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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGCGAGGGCGCCGGTCCCGCCCCCCGGCGTCGCGGGCAACCTTGAGCGGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctgccctttgacttcctcgcgtggtagggttagatcgtagtaattacttgcggcagtgcgaccatttctgaatcggcggtggatttgggatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g33000.1
intron # 1
splice site 5'
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|58601872|gb|CK012400.1|CK012400
EST:     GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAG                         ATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
genomic: GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctg ... tgggatgcagATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
EST: gi|29639168|gb|CB644177.1|CB644177
EST:     GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAG                         ATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
genomic: GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctg ... tgggatgcagATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
EST: gi|58599084|gb|CK009612.1|CK009612
EST:     GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAG                         ATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
genomic: GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctg ... tgggatgcagATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
EST: gi|218494823|gb|FG945584.1|FG945584
EST:     GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAG                         ATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
genomic: GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctg ... tgggatgcagATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
EST: gi|29613964|gb|CB618977.1|CB618977
EST:     GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAG                         ATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
genomic: GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctg ... tgggatgcagATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
EST: gi|58656734|gb|CK045414.1|CK045414
EST:     GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAG                         ATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
genomic: GGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctg ... tgggatgcagATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
EST: gi|218480683|gb|FG945057.1|FG945057
EST:     CGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAG                         ATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG
genomic: CGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctg ... tgggatgcagATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGG

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: 29 (upstream exon), 52 (downstream exon)
Score: 3

GCCGGCGAGGGCGCCGGTCCCGCCCCCCGGCGTCGCGGGCAACCTTGAGCGGTTCGTGGCCGCCGTGACGCCGTTCGTGCCTGCTCAGTTCCCCTCCAAGgttcgccctg ... tgggatgcagATGCAGAGAGCCGCGAGGGGGTGGCGGGGCTGCGGCGTGGATGCCGAGCGGGAGGAGGCCCCGCACTTCTTCCTCAGAGACGTGTGGGAGGCGTACAGGG




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