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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCTCCACTGATATTGTATGCCCAATGTACATGCGTGTCTGGGATATTCTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaatgcagcctcacatgttaacttgttccccttttttgtattaaaattccagaaatgttaaagaaaattttccattttgttttcaag

Basic information

species Oryza sativa
transcript LOC_Os01g72340.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G032496_T01 (Zea mays), 5'ss of exon 3
CATCCTCCACTGATATTGTATGCCCAATGTACATGCGTGTCTGGGATATTCTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaatgcagcctcacatgttaacttgttccccttttttgtattaaaattccagaaatgttaaagaaaattttccattttgttttcaag
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CATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGTCTGGGATGTTGTTAAGATAGCAAAAGATCCATCTGAAACAAGGCCTCTAATTCTTTGCGAgtatgctaagcatgacctcacatattaata---accctttatccgtattcatat----gatttgatgaaagaactttttccttttgctttcaag
















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|58688410|gb|CK077097.1|CK077097
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|58692909|gb|CK081596.1|CK081596
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|14571259|gb|BI118627.1|BI118627
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|58687216|gb|CK075903.1|CK075903
EST:     CTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|58663708|gb|CK052394.1|CK052394
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|38568808|gb|CD671023.1|CD671023
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|29657376|gb|CB653651.1|CB653651
EST:     CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: CTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
EST: gi|58670588|gb|CK059274.1|CK059274
EST:     GAAAATAGGCCCCTCATTCTTTGCGA                         ATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT
genomic: GAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGAT

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: 69 (upstream exon), 71 (downstream exon)
Score: 28

CATCCTCCACTGATATTGTATGCCCAATGTACATGCGTGTCTGGGATATTCTTAAGATCGCACAAGACCCTTCTGAAAATAGGCCCCTCATTCTTTGCGAgtatgttcaa ... tgttttcaagATATTCACATGCTATGGGAAACAGTAATGGAAATATTGATGCATATTGGATGGCCATAGACAACACTGTTGGACTCCAAGGTGGTTTTATATGGGACTGG




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