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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacctaccccctccttccccaccgccctctctctccccaccctagggtttccccgtctgacctcgattccgccttcgatccgtccgcgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGACCCCTCCCCCGAGCCCCAGCAGCAGCCCTACGACGACCTCGAGGACGAC

Basic information

species Oryza sativa
transcript LOC_Os01g05420.1
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|95101009|gb|CI692735.1|CI692735
EST:     CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
EST: gi|88400934|gb|CI616939.1|CI616939
EST:     CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
EST: gi|86894950|gb|CI310258.1|CI310258
EST:     CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
EST: gi|88337836|gb|CI676808.1|CI676808
EST:     CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
EST: gi|88718158|gb|CI741668.1|CI741668
EST:     GGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: GGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
EST: gi|88336779|gb|CI644206.1|CI644206
EST:     CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
EST: gi|88429087|gb|CI689967.1|CI689967
EST:     CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
EST: gi|88326162|gb|CI659974.1|CI659974
EST:     CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
EST: gi|88569692|gb|CI660867.1|CI660867
EST:     CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCC                         CTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA
genomic: CTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGA

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: 74 (upstream exon), 75 (downstream exon)
Score: 10

CGTCTCCTTCCTCGTCATCTCCAAGTTCACCAGCTCCCCCTCCTCGCCTGCTCGCCTAGGGTTTCGATTCGGATCTCGCCGCCGTCGCCATGGATGACCCgtaagtacct ... cgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGACCCCTCCCCCGAGCCCCAGCAGCAGCCCTACGACGACCTCGAGGACGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagggtttccccgtctgacctcgattccgccttcgatccgtccgcgccttgcagCTACATCGACGAGGACGGCGAGCCGCTCATGGACCCCTACGACACGCGCGACCCCTCCCCCGAGCCCCAGCAGCAGCCCTACGACGACCTCGAGGACGAC
             gtctgac  putative branch site (score: 10)