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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttttcttctcatcaatctcttctcaatttggacattattaggaagacattgttcatcatcatcatcatgtcaatgtaacatagaattaatgttgctcatggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGATCCAGATCGAG

Basic information

species Oryza sativa
transcript LOC_Os02g02560.1
intron # 3
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|88370657|gb|CI590235.1|CI590235
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88401596|gb|CI588537.1|CI588537
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCG
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCG
EST: gi|88417942|gb|CI596619.1|CI596619
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88371009|gb|CI595121.1|CI595121
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATT
EST: gi|88377046|gb|CI597830.1|CI597830
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88426949|gb|CI601910.1|CI601910
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88433235|gb|CI591675.1|CI591675
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGA
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGA
EST: gi|88415469|gb|CI589061.1|CI589061
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|3090613|gb|C93600.1|C93600
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGNCCAAA                         ATCGGTCATCGAAGTTCGCAACGGATTCACATTCCTCGGCTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88391611|gb|CI600800.1|CI600800
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTC-TCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88433205|gb|CI591645.1|CI591645
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTTGTGA
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATT-GTGA
EST: gi|88389523|gb|CI600692.1|CI600692
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88387609|gb|CI585312.1|CI585312
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88314463|gb|CI604947.1|CI604947
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATT-ACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88314385|gb|CI604869.1|CI604869
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATTGAAGTGCGCAACGGATTCACATTCCTCGA
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGA
EST: gi|88300805|gb|CI589797.1|CI589797
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATGGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|66922584|gb|CX109432.1|CX109432
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88434257|gb|CI589322.1|CI589322
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAA
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAA
EST: gi|88433214|gb|CI591654.1|CI591654
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGA
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGA
EST: gi|88389649|gb|CI603148.1|CI603148
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTG
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTG
EST: gi|88370364|gb|CI587754.1|CI587754
EST:     CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: CTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
EST: gi|88405310|gb|CI586131.1|CI586131
EST:     TCAAGCTCAACGGCGGCCTCGGCCACCACCATGGGATGCACCGGACCAAA                         ATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT
genomic: TCAAGCTCAACGGCGGCCTCGGC-ACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGAT

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: 71 (upstream exon), 71 (downstream exon)
Score: 39

CGCCGGAGGACTTGGAGGAGACCAAGAAGCTGCTCAACAAGCTCGCCGTGCTCAAGCTCAACGGCGGCCTCGGCACCACCATGGGATGCACCGGACCAAAgtatgtgttt ... ggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGATCCAGATCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatcatcatcatgtcaatgtaacatagaattaatgttgctcatggcctcgcagATCGGTCATCGAAGTGCGCAACGGATTCACATTCCTCGACTTGATTGTGATCCAGATCGAG
                             aattaat  putative branch site (score: 39)
                     taacatagaattaat  TA-rich tract