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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTATCCCCGAACTTCATGTGTTAGAAAAGGTTGGCTGATTCGTCAAATTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAAgtaagctattctgttatgttttggtcttctagaataccctcatgcacttcttaaccatttattaattttatatgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g10810.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g10810.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G130749_T01 (Zea mays), 5'ss of exon 8
AAGCTATCCCCGAACTTCATGTGTTAGAAAAGGTTGGCTGATTCGTCAAATTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAAgtaagctattc---tgtt---atgttttggtcttctagaataccctcatgcacttcttaaccatttattaattttatatgtttgcag
||| ||||| |||||  | | ||||||||||||||||||| | |||||| ||||||| |||||||| ||||||||||| ||||| |||||||||||||||||||||| ||    |||    || | |   |||| || |||| |||||| || ||||||||| |||||| |||||| |   ||||||
AAGTTATCCTCGAACACCTTATGTTAGAAAAGGTTGGCTGGTCCGTCAAGTTATTCTATACTTGATATTTACTGGTCTCCAAGGATTCATTATTGAGCAAgtaagctgtttatatgtctccatatatatatcttgtaaaatatcctcatacatttcttaaccttttattgattttacaatcttgcag
















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|29664361|gb|CB660636.1|CB660636
EST:     TTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAA                         TACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTC
genomic: TTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAAgtaagctatt ... atgtttgcagTACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTC
EST: gi|33796857|gb|CF324292.1|CF324292
EST:     TTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAA                         TACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTC
genomic: TTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAAgtaagctatt ... atgtttgcagTACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTC
EST: gi|29646483|gb|CB651490.1|CB651490
EST:     TTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAA                         TACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTC
genomic: TTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAAgtaagctatt ... atgtttgcagTACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTC
EST: gi|29664324|gb|CB660599.1|CB660599
EST:     TTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAA                         TACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTC
genomic: TTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAAgtaagctatt ... atgtttgcagTACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTC

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: 48 (upstream exon), 56 (downstream exon)
Score: 13

AAGCTATCCCCGAACTTCATGTGTTAGAAAAGGTTGGCTGATTCGTCAAATTATTCTGTACTTGATCTTTACTGGTCTTCAAGGCTTCATTATTGAGCAAgtaagctatt ... atgtttgcagTACATAAATCCAATTGTTGTGAATTCTCAGCATCCATTGAAAGGAGGACTCCTAAATGCTGTAGAGACTGTTTTGAAACTCTCATTACCAAATGTTTACC




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