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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctaccttgtgcctttttaattctgactatatcagaaataattgatatgaaaataaactggaaaactgatgcaagttttctatcttgtgaatgatgtcatctctgtacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAGGGATAAGGGTTATTCCTCCCCCATTTGGCACCGATTCTGCCTGGTTTGG

Basic information

species Oryza sativa
transcript LOC_Os04g57210.3
intron # 8
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|87033311|gb|CI187935.1|CI187935
EST:     GATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: GATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29626709|gb|CB631720.1|CB631720
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29663904|gb|CB660179.1|CB660179
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29663905|gb|CB660180.1|CB660180
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29618214|gb|CB623226.1|CB623226
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29626176|gb|CB631187.1|CB631187
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29679980|gb|CB676255.1|CB676255
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTTTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29624048|gb|CB629059.1|CB629059
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|58589122|gb|CF987430.1|CF987430
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29671067|gb|CB667342.1|CB667342
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29663603|gb|CB659878.1|CB659878
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG
EST: gi|29679981|gb|CB676256.1|CB676256
EST:     CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAG                         AGAGACTGGAAAAGGAGCTCCGTGAACTTTTTCCAGCACATATTTCAGAAG
genomic: CAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAG

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), 73 (downstream exon)
Score: 62

TGTATGGATCACTGCTACAATTCAGAAGTGTTCGGTGATGACAACTGGTACAAGACAGTAGTTTTATCCGGTGGATCTTCATGCTTACCTGGTTTATCAGgtatgctacc ... tacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAGGGATAAGGGTTATTCCTCCCCCATTTGGCACCGATTCTGCCTGGTTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaactgatgcaagttttctatcttgtgaatgatgtcatctctgtacattacagAGAGACTGGAAAAGGAGCTCCGTGAACTTCTTCCAGCACATATTTCAGAAGGGATAAGGGTTATTCCTCCCCCATTTGGCACCGATTCTGCCTGGTTTGG
   aactgat  putative branch site (score: 62)
                                       tctctgt  putative PPT
               ttttctat  TA-rich tract