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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacggaaattaaaaatgattactatggtcaaggcattttttttttgcttatattcttcgatgcatagatatttggttgtattgttgacaaaaatatttgatataacattttattgattcacgcagATTAAAAATTGATTTCACAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTACTGGCTGAAGAGAGTACCAACTAACACAAGAACAGATCTAAGCATGGCAC

Basic information

species Oryza sativa
transcript LOC_Os02g04420.1
intron # 1
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|88291705|gb|CI539876.1|CI539876
EST:     AGCTCCATCAAAGCTGTAGGGCTTGGGATAGACTAATG                         ATTAAAAATTGATTTCACAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTAC
genomic: AGCTCCATCAAAGCTGTAGGGCTTGGGATAGACTAATGgtatgacgga ... attcacgcagATTAAAAATTGATTTCACAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTAC
EST: gi|88274809|gb|CI388267.1|CI388267
EST:     GATTCATCAAACAGCTCCATCAAAGCTGTAGGGCTTGGGATAGACTAATG                         ATTAAAAATTGATTTCACAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTAC
genomic: GATTCATCAAACAGCTCCATCAAAGCTGTAGGGCTTGGGATAGACTAATGgtatgacgga ... attcacgcagATTAAAAATTGATTTCACAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTAC
EST: gi|25805677|gb|CA761638.1|CA761638
EST:     ATTCATCAAACAGCTCCCATCAGAGCTGTAGGGCTTGGGATAGACTAATG                         ATTAAAAATTGATTTCNCAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTAC
genomic: ATTCATCAAACAGCT-CCATCAAAGCTGTAGGGCTTGGGATAGACTAATGgtatgacgga ... attcacgcagATTAAAAATTGATTTCACAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggttgtattgttgacaaaaatatttgatataacattttattgattcacgcagATTAAAAATTGATTTCACAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTACTGGCTGAAGAGAGTACCAACTAACACAAGAACAGATCTAAGCATGGCAC
                                        tattgat  putative branch site (score: 3)
        tattgttgacaaaaat  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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacggaaattaaaaatgattactatggtcaaggcattttttttttgcttatattcttcgatgcatagatatttggttgtattgttgacaaaaatatttgatataacattttattgattcacgcagATTAAAAATTGATTTCACAAGCAAACGGAAGCGTTGTCTCTGCTAGTTTACTGGCTGAAGAGAGTACCAACTAACACAAGAACAGATCTAAGCATGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC