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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacccaccctcaatttttttcttgcaataacaatagtgttatttgttaattaaaaatgactaaaactgagctttacaagaacaacaaagatttgtgctaaaaaccgtgtatatccttgttaagtgataagatatgcctactgcagattggtttgatgtaatacgtgctgcagATACTATTGAAGATGCTTCCAAAGTATTACAATCATGTCAAAGCTTATGATAATACGCTCATTACAAAATTCTTTGGCGTGCACAGGATTACTCTGAAAC

Basic information

species Oryza sativa
transcript LOC_Os03g49510.1
intron # 5
splice site 3'
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|157651826|gb|EX451460.1|EX451460
EST:     CTC-AGATGAACGTTTTGTTATAAAAACATTGAGGAAAACTGAGCTGAAG                         AAACTATTGAAGATGCTTCCAAAGTATTACAATCATGTCAAAGCTTATGAT
genomic: CTCAAGATGAACGTTTTGTTATAAAAACATTGAGGAAAACTGAGCTGAAGgtatgaccca ... cgtgctgcagATACTATTGAAGATGCTTCCAAAGTATTACAATCATGTCAAAGCTTATGAT
EST: gi|29685719|gb|CB681994.1|CB681994
EST:     CTCAAGATGAACGTTTTGTTATAAAAACATTGAGGAAAACTGAGCTGAAG                         ATACTATTGAAGATGCTTCCAAAGTATTACAATCATG
genomic: CTCAAGATGAACGTTTTGTTATAAAAACATTGAGGAAAACTGAGCTGAAGgtatgaccca ... cgtgctgcagATACTATTGAAGATGCTTCCAAAGTATTACAATCATG

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: 54 (upstream exon), 55 (downstream exon)
Score: 4

TCTAAAGGAGCTTTCTTCACCTGGGAAAAGTGGCAGCATTTTCTATCTTTCTCAAGATGAACGTTTTGTTATAAAAACATTGAGGAAAACTGAGCTGAAGgtatgaccca ... cgtgctgcagATACTATTGAAGATGCTTCCAAAGTATTACAATCATGTCAAAGCTTATGATAATACGCTCATTACAAAATTCTTTGGCGTGCACAGGATTACTCTGAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaagtgataagatatgcctactgcagattggtttgatgtaatacgtgctgcagATACTATTGAAGATGCTTCCAAAGTATTACAATCATGTCAAAGCTTATGATAATACGCTCATTACAAAATTCTTTGGCGTGCACAGGATTACTCTGAAAC
                                gtttgat  putative branch site (score: 4)
        ataagatat  TA-rich tract