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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAATATATTAGCTAATTCCAACTGCAAACTGAAAATTTGTGATTTTGGACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACGgtatgctcatggaaatatctatctttaacttagttttgtctaaacctttggcttctggcttatttgtgtacgcggatcacctctgatgtctcttcatttgcctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g43910.1
intron # 3
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|66932207|gb|CX119055.1|CX119055
EST:     GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACG                         GATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
genomic: GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACGgtatgctcat ... ttgcctgcagGATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
EST: gi|58673221|gb|CK061907.1|CK061907
EST:     GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACG                         GATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
genomic: GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACGgtatgctcat ... ttgcctgcagGATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
EST: gi|33678274|gb|CF306513.1|CF306513
EST:     GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACG                         GATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
genomic: GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACGgtatgctcat ... ttgcctgcagGATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
EST: gi|58604024|gb|CK014552.1|CK014552
EST:     GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACG                         GATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
genomic: GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACGgtatgctcat ... ttgcctgcagGATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
EST: gi|29627445|gb|CB632456.1|CB632456
EST:     GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACG                         GATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC
genomic: GACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACGgtatgctcat ... ttgcctgcagGATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTC

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: 70 (upstream exon), 72 (downstream exon)
Score: 37

GAAGAATATATTAGCTAATTCCAACTGCAAACTGAAAATTTGTGATTTTGGACTGGCGCGAGTTGCATTCAATGATACTCCGACAACAATCTTTTGGACGgtatgctcat ... ttgcctgcagGATTATGTTGCAACAAGATGGTACAGGGCTCCAGAGCTCTGTGGATCCTTCTTTTCAAAG




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