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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctctcataactctgttattttctcttctccatagttaagtcccccaatgttgataatcttgtgacctgtgcaccattttttttttgcagGGTTTGCGCCTGTATGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g03180.1
intron # 6
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|29656759|gb|CB653034.1|CB653034
EST:     TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|88832654|gb|CI008250.1|CI008250
EST:     ATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: ATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|25797080|gb|CA753041.1|CA753041
EST:     TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|58592334|gb|CF990642.1|CF990642
EST:     TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|86259413|gb|CI008090.1|CI008090
EST:     CCTTTCCTGCTTGTCTGATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: CCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|29623019|gb|CB628030.1|CB628030
EST:     TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|325493801|gb|JG458325.1|JG458325
EST:     TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: TCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|87008224|gb|CI299192.1|CI299192
EST:     AAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: AAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|86527924|gb|CI168130.1|CI168130
EST:     ATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: ATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG
EST: gi|88994723|gb|CI036304.1|CI036304
EST:     GATATGGTCTACTGCTC                         GGTTTGCGCCTGTATGCAG
genomic: GATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG

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: 57 (upstream exon), 22 (downstream exon)
Score: 24

TTGCTTGTATCTTCTCTATAGTTGCCGCTATTGTTGGTAGTGAAGAGCTTTCAGAGGCTTCCCAAATCCTTTCCTGCTTGTCTGATATGGTCTACTGCTCgtaagctctc ... ttttttgcagGGTTTGCGCCTGTATGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagtcccccaatgttgataatcttgtgacctgtgcaccattttttttttgcagGGTTTGCGCCTGTATGCAG
             tgttgat  putative branch site (score: 24)
                                    caccatttttttttt  putative PPT
                                     accatttttttttt  TA-rich tract