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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagattcgatatctctctctctatatatatattttattttcctacacatcaattaaatcgtctgatttggcataaacatgcactcctatgtttttgcagGTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGAGCGAGGTCGTGCAGCTGTACAAGTCCAATGGTATCGGTGCTATGCGCAT

Basic information

species Oryza sativa
transcript LOC_Os01g71810.1
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|88570274|gb|CI661449.1|CI661449
EST:     ATCAAGCAGATCAGAGCTCGAGTTATCATAGCTATTTGATCAAATGGGAG                         GTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGA
genomic: ATCAAGCAGATCAGAGCTCGAGTTATCATAGCTATTTGATCAAATGGGAGgtatattcag ... gtttttgcagGTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGA
EST: gi|88573225|gb|CI664796.1|CI664796
EST:     ATCAAGCAGATCAGAGCTCGAGTTATCATAGCTATTTGATCAAATGGGAG                         GTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGA
genomic: ATCAAGCAGATCAGAGCTCGAGTTATCATAGCTATTTGATCAAATGGGAGgtatattcag ... gtttttgcagGTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGA
EST: gi|88328969|gb|CI649416.1|CI649416
EST:     ATCAAGCAGATCAGAGCTCGAGTTATCATAGCTATTTGATCAAATGGGAG                         GTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGA
genomic: ATCAAGCAGATCAGAGCTCGAGTTATCATAGCTATTTGATCAAATGGGAGgtatattcag ... gtttttgcagGTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGA
EST: gi|88587883|gb|CI705663.1|CI705663
EST:     ATCAAGCAGATCAGAGCTCGAGTTATCATAGCTATTTGATCAAATGGGAG                         GTGTCCACGGTGTTTGCTACGGNATGAACGGCGACAACCTCCCGTCGCAGA
genomic: ATCAAGCAGATCAGAGCTCGAGTTATCATAGCTATTTGATCAAATGGGAGgtatattcag ... gtttttgcagGTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatcaattaaatcgtctgatttggcataaacatgcactcctatgtttttgcagGTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGAGCGAGGTCGTGCAGCTGTACAAGTCCAATGGTATCGGTGCTATGCGCAT
               gtctgat  putative branch site (score: 4)
                                            tgttttt  putative PPT
      aattaaat  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagattcgatatctctctctctatatatatattttattttcctacacatcaattaaatcgtctgatttggcataaacatgcactcctatgtttttgcagGTGTCCACGGTGTTTGCTACGGCATGAACGGCGACAACCTCCCGTCGCAGAGCGAGGTCGTGCAGCTGTACAAGTCCAATGGTATCGGTGCTATGCGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - -cctacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaca