTCGGGGAGGGCAAGTCGACCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgagaggctttccatgccactttcgcttgttctataatcgacagggtatcttggtt--acttattggttatagataaagtttgtgattggtgttgaggtaa
||| ||||| | ||| || |||||||||||||| || |||||||| ||||||||||| ||||||||  | || ||  |||| ||   ||| |  || ||||||||    || |    | ||| | |  | |    | |  ||    |  || |  ||   |||  |   ||| |  |||   |||    | | ||  |    
CGTCGTGGTGGCCGGGATTACGCCGACGCCGCTGGGAGAGGGCAAATCGACCACCACTGTTGGGCTCGGGCAAGCCATGGGGGCTCATCTCGGAAAGAAGgtgagctctttcctcctctactgtaggatctagagtgagtgatctagagtcctcctttggcttgctttctatcg-caaacactgtttgcgatatttcgtcg-

upper sequence: LOC_Os09g27420.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ37206 (Selaginella moellendorffii), 5'ss of exon 2
CGTGGTGGTCGGCGGCATCACGCCGACGCCGCTCGGGGAGGGCAAGTCGACCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgagaggctttccatgccactttcgcttgttctataatcgacagggtatcttggttacttattggttatagataaagtttgtgattggtgtt-gaggtaa
||| ||||| | ||| || |||||||||||||| || |||||||| ||||||||||| ||||||||  | || ||  |||| ||   ||| |  || ||||||||    || |      ||| | |  | |    |  |   |   |  ||| |  | ||  || |   ||  |    |  |  |    |||| | | || 
CGTCGTGGTGGCCGGGATTACGCCGACGCCGCTGGGAGAGGGCAAATCGACCACCACTGTTGGGCTCGGGCAAGCCATGGGGGCTCATCTCGGAAAGAAGgtgagctcgttcctcctttactgtaggatctagagtggtgatcttcgcgtctagagtcctcctttggcttactttctatc-gcaaacactgtttgcgatat

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|1631916|gb|C19645.1|C19645
EST:     GCCAGGCGCTGGGTGCGTTTCTTGATAAAAAG                         GTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAG
genomic: GCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgagaggct ... gctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAG
EST: gi|29657308|gb|CB653583.1|CB653583
EST:     CCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAG                         GTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAG
genomic: CCACCACCGTTGGGCTGTGCCAGGCGCTGGGTGCGTTTCTTGATAAAAAGgtgagaggct ... gctattatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAG