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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcccttcttgatctgactctgtaaaacatctagtaacattcttgttttgagtagttattaggttcttacccttctaactttagtgatcaaaatttcagGTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCATATGCAAGGGCAACTTCCGTGTATCCCATCGATAAGCCAAATTCCAATGG

Basic information

species Oryza sativa
transcript LOC_Os09g29470.3
intron # 4
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|29623683|gb|CB628694.1|CB628694
EST:     TGAGGAGCTTTCTCAAGATAGCATCTTACTTGTCTATCTATCAGCATCAG                         GTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCAT
genomic: TGAGGAGCTTTCTCAAGATAGCATCTTACTTGTCTATCTATCAGCATCAGgttcccttct ... aaaatttcagGTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCAT
EST: gi|29637839|gb|CB642848.1|CB642848
EST:     TGAGGAGCTTTCTCAAGATAGCATCTTACTTGTCTATCTATCAGCATCAG                         GTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCAT
genomic: TGAGGAGCTTTCTCAAGATAGCATCTTACTTGTCTATCTATCAGCATCAGgttcccttct ... aaaatttcagGTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCAT
EST: gi|58673945|gb|CK062631.1|CK062631
EST:     TGAGGAGCTTTCTCAAGATAGCATCTTACTTGTCTATCTATCAGCATCAG                         GTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCAT
genomic: TGAGGAGCTTTCTCAAGATAGCATCTTACTTGTCTATCTATCAGCATCAGgttcccttct ... aaaatttcagGTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCAT

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: 67 (upstream exon), 74 (downstream exon)
Score: 16

GTTCTAGCCACAGTCTGTGAGGAGCTTTCTCAAGATAGCATCTTACTTGTCTATCTATCAGCATCAGgttcccttct ... aaaatttcagGTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCATATGCAAGGGCAACTTCCGTGTATCCCATCGATAAGCCAAATTCCAATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgagtagttattaggttcttacccttctaactttagtgatcaaaatttcagGTTTTTCCGAGCAGAACATTACTTCTCAAAAGTATGCCTCAAGCTCATCATATGCAAGGGCAACTTCCGTGTATCCCATCGATAAGCCAAATTCCAATGG
                            ttctaac  putative branch site (score: 16)
                                          atcaaaattt  TA-rich tract