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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagctattttatgcaagaaaatatcaacttctcttttccaatatatatcttctgccatacatgtgttcaattgcaattctggggcaagctttataaagtcctgtttttacatgaataataggtttgcttcttattttccactgttatgctgtaccatgcag

Basic information

species Oryza sativa
transcript LOC_Os10g35960.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G085747_T01 (Zea mays), 5'ss of exon 10
GATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagcta-ttttatgcaagaaaatatcaac-ttctcttttccaatatatatcttctgccatacatgtgttcaattgcaattctggggcaagct--ttataaagtcctgtttttacatgaataataggtttgcttcttattttccactgttatgctgtaccatgcag
||||||||||||||  |||||||||||||| ||| |||||||||| |||||  |||| | |||||||||||||||||||||||||||||||||||||||||||||| |  ||||  |||  ||| |  ||  | ||  |||  | | || ||    || |||   | |||  |  || |   |   |||       || |    ||||||| |    | | |  |||                                        
GATAGGTGTGCTTAGCATGGCTAAACAGGCAATGTTAAGGATGCCTGGGATCCACAGAACCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagccaactttagacaaacaaacaaaaaaatcctgctttttactctaaataaa-tgtcatttttatgtcaatctgaatggcaaaggctgataaattgtgcgctcctgttgtgctgt-acttgtag----------------------------------------
















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|58596497|gb|CK007025.1|CK007025
EST:     TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGAT                         GGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
genomic: TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagctatt ... taccatgcagGGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
EST: gi|58673493|gb|CK062179.1|CK062179
EST:     TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGAT                         GGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
genomic: TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagctatt ... taccatgcagGGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
EST: gi|58665242|gb|CK053928.1|CK053928
EST:     TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGAT                         GGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
genomic: TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagctatt ... taccatgcagGGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
EST: gi|58601869|gb|CK012397.1|CK012397
EST:     TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACGAAGAT                         GGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
genomic: TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagctatt ... taccatgcagGGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
EST: gi|29678813|gb|CB675088.1|CB675088
EST:     TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGAT                         GGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT
genomic: TAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagctatt ... taccatgcagGGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTAT

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), 75 (downstream exon)
Score: 118

GATAGGTGTGCTTAATATGGCTAAACAGGCGATGCTAAGGATGCCAGGGATAAACAGGAGCGGGGAAGGGCATAATCAATTCTGGGTTCTGGACAAAGATgtaagctatt ... taccatgcagGGACTTATTACCAAATCCAGAAAGGGCCTGGATCCTGCAGTTGCTCGCTATGCCAGAGGTTTTGGTCCTGAAGAGGTGCAAGATCTCCATGAGGGGGCTA




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