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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcctaacataatttttcctttgaaattccttccggttattatcttttgttttattggcttatatttccttttctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG

Basic information

species Oryza sativa
transcript LOC_Os03g63020.1
intron # 14
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|29628841|gb|CB633852.1|CB633852
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29638287|gb|CB643296.1|CB643296
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29613155|gb|CB618168.1|CB618168
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29613395|gb|CB618408.1|CB618408
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29644979|gb|CB649986.1|CB649986
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29613120|gb|CB618133.1|CB618133
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|33801021|gb|CF326384.1|CF326384
EST:     TGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: TGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29633044|gb|CB638053.1|CB638053
EST:     AAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: AAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29666009|gb|CB662284.1|CB662284
EST:     AACTACCCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: AACTA-CCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|34996388|gb|CF569133.1|CF569133
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29666008|gb|CB662283.1|CB662283
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|89167683|gb|CI018289.1|CI018289
EST:     AAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: AAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|218497584|gb|FG955131.1|FG955131
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|8856640|gb|AU093958.1|AU093958
EST:     AACTACCTTGGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: AACTACCTT-GATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29663527|gb|CB659802.1|CB659802
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|29656192|gb|CB652467.1|CB652467
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
EST: gi|33381337|gb|CF196680.1|CF196680
EST:     CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAG                         ATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
genomic: CAACTACCTTGATTTAACTCTGAGTCTAAAGCCAAGTTTTCCTGGAACAGgtgcctaaca ... ctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttccggttattatcttttgttttattggcttatatttccttttctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG
                              cttatatttccttttc  CT-rich tract
        ttattatcttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctaacataatttttcctttgaaattccttccggttattatcttttgttttattggcttatatttccttttctgcttgtagATTTTTCTAACAATGTTCCAGAGCATACAAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA