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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTGGTGTTACTCATGTCTTAGTAACAGGAGGAGCTGGCTATATTGGGTCACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTGgtaattaagttttcctttgtactgaatttctgaactggtttgttcttcaaatgccacccttgatggttaattgtgatttttag

Basic information

species Oryza sativa
transcript LOC_Os08g03570.1
intron # 4
splice site 5'
intron type U2

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|29639521|gb|CB644530.1|CB644530
EST:     CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTG                         GACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
genomic: CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTGgtaattaagt ... tgatttttagGACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
EST: gi|218499746|gb|FG949515.1|FG949515
EST:     CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTG                         GACAATCTTTCTAAAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
genomic: CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTGgtaattaagt ... tgatttttagGACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
EST: gi|58693033|gb|CK081720.1|CK081720
EST:     CACATGCTTCATTACGCCTGTTAAAGGACAATAATCGAGTTACCATTGTG                         GACAATCTTTCTAGAGGAAACATGGGAGCAGTACAGGTTCTCCAAGAGTTG
genomic: CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTGgtaattaagt ... tgatttttagGACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
EST: gi|29660517|gb|CB656792.1|CB656792
EST:     CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTG                         GACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
genomic: CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTGgtaattaagt ... tgatttttagGACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
EST: gi|117233153|gb|CT848014.1|CT848014
EST:     CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTG                         GACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
genomic: CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTGgtaattaagt ... tgatttttagGACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG
EST: gi|58695746|gb|CK084433.1|CK084433
EST:     CACATGCTTCATTACGCCTGTTAAAGGACAATAATCGAGTTACCATTGTG                         GACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTAG
genomic: CACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTGgtaattaagt ... tgatttttagGACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTG

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), 54 (downstream exon)
Score: 21

ACCTGGTGTTACTCATGTCTTAGTAACAGGAGGAGCTGGCTATATTGGGTCACATGCTTCATTACGCCTGTTAAAGGACAATTATCGAGTTACCATTGTGgtaattaagt ... tgatttttagGACAATCTTTCTAGAGGAAACATGGGAGCAGTAAAGGTTCTCCAAGAGTTGTTCCCCCAGCCAGGAAGACTTCAGTTTATCTATGCTGATCTTGGAGATC




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