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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacattttttttgcagatgttttattctagtgtcttatgaccttttatttggcttacacatatgctattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATCGCTAGAAGTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGG

Basic information

species Oryza sativa
transcript LOC_Os10g40780.1
intron # 37
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|58666011|gb|CK054697.1|CK054697
EST:     AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAA                         CTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
genomic: AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAAgtaagacatt ... tattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
EST: gi|29616067|gb|CB621079.1|CB621079
EST:     TCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAA                         CTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
genomic: TCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAAgtaagacatt ... tattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
EST: gi|58672311|gb|CK060997.1|CK060997
EST:     GAGG-TTATAATGTTGTTGATGCCTTATCAAAA                         CTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
genomic: GAGGTTTATAATGTTGTTGATGCCTTATCAAAAgtaagacatt ... tattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
EST: gi|29615806|gb|CB620818.1|CB620818
EST:     AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAA                         CTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
genomic: AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAAgtaagacatt ... tattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
EST: gi|29629737|gb|CB634746.1|CB634746
EST:     AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAA                         CTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
genomic: AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAAgtaagacatt ... tattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
EST: gi|29674318|gb|CB670593.1|CB670593
EST:     AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAA                         CTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
genomic: AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAAgtaagacatt ... tattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
EST: gi|58604721|gb|CK015249.1|CK015249
EST:     AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAG                         CTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
genomic: AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAAgtaagacatt ... tattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
EST: gi|58672055|gb|CK060741.1|CK060741
EST:     AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAA                         CTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC
genomic: AATCTATTAGCATCGCAGAGGTTTATAATGTTGTTGATGCCTTATCAAAAgtaagacatt ... tattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattctagtgtcttatgaccttttatttggcttacacatatgctattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATCGCTAGAAGTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGG
                              ggcttac  putative branch site (score: 3)
                                            ctatttt  putative PPT
                      ttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacattttttttgcagatgttttattctagtgtcttatgaccttttatttggcttacacatatgctattttgcagCTTGCAATCAGGCCCAGTTCTCCTGAATCGCTGCAGCAGTTGATTGAAATCGCTAGAAGTTTTGCTTCCGTGAAGGATGAAAATATTAGACAGTCAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG