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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_Os08g40140.1
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|86255970|gb|CI068419.1|CI068419
EST:     AATTCATACTAAATTGCCAG                         GACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
genomic: AATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
EST: gi|58594582|gb|CF992890.1|CF992890
EST:     TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG                         GACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
genomic: TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
EST: gi|88220590|gb|CI220150.1|CI220150
EST:     TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG                         GACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
genomic: TGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
EST: gi|88227738|gb|CI227218.1|CI227218
EST:     CTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAG                         GACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC
genomic: CTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATC

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: 59 (upstream exon), 75 (downstream exon)
Score: 23

GTGTGCTACTCCTGGTGGGTGCTCTCAAGCTTGATAATGATTGATAGAGTGCACTGGATTGACAAGGACAAACTTGCAAAATTCATACTAAATTGCCAGgtaaatgctt ... tcattggtagGACAAGGAAAATGGTGGAATTTCAGATAGACCAGATAATGCGGTAGATATCTACCACACATACTTTGGAGTTGCAG




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