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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacgcaccaaattcttgatgcccatggcgaatctatcttttgcaagagaactaaagaacgagcggtgtgtttccggattattcgggagtgcaggttgttttcttggaggagtctcttttgaaatttcgcttctctttattaactctgttagATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGGAGCGGATTCTGTGGCCGGCGTCGGTTCTTGCCGGCATCGCCATGTGCGC

Basic information

species Oryza sativa
transcript LOC_Os01g60120.3
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|29664737|gb|CB661012.1|CB661012
EST:     GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAG                         ATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
genomic: GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAGgtaagtacgc ... actctgttagATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
EST: gi|29669063|gb|CB665338.1|CB665338
EST:     GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAG                         ATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
genomic: GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAGgtaagtacgc ... actctgttagATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
EST: gi|88328819|gb|CI646890.1|CI646890
EST:     GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAG                         ATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
genomic: GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAGgtaagtacgc ... actctgttagATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
EST: gi|88572980|gb|CI664551.1|CI664551
EST:     GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAG                         ATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
genomic: GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAGgtaagtacgc ... actctgttagATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
EST: gi|88340802|gb|CI636962.1|CI636962
EST:     GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAG                         ATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG
genomic: GAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAGgtaagtacgc ... actctgttagATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGG

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: 42 (upstream exon), 60 (downstream exon)
Score: 10

AAACCCAACCCGCGCGAAGCACAAGCACAGAAGCAAAAGCGAACGACGAGGAGAGACGCGACCACCGCCGCGGGTCACTCCCCATCCCAATCTCATCCAGgtaagtacgc ... actctgttagATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGGAGCGGATTCTGTGGCCGGCGTCGGTTCTTGCCGGCATCGCCATGTGCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttcttggaggagtctcttttgaaatttcgcttctctttattaactctgttagATTGGATTTGAGCGGATAGAGGAGGGATGGATGGGAATTTCGGGAGCGAGGAGCGGATTCTGTGGCCGGCGTCGGTTCTTGCCGGCATCGCCATGTGCGC
                                        tattaac  putative branch site (score: 10)
                                              ctctgtt  CT-rich tract
                   ttttgaaattt  TA-rich tract