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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgcttgaaatcttgcatctgatttttgtgtaaccatgtgtccattaatcaaataaaaatatctgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattggtag

Basic information

species Oryza sativa
transcript LOC_Os08g40140.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G124557_T02 (Zea mays), 5'ss of exon 8
GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgcttga--aatcttgcatctgatttttgtgtaacc-atgtgtccattaatcaaataaaaatatctgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattggtag
|| |||||||| ||||||||||| || ||| |  | |||||||| |||||||| |||||||||||||| || ||  | ||||||||||| || || ||||||| || |  |  | ||   |  |||   |||| ||||||  | ||||| || |   |  | || ||       |  ||||| | ||||  |||| |  ||  |                           
GTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttctattattcccaccactgccatttgcgtaacccgtatgtcccttgacttataacaagta-------ctggttccaactcttctcattcatgttgatcggcag---------------------

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G124557_T04 (Zea mays), 5'ss of exon 5
-GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgcttga--aatcttgcatctgatttttgtgtaacc-atgtgtccattaatcaaataaaaatatctgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattggtag
 || |||||||| ||||||||||| || ||| |  | |||||||| |||||||| |||||||||||||| || ||  | ||||||||||| || || ||||||| || |  |  | ||   |  |||   |||| ||||||  | ||||| || |   |  | || ||       |  ||||| | ||||  |||| |  ||  |                           
GGTTTGCTACTCGTGGTGGGTGCTATCGAGCCTAGTCATGATTGACAGAGTGCATTGGATTGACAAGGAAAAGCTAACGAAATTCATACTGAACTGTCAGgtaactgttctattattcccaccactgccatttgcgtaacccgtatgtcccttgacttataacaagta-------ctggttccaactcttctcattcatgttgatcggcag---------------------

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv12s0134g00150.t01 (Vitis vinifera), 5'ss of exon 8
GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgcttgaaatcttgcatctgatttttgtgtaaccatgtgtccattaatcaaataaaaatatc---tgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattggtag-----------
|| || ||||| ||||||||||| ||||||||||| |||||||| ||||  || |||||||||||||| || ||    ||||| ||| || | || ||||| | | ||  |     || |       || || | |   |   | |||  |  ||   | ||| |      |  ||| |   | |  ||| ||||||||   |  ||||||  |  ||   | |||||  |           
GTCTGTTACTCATGGTGGGTGCTTTCAAGCTTGATCATGATTGACAGAGCTCATTGGATTGACAAGGATAAGCTCATTAAATTTATAATAGACTGTCAGgtcagttctaaactaaatgaactgttacttagtttcagtttaatttcatagaaaaacctagaattttgcaccttacctctctgctgctttttcatttacaaggt--aaatatg-atcctcagttattggctgaaaaattgcag

upper sequence: LOC_Os08g40140.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv15s0024g00080.t01 (Vitis vinifera), 5'ss of exon 8
GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgcttgaaatcttgcatctgatttttgtgtaaccatgtgtccattaatcaaataaaaatatctgtctcctgttcccagtctttccatttacattttttaaatatataatcttgttcattg-gtag
|| || ||||| ||||||||||| |||||| |||| |||||||| ||||  || |||||||||||||| || ||    ||||||||  || |||| ||||| | | ||  |||    |        | || | ||        |   |||  || | ||   || |  |    |      ||| |  |     |   |  |||||  | | |  ||||  |    | ||
GTCTGTTACTCATGGTGGGTGCTATCAAGCCTGATCATGATTGACAGAGCTCATTGGATTGACAAGGAAAAGCTCATTAAATTCATCTTAGATTGTCAGgtcagttct--aaactaagtg---agctgttatttagattcagataacttacacaga-aatcctagcccttatttagatttagtttaacttaaaaaggtggttaaaattctcagtttgtggaaaatgcag

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|58681560|gb|CK070247.1|CK070247
EST:     TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG                         GACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
genomic: TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
EST: gi|33381466|gb|CF196809.1|CF196809
EST:     TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG                         GACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
genomic: TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC