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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGATAATAGAGACTGGTAATCCAGATGCATTCAAGCAGTACCTGCAAGAGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttgtgacgatctaactagtgttctctcttcatttctacttctataacttcatcatctttatgtaatataatgttccag

Basic information

species Oryza sativa
transcript LOC_Os08g20270.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g20270.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G016827_T03 (Zea mays), 5'ss of exon 7
GGAGATAATAGAGACTGGTAATCCAGATGCATTCAAGCAGTACCTGCAAGAGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcg-------ttgtgacgatctaactagtgttctctcttcatttctacttctataacttcatcatctttatgtaatataat-gttccag
|||||| |||||||||||  |||| |  || |||||  | |||||||| ||||| ||||| |||||||| |||||||||||||||||||| |||||   ||||||         || ||    || ||    |  ||||  |  ||  || |   | || ||||| |  ||  || |  | |  | | | |||
GGAGATCATAGAGACTGGCGATCCCGTAGCGTTCAAAGAATACCTGCAGGAGTACGAGAACACCATATGCGGACGCCACCCCATCAGCGTCTTCCTTCACgtaagtaaatgactttctgcttgtcaaaaacctactctcgatgaatgccttccgtttta-cttcagccactgcattttttttgtttgcttcag
















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|88980011|gb|CI026301.1|CI026301
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88258046|gb|CI360632.1|CI360632
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88849155|gb|CI087677.1|CI087677
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88482578|gb|CI419849.1|CI419849
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88967223|gb|CI392178.1|CI392178
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|86254986|gb|CI017106.1|CI017106
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|55408283|gb|CV720659.1|CV720659
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88385073|gb|CI561729.1|CI561729
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88846859|gb|CI005838.1|CI005838
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|12404774|gb|AU166375.1|AU166375
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88380314|gb|CI518684.1|CI518684
EST:     ATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTTTTCGGTATGA
genomic: ATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagAT-GCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGA
EST: gi|86872979|gb|CI326976.1|CI326976
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|89179701|gb|CI043980.1|CI043980
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|218488302|gb|FG946415.1|FG946415
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTCGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|55411914|gb|CV724290.1|CV724290
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88438074|gb|CI536233.1|CI536233
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|55409410|gb|CV721786.1|CV721786
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|86251794|gb|CI018986.1|CI018986
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|33810212|gb|CF330997.1|CF330997
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|38476889|gb|CF961022.1|CF961022
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTCGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|89184631|gb|CI007056.1|CI007056
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTTCGGTATGA
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTG-TTCGGTATGA
EST: gi|86600974|gb|CI356731.1|CI356731
EST:     AGTATGAGAATACCATATGTGGACCCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|86835196|gb|CI346671.1|CI346671
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|86886372|gb|CI336075.1|CI336075
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88509956|gb|CI437462.1|CI437462
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|87029686|gb|CI257481.1|CI257481
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88491183|gb|CI428455.1|CI428455
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
EST: gi|88470881|gb|CI408152.1|CI408152
EST:     AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGC                         ATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG
genomic: AGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 64 (downstream exon)
Score: 33

GGAGATAATAGAGACTGGTAATCCAGATGCATTCAAGCAGTACCTGCAAGAGTATGAGAATACCATATGTGGACGCCACCCCATCAGCGTTTTCCTCAGCgtaagcgttg ... aatgttccagATGCTGAAACATTGTTTGACAAAGATCAAGATCGGATTTGTTCGGTATGAGCAGTCAAGCCAGTGCAAGAGCATGAGGGACAGCAGCGTGAGCTACGCTT




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