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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtagatgcaatccatttcattccatatgtctacccagttgatatacttgggtgtgcaaaaacaacattaggcgcgttatacaatttctataattggattgttttttaagcttttgagctttgactaaactactcctatttttatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG

Basic information

species Oryza sativa
transcript LOC_Os08g23810.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 6
gtgtgtagatgcaatccatttcattccatatgtctacccagttgatatacttgggtgtgcaaaaacaacattaggcgcgtta-tacaatttctataattggattgttttttaagcttttgagctttgactaaactactcctatttttatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG
|| || ||  || |  |||||  |||||||||| || |    |    |   ||  ||    || | ||   |         | | || |   | | |   | || |  |  ||||||| |||||   | |||  |    || | || |||| | ||||||||| ||| ||||| | |||||| |||||||||||||||||  | ||||||||||| |||||||| ||||||
gtatgcagtcgccaatcattt--ttccatatgtatagctgcctaggttctatgcttgctagaagaaaatgctgaagatacaactgcagtg--tgttacctgtttctcataaaagctttagagctgacaataacattgagctttcttaatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 4
gtgtgtagatgcaatccatttcattccatatgt--ctacccagttgatatacttgggtgtgcaaaaacaacattaggcgcgttatacaatttctataattggattgttttttaagcttttgagcttt----gactaaactactcctattttt-atttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG
||||||   ||| |  |||||   |  || |||  || || || |  ||||||      ||| | || || ||   || |   |||||    ||  |    | || |  |  ||||||| ||||       ||| | |  | |  | |  || |||| | ||||||||| ||| ||||| |||||||| |||||||||||||||||  | ||||| ||||| |||||||| ||||||
gtgtgtgattgccaatcatttttctatatctgtagctgcctaggttttatact------tgctagaagaaaat---gctcaaaatacag---ctgcagagtgtttctcctgaaagctttagagcggacaaggacaataacattggtctccttgatttaacagGAAGTTGTTGAATCAGTGAAGAATGATTTTGGCAGCATTGACATACTAGTGCACTCTCTTGCTAATGGCCCAGAG

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ25882 (Selaginella moellendorffii), 3'ss of exon 5
gtgtgtagatgcaatccatttcattccatatgtctacccagttgatatacttgggtgtgcaaaaacaacattaggcgcgttatacaatttctataattggattgttttttaagcttttgagctttgactaaactactcctatttttatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG
                                                                                         |    ||  |  || ||  || |      | | |||   |   ||     | ||      ||  ||||||| |  ||    || || || ||||||||||||||||| ||| | || |||||||| || ||||||||||| 
----------------------------------------------------------------------------------------gtacgaaaaagctttattgcttgaatcgaagcgattttgtt---ctcgcattgttgcggcctg-cagGAAGTGGTGGACAGCGTGAAAAAAGACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAA

upper sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ10940 (Selaginella moellendorffii), 3'ss of exon 5
gtgtgtagatgcaatccatttcattccatatgtctacccagttgatatacttgggtgtgcaaaaacaacattaggcgcgttatacaatttctataattggattgttttttaagcttttgagctttgactaaactactcctatttttatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG
                                                                                         |    ||  |  || ||  || |      | | |||   |   ||     | ||      ||  ||||||| |  ||    || || || ||||||||||||||||| ||| | || |||||||| || ||||||||||| 
----------------------------------------------------------------------------------------gtacgaaaaagctttattgcttgaatcgaagcgattttgtt---ctcgcaatgttgccgcctg-cagGAAGTGGTGGACAGCGTGAAAAAAGACTTTGGCAGCATTGATATTCTCGTTCATTCTCTTGCGAATGGTCCAGAA

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|58686263|gb|CK074950.1|CK074950
EST:     GTCAAAGGAAACAAAAGGTATGCTGGGTCATCAAATTGGACTGTTAAG                         GAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTG
genomic: GTCAAAGGAAACAAAAGGTATGCTGGGTCATCAAATTGGACTGTTAAGgtgtgtagat ... tatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTG
EST: gi|38479842|gb|CF963931.1|CF963931
EST:     GTCAAAGGAAACAAAAGGTATGCTGGGTCATCAAATTGGACTGTTAAG                         GAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTG
genomic: GTCAAAGGAAACAAAAGGTATGCTGGGTCATCAAATTGGACTGTTAAGgtgtgtagat ... tatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTG
EST: gi|29613728|gb|CB618741.1|CB618741
EST:     GTCAAAGGAAACAAAAGGTATGCTGGGTCATCAAATTGGACTGTTAAG                         GAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTG
genomic: GTCAAAGGAAACAAAAGGTATGCTGGGTCATCAAATTGGACTGTTAAGgtgtgtagat ... tatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTG
EST: gi|29613729|gb|CB618742.1|CB618742
EST:     TCATCAAATTGGACTGTTAGG                         GAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTG
genomic: TCATCAAATTGGACTGTTAAGgtgtgtagat ... tatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttttttaagcttttgagctttgactaaactactcctatttttatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG
                         gactaaa  putative branch site (score: 2)
                                   ctcctatttttattt  putative PPT
                                       tatttttatttgata  TA-rich tract