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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAGAGATAGGAATGGAATCCTTACGAAGCCAAAATTTCGCAGAGAGGAGGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatgaagtccaacatatgattagtgaagtactactagtagcctatttgctctgctttcatttcttctctggtgtttgattgattgggtgtgttga...

Basic information

species Oryza sativa
transcript LOC_Os01g71630.1
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|88726524|gb|CI750179.1|CI750179
EST:     GGATATCTGTTTGAGGNNNNNNNGGACGGGGTCTCCCTTCCTGCAACAGA                         ACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
genomic: GGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
EST: gi|88421497|gb|CI618621.1|CI618621
EST:     GGATATCTGTTTGAGGNNNNNNNGGACGGGGTCTCCCTTCCTGCAACAGA                         ACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
genomic: GGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
EST: gi|88447616|gb|CI577133.1|CI577133
EST:     GGATATCTGTTTGAGGAACAAAAGGACGGGGTCTCCCTTCCTGCA-CAGA                         ACCGCGTGATGATGTTACCGTCTGATGTGACGTCCCTTA
genomic: GGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTA
EST: gi|88571115|gb|CI662488.1|CI662488
EST:     GGATATCTGTTTGAGGNNNNNNNGGACGGGGTCTCCCTTCCTGCAACAGA                         ACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
genomic: GGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
EST: gi|88325963|gb|CI649814.1|CI649814
EST:     GGATATCTGTTTGAGGNNNNNNNGGACGGGGTCTCCCTTCCTGCAACAGA                         ACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
genomic: GGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
EST: gi|163928005|gb|EG714277.1|EG714277
EST:     GGATATCTGTTTGAGGNNNNNNNGGACGGGGTCTCCCTTCCTGCAACAGA                         ACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
genomic: GGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
EST: gi|88367908|gb|CI572629.1|CI572629
EST:     GGATATCTGTTTGAGGNNNNNNNGGACGGGGTCTCCCTTCCTGCAACAGA                         ACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
genomic: GGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
EST: gi|88413306|gb|CI581321.1|CI581321
EST:     GGATATCTGTTTGAGGNNNNNNNGGACGGGGTCTCCCTTCCTGCAACAGA                         ACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA
genomic: GGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGA

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: 75 (upstream exon), 68 (downstream exon)
Score: 113

CGCAGAGATAGGAATGGAATCCTTACGAAGCCAAAATTTCGCAGAGAGGAGGATATCTGTTTGAGGAAAAAAAGGACGGGGTCTCCCTTCCTGCAACAGAgtacggatga ... ttttttgcagACCGCGTGATGATGTTACCGTTTGATGTGACGTACCTTAGTTTGTACGCGAGATTCAACAAGATGAAG




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