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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttaatttttttcctcaggcagatttttttaaaaaaaaagacatactcataccctttcgttcttcaacatatggtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATGTAGGTGCTGGGGTGAAGCTTACTAGAGAATTTTGCAGATCCTAGACAGA

Basic information

species Oryza sativa
transcript LOC_Os03g52340.2
intron # 8
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|88531392|gb|CI459865.1|CI459865
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|88539718|gb|CI469698.1|CI469698
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|88512657|gb|CI440163.1|CI440163
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|29619060|gb|CB624072.1|CB624072
EST:     CAGAGCTCTTTTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGGAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|58593304|gb|CF991612.1|CF991612
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGGAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|58606099|gb|CK034132.1|CK034132
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGGAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|88470988|gb|CI408259.1|CI408259
EST:     CAGAGGTCTTGTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGGTAAAGTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|88485242|gb|CI422513.1|CI422513
EST:     CAGAGCTCTTGTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|88277321|gb|CI398123.1|CI398123
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAAGTGAGATGTATTTACAACTTTGATCCATAGTAGGACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|86500373|gb|CI143006.1|CI143006
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|88472627|gb|CI409898.1|CI409898
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|29657857|gb|CB654132.1|CB654132
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|88553381|gb|CI483489.1|CI483489
EST:     AGAGCTCTTCTACTGTGAAAGCCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGNACAATGATG
genomic: AGAGCTCTTCTACTGTGAAA-CCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|88503492|gb|CI430998.1|CI430998
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
EST: gi|33679109|gb|CF307348.1|CF307348
EST:     CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATA                         GCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG
genomic: CAGAGCTCTTCTACTGTGAAACCGGTGTTTCCTATCTGAATCGTGAAATAgtaagtgtta ... gtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaaaaaaagacatactcataccctttcgttcttcaacatatggtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATGTAGGTGCTGGGGTGAAGCTTACTAGAGAATTTTGCAGATCCTAGACAGA
                                              tttctgc  CT-rich tract
     aaaaaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttaatttttttcctcaggcagatttttttaaaaaaaaagacatactcataccctttcgttcttcaacatatggtttctgcagGCGTTAAACTGAGATGTATTTACAACTTTGATCCATACTAGAACAATGATGTAGGTGCTGGGGTGAAGCTTACTAGAGAATTTTGCAGATCCTAGACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT