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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtcttagcaatttcagttcttgctctcagtctctctaagtttgtggatttttttccattgctcattgtaattgcag

Basic information

species Oryza sativa
transcript LOC_Os02g58590.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58590.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G426275_T01 (Zea mays), 5'ss of exon 7
GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtcttagcaatttcagttcttgctctcagtctctctaagtttgtggatttttttccattgctcattgtaattgcag
||||||||||||||| ||||| |||||||| || |||||||||||||||||||   || |||||||  ||||||  | ||     | |  |   |  |   ||||| ||||| |  |||| |  |   
GTATCAGACATCAGTTGCTTCGAAGTTTCCGCTTTTTATATCTCAGgtactggcaataccaatttcttttcttgggcccatgaagtgtgtggg-gaagtccttttttcattggttcttgtcacag---
















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|58586999|gb|CF985307.1|CF985307
EST:     GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAG                         GATGGAATAAATGGA
genomic: GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtct ... gtaattgcagGATGGAATAAATGGA
EST: gi|33795166|gb|CF323456.1|CF323456
EST:     GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAG                         GATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA
genomic: GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtct ... gtaattgcagGATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA
EST: gi|29626072|gb|CB631083.1|CB631083
EST:     GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAG                         GATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA
genomic: GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtct ... gtaattgcagGATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA
EST: gi|29628398|gb|CB633409.1|CB633409
EST:     GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAG                         GATGGAATACATGGAGAAGTGAAGAAAAA-GCTTTGAGTTATAATGAAATA
genomic: GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtct ... gtaattgcagGATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA
EST: gi|29666803|gb|CB663078.1|CB663078
EST:     GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAG                         GATGGAATANATGGAGAAGTGA
genomic: GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtct ... gtaattgcagGATGGAATAAATGGAGAAGTGA
EST: gi|33797216|gb|CF324472.1|CF324472
EST:     GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAG                         GATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA
genomic: GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtct ... gtaattgcagGATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA
EST: gi|29681006|gb|CB677281.1|CB677281
EST:     GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAG                         GATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA
genomic: GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtct ... gtaattgcagGATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATA

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: 62 (upstream exon), 75 (downstream exon)
Score: 24

GTATCAGACATCAGTGGCTTCAAAGTTTCCACTATTTATATCTCAGgtactggtct ... gtaattgcagGATGGAATAAATGGAGAAGTGAAGAAAAAAGCTTTGAGTTATAATGAAATAACATATATGCAG




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