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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACACTTTCCGTGGTAGAGTGTGTGAATGCCCTACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttctttctgtatccatgctcgtatccttccatagtctcagaaatattactcctgtatcagctatgtctacaaattacaacatgcataaacaag...

Basic information

species Oryza sativa
transcript LOC_Os10g20630.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g20630.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 7
GACACTTTCCGTGGTAGAGTGTGTGAATGCCCTACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttctttctgtatccatgctcgtatc--cttccatagtctcagaaatattactcctgtatcagctatgtctacaaattacaacatgcataaacaag
||||| |||||||||||||||||||||||||| || |||||||| || || |||||||||||||||||||||||||||||||||||| | | ||  | |||     | | |     ||   | |   | | |||||| ||    || |||||||| |  |||| || ||   || |   | |  
GACACCTTCCGTGGTAGAGTGTGTGAATGCCCCACTTTCAATGGCGTACAATTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatgtcttttgttctattttcccacattctaactctgaaatatttaaaaatataaccttagtgtcagctatattaacaagttgcattttggaatgaaa--
















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|218783354|gb|GE329406.1|GE329406
EST:     TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAAC                         CTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA
genomic: TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttc ... ttatttgcagCTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA
EST: gi|58594426|gb|CF992734.1|CF992734
EST:     TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAAC                         CTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTCGGCATGAGA
genomic: TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttc ... ttatttgcagCTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA
EST: gi|33692858|gb|CF321097.1|CF321097
EST:     TACATTCAATGGTGTGCAGTTTAAAGGCGACGGCTACAGCAATTGTGAAC                         CTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA
genomic: TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttc ... ttatttgcagCTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA
EST: gi|33796525|gb|CF324129.1|CF324129
EST:     TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAAC                         CTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA
genomic: TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttc ... ttatttgcagCTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA
EST: gi|300215523|gb|HO088149.1|HO088149
EST:     TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAAC                         CTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTG
genomic: TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttc ... ttatttgcagCTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTG
EST: gi|29674931|gb|CB671206.1|CB671206
EST:     TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAAC                         CTGCTGGACCACGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA
genomic: TACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttc ... ttatttgcagCTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGA

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), 71 (downstream exon)
Score: 66

GACACTTTCCGTGGTAGAGTGTGTGAATGCCCTACATTCAATGGTGTGCAGTTTAAAGGCGATGGCTACAGCAATTGTGAACgtaatatttc ... ttatttgcagCTGCTGGACCAGGAAAGTGCTTGATAAATCATGGCGGCTGTTGGCATGAGACTCGCAATGGCAAAACATTTTCTGCTTGTCAG




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