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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccttttgaaactgagcaatcaaactaatgttttatattctggtaatatgtttatttaatccatgaactatccaactttatttatcttactgaaacttagGGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGATAGCTTATGGCGGCTATGCTCGCAAG

Basic information

species Oryza sativa
transcript LOC_Os05g06510.1
intron # 10
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|29655960|gb|CB652235.1|CB652235
EST:     CATAGAATCCCTAAAGAAAGCTGGTCTTTTCCAATCTACAACTTTTCCTG                         GGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGA
genomic: CATAGAATCCCTAAAGAAAGCTGGTCTTTTCCAATCTACAACTTTTCCTGgtattttgtt ... tgaaacttagGGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGA
EST: gi|29667816|gb|CB664091.1|CB664091
EST:     CAACTTTTCCTG                         GGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGA
genomic: CAACTTTTCCTGgtattttgtt ... tgaaacttagGGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGA
EST: gi|29667169|gb|CB663444.1|CB663444
EST:     CATAGAATCCCTAAAGAAAGCTGGTCTTTTCCAATCTACAACTTTTCCTG                         GGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGA
genomic: CATAGAATCCCTAAAGAAAGCTGGTCTTTTCCAATCTACAACTTTTCCTGgtattttgtt ... tgaaacttagGGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGA
EST: gi|29661373|gb|CB657648.1|CB657648
EST:     CATAGAATCCCTAAAGAAAGCTGGTCTTTTCCAATCTACAACTTTTCCTG                         GGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGA
genomic: CATAGAATCCCTAAAGAAAGCTGGTCTTTTCCAATCTACAACTTTTCCTGgtattttgtt ... tgaaacttagGGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtttatttaatccatgaactatccaactttatttatcttactgaaacttagGGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGATAGCTTATGGCGGCTATGCTCGCAAG
                                      atcttac  putative branch site (score: 3)
                                       tcttact  CT-rich tract
                            aactttatttatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccttttgaaactgagcaatcaaactaatgttttatattctggtaatatgtttatttaatccatgaactatccaactttatttatcttactgaaacttagGGGCAGCAACCTCTGGAGTGACTGATTGTCAGCAAGCCTTTATTGGAGGGATAGCTTATGGCGGCTATGCTCGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - -tattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atccatg