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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGTGAGTCCAGATGGGAAAAGGGTCAGGAGGTTACATCCATTGCCAAATAATGAATTGAATGATGTTAAGgtcaatttccagcccactccttgctgaaatgcattatttatatgtattgtggaatatctgtgttctaagttttaactttaacttgcacgcag

Basic information

species Oryza sativa
transcript LOC_Os01g55170.1
intron # 4
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|29643680|gb|CB648687.1|CB648687
EST:     GGGTCAGGAGGTTACATCCATTGCCAAATAATGAATTGAATGATGTTAAG                         AAAAGGATAGTCGTGGTGGAAAATCTGCCTTCTGATTTCTCCATGGAAAGC
genomic: GGGTCAGGAGGTTACATCCATTGCCAAATAATGAATTGAATGATGTTAAGgtcaatttcc ... ttgcacgcagAAAAGGATAGTCGTGGTGGAAAATCTGCCTTCTGATTTCTCCATGGAAAGC
EST: gi|2280557|gb|C25052.1|C25052
EST:     GGTCAGGAGGTTACATCCATTGCCAAATAATGAATTGAATGATTGTTAAG                         AAAAGGATAGTCCGTGGTGGGAAAATCTGCCTTCTGATTTCTCCATGGAA
genomic: GGTCAGGAGGTTACATCCATTGCCAAATAATGAATTGAATGAT-GTTAAGgtcaatttcc ... ttgcacgcagAAAAGGATAGTC-GTGGTGG-AAAATCTGCCTTCTGATTTCTCCATGGAA
EST: gi|66915125|gb|CX101973.1|CX101973
EST:     GGGTCAGGAGGTTACATCCATTGCCAAATAATGAATTGAATGATGTTAAG                         AAAAGGATAGTCGTGGTGGAAAATCTGCCTTCTGATTTCTCCATGGAAAGC
genomic: GGGTCAGGAGGTTACATCCATTGCCAAATAATGAATTGAATGATGTTAAGgtcaatttcc ... ttgcacgcagAAAAGGATAGTCGTGGTGGAAAATCTGCCTTCTGATTTCTCCATGGAAAGC
EST: gi|58675641|gb|CK064328.1|CK064328
EST:     GGTCAGGAGTGTTACATCCATTGCCAAATAATGAATTGAATGATGTTAAG                         AAAAGGATAGTCGTGGTGGAAAATCTGCCTTCTGATTTCTCCATGGAAAGC
genomic: GGTCAGGAG-GTTACATCCATTGCCAAATAATGAATTGAATGATGTTAAGgtcaatttcc ... ttgcacgcagAAAAGGATAGTCGTGGTGGAAAATCTGCCTTCTGATTTCTCCATGGAAAGC

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: 48 (upstream exon), 73 (downstream exon)
Score: 67

GTCGTGAGTCCAGATGGGAAAAGGGTCAGGAGGTTACATCCATTGCCAAATAATGAATTGAATGATGTTAAGgtcaatttcc ... ttgcacgcagAAAAGGATAGTCGTGGTGGAAAATCTGCCTTCTGATTTCTCCATGGAAAGCATACATGCGAAATTTGAAACAGTTGGGAA




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