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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaaaaacatgaatttgtttcatctctttctggcctatgctaacaagatattattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 6
gtaagtttaaaaacatgaatt-tgtttcatctctttctggcctatgctaacaagatattattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
|||||||  |||    |  || | |||| || ||| || ||  |||||||     ||| | ||| ||||| ||||||||||| ||||||||||||||| ||||||| ||||||||||| ||||||||||||||||||||||||||||| || ||||||||| | ||||
gtaagttggaaatgtggggttatttttcttcacttgcttgcacatgctaaagctgtatcactttccagAACCATCTTGATCTTCATGCTGTGTTATGGCTAGAAACTTATCTCCTGAAGTGGCCAAAGACATTCATTGTTGTATCACACGCAAGGGAGTTTTTGAATA

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 5
gtaagtttaaaaacatgaatttgtttcatctctttctg--gcctatgctaacaagat-----------attattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
|| |  | |  |     | | | |||| |   |    |  ||||  | | | |  ||           ||| | |||||||||||||||||||| |||||||| |||||| | ||| | ||  |  | ||||||||||| ||||| || ||||| || |||||||| || ||| | || |
gtta-ctcatcattcccagtctctttcgtgattcatggatgccttggtttatagaatttatgaattttattttattgcagAATCATCTTGATCTTCATGCTGTCTTATGGCTTGAATCGTACTTGGTTAAATGGCCAAAAACATTTATCGTTGTTTCTCATGCTAGAGAATTTTTAAACA

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 5
gtaagtttaaaaacatgaatttgtttcatctctttctg--gcctatgctaacaagat-----------attattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
|| |  | |  |     | ||| ||||||   |    |  ||||  | | | |  ||            || | |||||||||||||||||||| |||||||| |||||| | ||| | ||  |  | ||||||||||| ||||| |||||||| || |||||||| || ||| | || |
gtta-ctcatcattccaagtttctttcatgattcatggatgccttggtttatagaatttatgaattttgttttattgcagAATCATCTTGATCTTCATGCTGTCTTATGGCTTGAATCTTACTTGGTTAAATGGCCAAAAACATTTATTGTTGTTTCTCATGCTAGAGAATTTTTAAACA

upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G64550.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------gtaagtttaaaaacatgaatttgtttcatctctttctggcctatgctaacaagatattattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
             ||||| ||      || |  |   |  || |     |  |  |   |       | |  ||| | |||| |||||||||||||||||||| ||||||||||||||||||||   ||| |||||||| ||||| || || || || ||||||||||| ||  | || |
gtgtgttttctttgtaaggtttcccttattagatcaatatattttcaggtttctgacattcttttcctctcttttggtagAACCATCTTGATCTCCATGCTGTCTTATGGTTAGAAACATATCTAACGAAGTGGCCAAAAACATTTATAGTCGTTTCCCATGCTAGGGAATTCTTGAACA

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|218482666|gb|FG970229.1|FG970229
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|29662747|gb|CB659022.1|CB659022
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|29644366|gb|CB649373.1|CB649373
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|24468674|gb|CA305623.1|CA305623
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|88311922|gb|CI577528.1|CI577528
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
EST: gi|58602069|gb|CK012597.1|CK012597
EST:     CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACA                         AATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA
genomic: CACGTGCTCTCTTCATTGAGCCTGATTTGTTGCTACTTGATGAGCCAACAgtaagtttaa ... tattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgaatttgtttcatctctttctggcctatgctaacaagatattattttgcagAATCATCTTGATCTCCATGCTGTGTTATGGTTAGAAACATATCTCCTGAAATGGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATA
                               tgctaac  putative branch site (score: 1)
                                            ttatttt  putative PPT
                                  taacaagatattattt  TA-rich tract