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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATCCTGTTATTTCACTATGATGGTCGGGTGAGTGAATGGGATGAATTTGAGTGGTCAAAGCGAGCTATACATGTTAGTGTACGGAGGCAAGCGAAATGgtacactctgctcctttgatatcctttataattgtctaaattggaaggtgattctaaagatactgttttgtttaaattgtag

Basic information

species Oryza sativa
transcript LOC_Os01g73970.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA12G29800.1 (Glycine max), 5'ss of exon 7
CTATCCTGTTATTTCACTATGATGGTCGGGTGAGTGAATGGGATGAATTTGAGTGGTCAAAGCGAGCTATACATGTTAGTGTACGGAGGCAAGCGAAATGgtacactctgctcctttgatatcctt---tataattgtctaaattggaaggtgat---tctaaagatactgttttgtttaaattgtag-------------------------------------------------------------------------------------------
| ||  || | ||||| ||||||||||||   |||||||||||| ||||||||||||||| |   || || |||||||||| | |||  ||| | |||||||| | | | ||||  | || |  ||   | ||| |    ||| |   ||||  |     |    |  || |||| |    ||   |                                                                                            
CAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAATGCAATCCATGTTAGTGCAAGGAAACAAACTAAATGgtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctattttttggtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgcttttatgcaatttcctcgtacttaatgttgtgcag

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA13G39990.1 (Glycine max), 5'ss of exon 7
CTATCCTGTTATTTCACTATGATGGTCGGGTGAGTGAATGGGATGAATTTGAGTGGTCAAAGCGAGCTATACATGTTAGTGTACGGAGGCAAGCGAAATGgtacactctgctcctttgatatcctt---tataattgtctaaattggaaggtgat---tctaaagatactgttttgtttaaattgtag--------------------------------------------------------------------------------------------------------
| ||  || | ||||| ||||||||||||   |||||||||||| ||||||||||||||| | | || || ||||| || | | |||  ||| | |||||||| | | | ||||  | || |  ||   | ||| |    ||| |   ||||  |     |    |  || |||| ||   ||   |                                                                                                         
CAATTTTGCTCTTTCATTATGATGGTCGGACTAGTGAATGGGATCAATTTGAGTGGTCAAGGAGTGCAATCCATGTCAGCGCAAGGAAACAAACTAAATGgtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcag

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 5'ss of exon 7
CTATCCTGTTATTTCACTATGATGGTCGGGTGAGTGAATGGGATGAATTTGAGTGGTCAAAGCGAGCTATACATGTTAGTGTACGGAGGCAAGCGAAATGgtac--actctgctc----ctttga---tatcctttataattgtctaaattggaaggtgattctaaagatactgttttgtttaaattgtag----------
  ||  || | |||||||||||||||||    |||||||||||| ||||||||||||||||    || || |||||||||| | | |  ||| | ||||||||   |||||   |     |||||   || |  |   |    | | | |  |||| | |  || |||||  |     | |    || ||           
AAATTTTGCTTTTTCACTATGATGGTCGAACAAGTGAATGGGATCAATTTGAGTGGTCAAAAACTGCAATTCATGTTAGTGCAAGAAAACAAACAAAATGgtaaggactctatacataattttgagcataacactctgacccctttcagtgagaagtttaaacttaagatg-taacaaggtcctcttataagaaggaaaag

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|58694661|gb|CK083348.1|CK083348
EST:     GCTATACATGTTAGTGTACGGAGGCAAGCGAAATG                         GTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTA
genomic: GCTATACATGTTAGTGTACGGAGGCAAGCGAAATGgtacactctg ... taaattgtagGTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTA
EST: gi|29641984|gb|CB646991.1|CB646991
EST:     GAGTGGTCAAAGCGAGCTATACATGTTAGTGTACGGAGGCAAGCGAAATG                         GTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTA
genomic: GAGTGGTCAAAGCGAGCTATACATGTTAGTGTACGGAGGCAAGCGAAATGgtacactctg ... taaattgtagGTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTA
EST: gi|29663566|gb|CB659841.1|CB659841
EST:     ATACATGTTAGTGTACGGAGGCAAGCGAAATG                         GTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTA
genomic: ATACATGTTAGTGTACGGAGGCAAGCGAAATGgtacactctg ... taaattgtagGTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTA

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: 75 (upstream exon), 66 (downstream exon)
Score: 34

CTATCCTGTTATTTCACTATGATGGTCGGGTGAGTGAATGGGATGAATTTGAGTGGTCAAAGCGAGCTATACATGTTAGTGTACGGAGGCAAGCGAAATGgtacactctg ... taaattgtagGTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAG




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