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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatacttgatacagttcactgaaaatctcttaatttgttatccaatagatcaaaagcaattaactcttcattaagtttatctcatagttgatatggaggaatcgtatgtaaaatgttataggcttatagcactgtaggtgaataaacagaggattcgacttgcttcgccgggcctaatatctgttttcacttgcagGAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCAAGATTTGTTAGCTTGTAATTAATTTGACCAACTTCATTCAACATGTAAC

Basic information

species Oryza sativa
transcript LOC_Os01g66330.1
intron # 14
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|88293117|gb|CI512882.1|CI512882
EST:     ACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATG                         GAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCA
genomic: ACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATGgtaggatact ... tcacttgcagGAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCA
EST: gi|88261032|gb|CI364608.1|CI364608
EST:     ACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATG                         GAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCA
genomic: ACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATGgtaggatact ... tcacttgcagGAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCA
EST: gi|25806957|gb|CA762918.1|CA762918
EST:     ACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATG                         GAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCA
genomic: ACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATGgtaggatact ... tcacttgcagGAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCA
EST: gi|88374353|gb|CI513440.1|CI513440
EST:     ACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATG                         GAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCA
genomic: ACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATGgtaggatact ... tcacttgcagGAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCA

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: 62 (upstream exon), 67 (downstream exon)
Score: 11

AATAGGTTCAATTGATAGGCCAGGATGTGGAGCCAAAATTCTTCGGGGTGACGGTGCATTGGAGCAGTACATAACAAACACTAACATGAAGAATTCCATGgtaggatact ... tcacttgcagGAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCAAGATTTGTTAGCTTGTAATTAATTTGACCAACTTCATTCAACATGTAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaacagaggattcgacttgcttcgccgggcctaatatctgttttcacttgcagGAAGCTAACGAGGGTTTGGCGGGTGAACTTGAAGATGCATATATGATGTCAAGATTTGTTAGCTTGTAATTAATTTGACCAACTTCATTCAACATGTAAC
                              gcctaat  putative branch site (score: 11)
                                      tctgttttc  CT-rich tract
                                 taatatct  TA-rich tract