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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatttcatacctctatgatttatatatgtcaagtttggtggatatagttgtttggccttttactaatattgtgtccatggatgaccaaaatgcatccagGTGAAAGTTTAAACATAGGTTATTTGAGTCCGTACCTGAAGGCATTGGGTTCTGACTACAGTAATGGTGCAAATTTTGCCATTGCCGGTTCAGCGACATT

Basic information

species Oryza sativa
transcript LOC_Os01g22660.1
intron # 1
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|58684763|gb|CK073450.1|CK073450
EST:     CCACCCCACCGGCCGGTTCTGCGACGGCCGCCTCACCATCGACTTCCTCT                         GTGAAAGTTTAAACATAGGTTATTTGAGTCCGTACCTGAAGGCATTGGGTT
genomic: CCACCCCACCGGCCGGTTCTGCGACGGCCGCCTCACCATCGACTTCCTCTgtcagttaat ... atgcatccagGTGAAAGTTTAAACATAGGTTATTTGAGTCCGTACCTGAAGGCATTGGGTT
EST: gi|58685309|gb|CK073996.1|CK073996
EST:     CCACCCCACCGGGCGGTTCTGCGACGGCCGCCTCACCATCGACTTCCTCT                         GTGAAAGTTTAAACATAGGTTATTTGAGTCCGTACCTGAAGGCATTGGGTT
genomic: CCACCCCACCGGCCGGTTCTGCGACGGCCGCCTCACCATCGACTTCCTCTgtcagttaat ... atgcatccagGTGAAAGTTTAAACATAGGTTATTTGAGTCCGTACCTGAAGGCATTGGGTT

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: 20 (upstream exon), 56 (downstream exon)
Score: 2

GCGGCGATGGGGTGGCGCATCAGGCGGCCGGAGGGCCGCGCCTTCTTCCACCACCCCACCGGCCGGTTCTGCGACGGCCGCCTCACCATCGACTTCCTCTgtcagttaat ... atgcatccagGTGAAAGTTTAAACATAGGTTATTTGAGTCCGTACCTGAAGGCATTGGGTTCTGACTACAGTAATGGTGCAAATTTTGCCATTGCCGGTTCAGCGACATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttgtttggccttttactaatattgtgtccatggatgaccaaaatgcatccagGTGAAAGTTTAAACATAGGTTATTTGAGTCCGTACCTGAAGGCATTGGGTTCTGACTACAGTAATGGTGCAAATTTTGCCATTGCCGGTTCAGCGACATT
                tactaat  putative branch site (score: 2)
             ttttactaatattgt  TA-rich tract