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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaagctactaatccgcatttttttaaaaaaagattcaaagtgcatccaaatcatatctgatctgaatttgaatgtcaattgtgattttctgcagGAGGATTTTTTGGTTGGGTGATCTGAATTATCGCATCGACGTCGCGTACGAGAGAGCACACGAGCTGATTTCGACGATGGATTGGACTCAGCTGGCAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g08780.1
intron # 4
splice site 3'
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|87040614|gb|CI195236.1|CI195236
EST:     CGGACGCACTTCGCCGGCGTCGGCATGCCGAGAAACATCTATGACCATGA                         GAGGATTTTTTGCTTGGGTGATCTGAATTATCGCATCGACGTCGCGTACGA
genomic: CGGACGCACTTCGCCGGCGTCGGCATGCCGAGAAACATCTATGACCATGAgtaagaagct ... ttttctgcagGAGGATTTTTTGGTTGGGTGATCTGAATTATCGCATCGACGTCGCGTACGA
EST: gi|87038774|gb|CI193396.1|CI193396
EST:     CGGACGCACTTCGCCGGCGTCGGCATGCCGAGAAACATCTATGACCATGA                         GAGGATTTTTTGGTTGGGTGATCTGAATTATCGCATCGACGTCGCGTACGA
genomic: CGGACGCACTTCGCCGGCGTCGGCATGCCGAGAAACATCTATGACCATGAgtaagaagct ... ttttctgcagGAGGATTTTTTGGTTGGGTGATCTGAATTATCGCATCGACGTCGCGTACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcatccaaatcatatctgatctgaatttgaatgtcaattgtgattttctgcagGAGGATTTTTTGGTTGGGTGATCTGAATTATCGCATCGACGTCGCGTACGAGAGAGCACACGAGCTGATTTCGACGATGGATTGGACTCAGCTGGCAGAG
               atctgat  putative branch site (score: 4)
                                             ttttctgc  putative PPT
        aaatcatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaagctactaatccgcatttttttaaaaaaagattcaaagtgcatccaaatcatatctgatctgaatttgaatgtcaattgtgattttctgcagGAGGATTTTTTGGTTGGGTGATCTGAATTATCGCATCGACGTCGCGTACGAGAGAGCACACGAGCTGATTTCGACGATGGATTGGACTCAGCTGGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG