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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACAAACAGCCCTGTTTCCTATGGTTCATCCAACACACACAAACAATTGTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgatgttcagctcaaaatcccggtacatctatgtatgttgacaatttttatggtggtctctgctgttactatgttccctgttatgtttttgttt...

Basic information

species Oryza sativa
transcript LOC_Os02g35470.4
intron # 8
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|29630725|gb|CB635734.1|CB635734
EST:     GCAAAAGCA-GGCAAACTTCTACAGGCACTACAAGTGAAGCAG                       
genomic: GCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTG-A--AGgtaatatgat ... ttttcagc
EST: gi|33674902|gb|CF303141.1|CF303141
EST:     GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAG                         ATGGATCTACAAGTGCATACAATGGAAATCAGGCAGGACGATATGCAGTCA
genomic: GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgat ... ttttcagcagATGGATCTACAAGTGCATACAATGGAAATCAGGCAGGACGATATGCAGTCA
EST: gi|29667009|gb|CB663284.1|CB663284
EST:     GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAG                         C
genomic: GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgat ... ttttcagcag-
EST: gi|29667009|gb|CB663284.1|CB663284
EST:     GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAG                         C
genomic: GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgat ... ttttcagcag-
EST: gi|58607528|gb|CK035561.1|CK035561
EST:     GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAG                         C
genomic: GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgat ... ttttcagcag-
EST: gi|58607528|gb|CK035561.1|CK035561
EST:     GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAG                         C
genomic: GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgat ... ttttcagcag-
EST: gi|29666753|gb|CB663028.1|CB663028
EST:     GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGCAG                       
genomic: GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTG-A--AGgtaatatgat ... ttttcagc
EST: gi|29668182|gb|CB664457.1|CB664457
EST:     GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAG                         ATGGATCTACAAGTGCATACAATGGAAATCAGGCAGGACGATATGCAGTCA
genomic: GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgat ... ttttcagcagATGGATCTACAAGTGCATACAATGGAAATCAGGCAGGACGATATGCAGTCA
EST: gi|3761547|gb|C98795.1|C98795
EST:     GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAG                         ATGGATCTACAAGTGCATACAATGGAAATCAGGCAGGACGATATGCAGTCA
genomic: GTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgat ... ttttcagcagATGGATCTACAAGTGCATACAATGGAAATCAGGCAGGACGATATGCAGTCA

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: 71 (upstream exon), 73 (downstream exon)
Score: 27

GCAACAAACAGCCCTGTTTCCTATGGTTCATCCAACACACACAAACAATTGTCTCAACCAGCAAAAGCAGGGCAAACTTCTACAGGCACTACAAGTGAAGgtaatatgat ... ttttcagcagATGGATCTACAAGTGCATACAATGGAAATCAGGCAGGACGATATGCAGTCAATTCTCAAAGCATACCTGCAAACGTCACTACACAATATGAGCGGAGTTC




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